From ee12a92b337e0769f62c186bb491f4b3a22359a8 Mon Sep 17 00:00:00 2001 From: Terazus Date: Fri, 24 May 2024 14:26:32 +0100 Subject: [PATCH] Fixed ontology source references comment in isa tab --- ...i-programmatic-BH2023-multiomics-isa.ipynb | 1871 +---------------- isatools/isatab/load/core.py | 5 +- 2 files changed, 109 insertions(+), 1767 deletions(-) diff --git a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb index 04bfbcee..e5c8b22e 100644 --- a/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb +++ b/isa-cookbook/content/notebooks/isa-api-programmatic-BH2023-multiomics-isa.ipynb @@ -33,169 +33,13 @@ { "cell_type": "code", "execution_count": 1, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Collecting git+https://github.com/isa-tools/isa-api.git@issue-511\n", - " Cloning https://github.com/isa-tools/isa-api.git (to revision issue-511) to /private/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/pip-req-build-mzr7j2ry\n", - " Running command git clone --filter=blob:none --quiet https://github.com/isa-tools/isa-api.git /private/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/pip-req-build-mzr7j2ry\n", - " Running command git checkout -b issue-511 --track origin/issue-511\n", - " Switched to a new branch 'issue-511'\n", - " branch 'issue-511' set up to track 'origin/issue-511'.\n", - " Resolved https://github.com/isa-tools/isa-api.git to commit 16ccc001fbdfaed073a6cb2f63d254c1b0b24a79\n", - " Preparing metadata (setup.py) ... \u001b[?25ldone\n", - "\u001b[?25hRequirement already satisfied: graphene==3.1.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.1.1)\n", - "Requirement already satisfied: graphql-core==3.2.3 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (3.2.3)\n", - "Requirement already satisfied: wheel~=0.36.2 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (0.36.2)\n", - "Requirement already satisfied: setuptools~=57.1.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (57.1.0)\n", - "Requirement already satisfied: numpy~=1.23.3 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.23.5)\n", - "Requirement already satisfied: jsonschema~=4.18.4 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (4.18.6)\n", - "Requirement already satisfied: pandas==1.5.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (1.5.0)\n", - "Requirement already satisfied: openpyxl>=2.5.0 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2.6.4)\n", - "Requirement already satisfied: networkx~=2.5.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (2.5.1)\n", - "Requirement already satisfied: lxml~=4.9.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from isatools==0.14.2) (4.9.3)\n", - 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"Requirement already satisfied: greenlet!=0.4.17 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from sqlalchemy>=1.4.18->flask_sqlalchemy~=3.0.2->isatools==0.14.2) (3.0.1)\n", - "Building wheels for collected packages: isatools\n", - " Building wheel for isatools (setup.py) ... \u001b[?25ldone\n", - "\u001b[?25h Created wheel for isatools: filename=isatools-0.14.2-py3-none-any.whl size=2696947 sha256=ee443afda16dd3f9fa177a627370eb88ca515f6315e27eda76cc50de31b244fc\n", - " Stored in directory: /private/var/folders/5n/rl6lqnks4rqb59pbtpvvntqw0000gr/T/pip-ephem-wheel-cache-qi3jve2_/wheels/ee/20/69/6f853ca26fa5c0d6a848162269e5640761b26197e3a5dde721\n", - "Successfully built isatools\n", - "Installing collected packages: isatools\n", - " Attempting uninstall: isatools\n", - " Found existing installation: isatools 0.12.0a0\n", - "\u001b[31mERROR: Exception:\n", - "Traceback (most recent call last):\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/cli/base_command.py\", line 167, in exc_logging_wrapper\n", - " status = run_func(*args)\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/cli/req_command.py\", line 205, in wrapper\n", - " return func(self, options, args)\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/commands/install.py\", line 405, in run\n", - " installed = install_given_reqs(\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/req/__init__.py\", line 68, in install_given_reqs\n", - " uninstalled_pathset = requirement.uninstall(auto_confirm=True)\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/req/req_install.py\", line 637, in uninstall\n", - " uninstalled_pathset = UninstallPathSet.from_dist(dist)\n", - " File \"/Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages/pip/_internal/req/req_uninstall.py\", line 530, in from_dist\n", - " assert link_pointer == dist_location, (\n", - "AssertionError: Egg-link /Users/philippe/Documents/git/isa-api2/isa-api/src/isatools does not match installed location of isatools (at /Users/philippe/Documents/git/isa-api2/isa-api)\u001b[0m\u001b[31m\n", - "\u001b[0m\u001b[33mWARNING: You are using pip version 22.0.3; however, version 24.0 is available.\n", - "You should consider upgrading via the '/Users/philippe/.pyenv/versions/3.9.0/bin/python3.9 -m pip install --upgrade pip' command.\u001b[0m\u001b[33m\n", - "\u001b[0m" - ] - } - ], - "source": [ - "!pip install git+https://github.com/isa-tools/isa-api.git@issue-511" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Name: isatools\r\n", - "Version: 0.12.0a0\r\n", - "Summary: Metadata tracking tools help to manage an increasingly diverse set of life science, environmental and biomedical experiments\r\n", - "Home-page: https://github.com/ISA-tools/isa-api\r\n", - "Author: ISA Infrastructure Team\r\n", - "Author-email: isatools@googlegroups.com\r\n", - "License: UNKNOWN\r\n", - "Location: /Users/philippe/Documents/git/isa-api2/isa-api\r\n", - "Requires: beautifulsoup4, biopython, chardet, deepdiff, iso8601, jinja2, jsonschema, lxml, mzml2isa, networkx, numpy, pandas, progressbar2, PyYAML, requests\r\n", - "Required-by: \r\n" - ] - } - ], - "source": [ - "!pip show isatools" - ] - }, - { - "cell_type": "code", - "execution_count": 3, "metadata": { "scrolled": true }, "outputs": [], "source": [ - "import isatools\n", - "\n", + "import os\n", + "from hashlib import md5, sha1, sha256, blake2b\n", "\n", "from isatools.model import (\n", " Comment,\n", @@ -211,7 +55,6 @@ " Source,\n", " Protocol,\n", " ProtocolParameter,\n", - " ProtocolComponent,\n", " ParameterValue,\n", " Process,\n", " Publication,\n", @@ -220,43 +63,43 @@ " DataFile,\n", " plink\n", ")\n", - "import datetime\n", - "import os\n", - "from hashlib import md5, sha1, sha256, blake2b\n", "\n", - "def compute_hash(path, file, hash_func):\n", + "\n", + "HASH_FUNCTIONS = {\n", + " \"md5\": md5,\n", + " \"sha1\": sha1,\n", + " \"sha256\": sha256,\n", + " \"blake2\": blake2b,\n", + "}\n", + "\n", + "\n", + "def compute_hash(file_path, file, hash_func):\n", " \"\"\"a subfunction generating the hash using hashlib functions\n", "\n", - " :param path:\n", + " :param file_path:\n", " :param file:\n", " :param hash_func:\n", " :return:\n", " \"\"\"\n", "\n", - " with open(os.path.join(path, file), \"rb\") as f:\n", + " with open(os.path.join(file_path, file), \"rb\") as f:\n", " for byte_block in iter(lambda: f.read(4096), b\"\"):\n", " hash_func.update(byte_block)\n", " return hash_func.hexdigest()\n", "\n", "\n", - "def update_checksum(path, isa_file_object: DataFile, checksum_type):\n", + "def update_checksum(file_path, isa_file_object: DataFile, checksum_type):\n", " \"\"\" a helper function to compute file checksum given a file path, an isa data file name and a type of algorithm\n", "\n", - " :param path:\n", + " :param file_path:\n", " :param isa_file_object:\n", " :param checksum_type: enum\n", " :return: isa_file_object:\n", " :raises ValueError: when the checksum is invalid\n", " \"\"\"\n", - " HASH_FUNCTIONS = {\n", - " \"md5\": md5,\n", - " \"sha1\": sha1,\n", - " \"sha256\": sha256,\n", - " \"blake2\": blake2b,\n", - " }\n", " if checksum_type in HASH_FUNCTIONS.keys():\n", " hash_type = HASH_FUNCTIONS[checksum_type]()\n", - " file_checksum = compute_hash(path, isa_file_object.filename, hash_type)\n", + " file_checksum = compute_hash(file_path, isa_file_object.filename, hash_type)\n", " isa_file_object.comments.append(Comment(name=\"checksum type\", value=checksum_type))\n", " else:\n", " raise ValueError(\"Invalid checksum type\")\n", @@ -264,15 +107,30 @@ "\n", " return isa_file_object\n", "\n", - "def md5_checksum(fname, path):\n", - " hash_md5 = hashlib.md5()\n", - " with open(os.path.join(path, fname), \"rb\") as f:\n", - " for byte_block in iter(lambda: f.read(4096),b\"\"):\n", - " hash_md5.update(byte_block)\n", - " return hash_md5.hexdigest()\n", "\n", - "def create_file():\n", - " return filename\n" + "def create_directories() -> None:\n", + " \"\"\" Creates all the directories required by the notebook \"\"\"\n", + " here_path: str = os.getcwd()\n", + " bh2023_output_path: str = os.path.join(here_path, \"output\", \"ISA-BH2023-ALL\")\n", + "\n", + " directories: dict[str, list[str]] = {\n", + " 'TAB': ['BH23-ISATAB_FROM_TAB'],\n", + " 'JSON': ['BH23-ISATAB', 'BH23-ISATAB_FROM_JSON'],\n", + " 'DERIVED_FILES': [],\n", + " 'RAW_FILES': []\n", + " }\n", + "\n", + " for directory, subdirectories in directories.items():\n", + " directory_path: str = os.path.join(bh2023_output_path, directory)\n", + " if not os.path.exists(directory_path):\n", + " os.makedirs(directory_path)\n", + " for subdirectory in subdirectories:\n", + " sub_directory_path: str = os.path.join(directory_path, subdirectory)\n", + " if not os.path.exists(sub_directory_path):\n", + " os.makedirs(sub_directory_path)\n", + "\n", + "\n", + "create_directories()" ] }, { @@ -292,7 +150,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 2, "metadata": { "scrolled": true }, @@ -300,22 +158,21 @@ "source": [ "investigation = Investigation()\n", "\n", - "chebi=OntologySource(name=\"CHEBI\",\n", - " description=\"Chemical Entity of Biological Interest\",\n", - " version=\"1.0\",\n", - " file=\"https://www.example.org/CHEBI\"\n", - " )\n", - "efo=OntologySource(name=\"EFO\", description=\"Experimental Factor Ontology\")\n", - "msio=OntologySource(name=\"MSIO\", description=\"Metabolomics Standards Initiative Ontology\")\n", + "chebi = OntologySource(\n", + " name=\"CHEBI\",\n", + " description=\"Chemical Entity of Biological Interest\",\n", + " version=\"1.0\",\n", + " file=\"https://www.example.org/CHEBI\"\n", + ")\n", + "efo = OntologySource(name=\"EFO\", description=\"Experimental Factor Ontology\")\n", + "msio = OntologySource(name=\"MSIO\", description=\"Metabolomics Standards Initiative Ontology\")\n", "obi = OntologySource(name='OBI', description=\"Ontology for Biomedical Investigations\")\n", "pato = OntologySource(name='PATO', description=\"Phenotype and Trait Ontology\")\n", - "ncbitaxon = OntologySource(name=\"NCIBTaxon\", description=\"NCBI Taxonomy\")\n", "uo = OntologySource(name=\"UO\", description=\"Unit Ontology\")\n", + "ncbitaxon = OntologySource(name=\"NCIBTaxon\", description=\"NCBI Taxonomy\")\n", + "ncbitaxon.comments.append(Comment(name=\"onto-test\", value=\"onto-value\"))\n", "\n", - "ontocomment = Comment(name=\"onto-test\", value=\"onto-value\")\n", - "ncbitaxon.comments.append(ontocomment)\n", - "\n", - "investigation.ontology_source_references=[chebi, efo, obi, pato, ncbitaxon, msio, uo]" + "investigation.ontology_source_references = [chebi, efo, obi, pato, ncbitaxon, msio, uo]" ] }, { @@ -327,7 +184,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -344,7 +201,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 4, "metadata": { "scrolled": true }, @@ -430,7 +287,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 5, "metadata": { "scrolled": true }, @@ -456,7 +313,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 6, "metadata": { "scrolled": true }, @@ -488,7 +345,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 7, "metadata": { "scrolled": true }, @@ -677,7 +534,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 8, "metadata": { "scrolled": true }, @@ -785,7 +642,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 9, "metadata": { "scrolled": true }, @@ -839,7 +696,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -847,111 +704,6 @@ "data_path = \"./output/\"" ] }, - { - "cell_type": "code", - "execution_count": 13, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "# ms_sw = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"ms software\")),\n", - "# value=OntologyAnnotation(term=\"IsoSolve\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "\n", - "\n", - "# ms_derivedDF = DataFile(filename=\"isotopologue-distribution-analysis.txt\", label=\"Derived Data File\")\n", - "\n", - "# f=open(os.path.join(main_path,\"DERIVED_FILES/\",\"isotopologue-distribution-analysis.txt\"),\"w+\")\n", - "# f.write(\"isotopologue-distribution-analysis.txt\")\n", - "# f.close\n", - "\n", - "# ms_da_process = Process(name=\"MS-DT-ident\",\n", - "# executes_protocol=study.protocols[6],\n", - "# parameter_values=[ms_sw],\n", - "# outputs=[ms_derivedDF])\n", - "\n", - "# assay.data_files.append(ms_derivedDF)\n", - "\n", - "# for i, sample in enumerate(study.samples):\n", - "\n", - "\n", - "\n", - "# # extraction process takes as input a sample, and produces an extract material as output\n", - "\n", - "# char_ext = Characteristic(category=OntologyAnnotation(term=\"Material Type\"),\n", - "# value=OntologyAnnotation(term=\"pellet\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "\n", - " \n", - "# char_ext1 = Characteristic(category=OntologyAnnotation(term=\"quantity\"),\n", - "# value=40, \n", - "# unit=mass_unit\n", - "# )\n", - "# ms_material = Material(name=\"extract-ms-{}\".format(i))\n", - "# ms_material.type = \"Extract Name\"\n", - "# ms_material.characteristics.append(char_ext)\n", - "# ms_material.characteristics.append(char_ext1)\n", - "# # create an extraction process that executes the extraction protocol\n", - "\n", - " \n", - "# extraction_process = Process(\n", - "# name=\"extract-process-{}\".format(i),\n", - "# executes_protocol=study.protocols[1],\n", - "# inputs=[sample],\n", - "# outputs=[ms_material]\n", - "# )\n", - "\n", - "# # create a ms acquisition process that executes the ms acquisition protocol\n", - "# column = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"chromatography column\")),\n", - "# value=OntologyAnnotation(term=\"Agilent C18 TTX\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "# ms_inst = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"mass spectrometry instrument\")),\n", - "# value=OntologyAnnotation(term=\"Agilent QTOF XL\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "# ms_anlzr = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"mass analyzer\")),\n", - "# value=OntologyAnnotation(term=\"Agilent MassDiscovery\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "\n", - "# datafile = DataFile(\n", - "# filename=\"ms-data-{}.mzml\".format(i),\n", - "# label=\"Raw Spectral Data File\"\n", - "# )\n", - "# f=open(os.path.join(main_path, \"RAW_FILES/\",\"ms-data-{}.mzml\".format(i)),\"w+\")\n", - "# f.write(\"ms-data-{}.mzml\".format(i))\n", - "# f.close\n", - "# data_comment = Comment(name=\"data_comment\",value=\"data_value\")\n", - "# datafile.comments.append(data_comment)\n", - " \n", - "# isotopologue_process = Process(\n", - "# name=\"assay-name-ms-{}\".format(i),\n", - "# executes_protocol=study.protocols[3],\n", - "# parameter_values=[column, ms_inst, ms_anlzr], \n", - "# inputs=[extraction_process.outputs[0]],\n", - "# outputs=[datafile]\n", - "# )\n", - "\n", - "# # ms acquisition process usually has an output mzml data file\n", - "# ms_da_process.inputs.append(datafile) \n", - "\n", - "# # Ensure Processes are linked forward and backward. plink(from_process, to_process) is a function to set\n", - "# # these links for you. It is found in the isatools.model package\n", - "\n", - "# assay.samples.append(sample)\n", - "# assay.other_material.append(ms_material)\n", - "# assay.data_files.append(datafile)\n", - "\n", - "# assay.process_sequence.append(extraction_process)\n", - "# assay.process_sequence.append(isotopologue_process)\n", - "# assay.process_sequence.append(ms_da_process)\n", - "# # create an extraction process that executes the extraction protocol\n", - "\n", - "# # plink(aliquoting_process, sequencing_process)\n", - "# plink(sample_collection_mbx, extraction_process)\n", - "# plink(extraction_process, isotopologue_process)\n", - "# plink(isotopologue_process, ms_da_process)\n", - "# # make sure the extract, data file, and the processes are attached to the assay\n", - "\n", - "# assay.characteristic_categories.append(char_ext.category)\n", - "# assay.characteristic_categories.append(char_ext1.category)\n", - "# assay.units.append(mass_unit)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -960,109 +712,6 @@ "make sure to used `ISA API plink function` to connects the protocols in a chain." ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "### The mass isotopomer distribution analysis assay using 1D 13C NMR acquisitions:" - ] - }, - { - "cell_type": "code", - "execution_count": 14, - "metadata": { - "scrolled": true - }, - "outputs": [], - "source": [ - "# nmr_sw = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"nmr software\")),\n", - "# value=OntologyAnnotation(term=\"https://pypi.org/project/IsoSolve\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "\n", - "# nmr_topo_DDF = DataFile(filename=\"isotopomer-analysis.txt\", label=\"Derived Data File\")\n", - "\n", - "\n", - "# f=open(os.path.join(main_path, \"DERIVED_FILES/\",\"isotopomer-analysis.txt\"),\"w+\")\n", - "# f.write(\"isotopomer-analysis.txt\")\n", - "# f.close\n", - "\n", - "\n", - "# nmr_topo_da_process = Process(\n", - "# name = \"NMR-TOPO-DT-ident\",\n", - "# executes_protocol=study.protocols[7],\n", - "# parameter_values=[nmr_sw],\n", - "# outputs=[nmr_topo_DDF]\n", - "# )\n", - "\n", - "# assay_nmr_topo.data_files.append(nmr_topo_DDF)\n", - "\n", - "# for i, sample in enumerate(study.samples):\n", - " \n", - "# # extraction process takes as input a sample, and produces an extract material as output\n", - "# material_nmr = Material(\n", - "# name=\"extract-nmr-topo-{}\".format(i),\n", - "# type_=\"Extract Name\"\n", - "# )\n", - " \n", - "# extraction_process_nmr = Process(\n", - "# name=\"extract-process-{}\".format(i),\n", - "# executes_protocol=study.protocols[1],\n", - "# inputs=[sample],\n", - "# outputs=[material_nmr]\n", - "# )\n", - "\n", - "# # create a nmr acquisition process that executes the nmr protocol\n", - "# magnet = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"magnetic field strength\")),\n", - "# value=6, unit=mag_field_unit)\n", - "# tube = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"nmr tube\")),\n", - "# value=OntologyAnnotation(term=\"Brucker 14 mm Oscar\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "# pulse_a = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"pulse sequence\")),\n", - "# value=OntologyAnnotation(term=\"HSQC\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "# pulse_b = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"pulse sequence\")),\n", - "# value=OntologyAnnotation(term=\"ZQF-TOCSY\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "# pulse_c = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"pulse sequence\")),\n", - "# value=OntologyAnnotation(term=\"HNCA\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "# pulse_d = ParameterValue(category=ProtocolParameter(parameter_name=OntologyAnnotation(term=\"pulse sequence\")),\n", - "# value=OntologyAnnotation(term=\"HACO-DIPSY\", term_source=obi, term_accession=\"https://purl.org/\"))\n", - "\n", - "# pulses=[pulse_a,pulse_b,pulse_c,pulse_d]\n", - "\n", - "# for j in range(len(pulses)):\n", - "\n", - "# # Sequencing process usually has an output data file\n", - "# datafile_nmr = DataFile(filename=\"nmr-data-topo\"+ pulses[j].value.term +\"-{}.nmrml\".format(i+1), label=\"Free Induction Decay Data File\")\n", - "# f=open(os.path.join(main_path,\"RAW_FILES/\",\"nmr-data-topo\"+ pulses[j].value.term +\"-{}.nmrml\".format(i+1)),\"w+\")\n", - "# f.write(\"nmr-data-topo\"+ pulses[j].value.term +\"-{}.nmrml\".format(i+1))\n", - "# f.close\n", - " \n", - "# isotopomer_process = Process(\n", - "# name = \"assay-name-nmr-topo-\"+ pulses[j].value.term +\"-{}\".format(i+1),\n", - "# executes_protocol=study.protocols[4],\n", - "# parameter_values=[magnet,tube,pulses[j]],\n", - "# inputs=[extraction_process_nmr.outputs[0]],\n", - "# outputs=[datafile_nmr]\n", - "# )\n", - "\n", - "# # Ensure Processes are linked forward and backward. plink(from_process, to_process) is a function to set\n", - "# # these links for you. It is found in the isatools.model package\n", - "\n", - "# assay_nmr_topo.samples.append(sample)\n", - "# assay_nmr_topo.other_material.append(material_nmr)\n", - "# assay_nmr_topo.data_files.append(datafile_nmr)\n", - "\n", - "# assay_nmr_topo.process_sequence.append(extraction_process_nmr)\n", - "# assay_nmr_topo.process_sequence.append(isotopomer_process)\n", - "# assay_nmr_topo.process_sequence.append(nmr_topo_da_process)\n", - " \n", - "# plink(sample_collection_mbx, extraction_process_nmr)\n", - "# plink(extraction_process_nmr, isotopomer_process)\n", - "# plink(isotopomer_process, nmr_topo_da_process)\n", - "# # make sure the extract, data file, and the processes are attached to the assay\n", - "\n", - " \n", - " \n", - "# assay_nmr_topo.units.append(mag_field_unit)" - ] - }, { "cell_type": "markdown", "metadata": {}, @@ -1072,7 +721,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 11, "metadata": { "scrolled": true }, @@ -1167,7 +816,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 12, "metadata": { "scrolled": true }, @@ -1308,7 +957,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 13, "metadata": { "scrolled": true }, @@ -1458,7 +1107,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 14, "metadata": { "scrolled": true }, @@ -1480,7 +1129,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 15, "metadata": { "scrolled": true }, @@ -1510,738 +1159,16 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 16, "metadata": { "scrolled": true }, "outputs": [ { "data": { - "text/plain": [ - "isatools.model.Investigation(identifier='', filename='', title='', submission_date='', public_release_date='', ontology_source_references=[isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), isatools.model.OntologySource(name='MSIO', file='', version='', description='Metabolomics Standards Initiative Ontology', comments=[]), isatools.model.OntologySource(name='UO', file='', version='', description='Unit Ontology', comments=[])], publications=[], contacts=[], studies=[isatools.model.Study(filename='s_BH2023-study.txt', identifier='BH2023', title='[U-13C6]-D-glucose labeling experiment in MCF7 cancer cell line', description='Probing cancer pathways of MCF7 cell line using 13C stable isotope resolved metabolomics study using isotopologue distribution analysis with mass spectrometry and isotopomer analysis by 1D 1H NMR.', submission_date='2021-08-15', public_release_date='2021-08-15', contacts=[isatools.model.Person(last_name='Min', first_name='Weng', mid_initials='', email='weng.min@bim.edu.cn', phone='', fax='', address='Prospect Street, Beijing, People's Republic of China', affiliation='Beijing Institute of Metabolism', roles=[isatools.model.OntologyAnnotation(term='principal investigator role', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='SRA Inform On Status', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='SRA Inform On Error', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='Study Person REF', value='')]), isatools.model.Person(last_name='Everest', first_name='Hillary', mid_initials='', email='', phone='', fax='', address='CCM, Edinborough, United Kingdom', affiliation='Centre for Cell Metabolism', roles=[isatools.model.OntologyAnnotation(term='principal investigator role', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='Study Person REF', value='')])], design_descriptors=[isatools.model.OntologyAnnotation(term='intervention design', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='http://purl.obolibrary.org/obo/OBI_0000115', comments=[]), isatools.model.OntologyAnnotation(term='stable isotope resolved metabolomics study', term_source=isatools.model.OntologySource(name='MSIO', file='', version='', description='Metabolomics Standards Initiative Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/MSIO_0000096', comments=[])], publications=[isatools.model.Publication(pubmed_id='36007233', doi='10.1371/journal.pone.0000000', author_list='Min,W. and Everest H', title='Decyphering new cancer pathways with stable isotope resolved metabolomics in MCF7 cell lines', status=isatools.model.OntologyAnnotation(term='indexed in PubMed', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), comments=[])], factors=[isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[])], protocols=[isatools.model.Protocol(name='cell culture and isotopic labeling', protocol_type=isatools.model.OntologyAnnotation(term='sample collection', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='tracer molecule', term_source=None, term_accession='', comments=[]), comments=[])], components=[], comments=[]), isatools.model.Protocol(name='intracellular metabolite extraction', 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isatools.model.DataFile(filename='nmr-data-metpro-CPMG-3.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-4.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-5.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), 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"\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-1.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-2.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-3.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-4.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-5.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/13f29395-3a03-412b-82e2-baef2236a9ba\". name=\"extract-process-6\", executes_protocol=Protocol(\n", - "\tname=intracellular metabolite extraction\n", - "\tprotocol_type=extraction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', 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outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/e1509bf1-f2fa-4614-85e0-eb962782bf3f\". name=\"NMR-metpro-DT-ident\", executes_protocol=Protocol(\n", - "\tname=NMR metabolite identification\n", - "\tprotocol_type=data transformation\n", - "\turi=https://doi.org/10.1021/acs.analchem.1c01064\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-1.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-2.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-3.nmrml', label='Free 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factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/aafb8e39-eac5-4abb-8843-b137bdd02dea\". name=\"rna-library-name-2\", executes_protocol=Protocol(\n", - "\tname=mRNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/ea023298-3774-4eef-8bde-984b02f1fd30\". name=\"assay-name-rna-seq-2\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-2.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/9d06139b-6ac4-4625-8cdd-dd7cb422c887\". name=\"RNASEQ-DT\", executes_protocol=Protocol(\n", - "\tname=transcription analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='rna-seq-data-2.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='rna-seq-DEA.txt', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='43c82c5a95957947f3132f49400c1d30'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/d306fbf2-6e3c-44c7-816c-aa8a1062691c\". name=\"extract-process-rna-seq-3\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', 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"\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/91657567-e020-42cd-a721-ba847950b7ae\". name=\"assay-name-rna-seq-3\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-3.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/121f9c37-b1d0-4200-b1b8-75820e31a76a\". name=\"RNASEQ-DT\", executes_protocol=Protocol(\n", - "\tname=transcription analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='rna-seq-data-3.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='rna-seq-DEA.txt', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='43c82c5a95957947f3132f49400c1d30'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/23e18f77-295f-464e-a025-ba399a464a3b\". name=\"extract-process-rna-seq-4\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), 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Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), 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"\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='rna-seq-data-6.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='rna-seq-DEA.txt', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='43c82c5a95957947f3132f49400c1d30'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/5a925721-2a47-404c-8e8e-778e34d7693e\". name=\"extract-process-rna-seq-7\", 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isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/d6c9eb50-4456-4a22-997b-60873edeaf30\". name=\"RNASEQ-DT\", executes_protocol=Protocol(\n", - "\tname=transcription analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='rna-seq-data-7.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='rna-seq-DEA.txt', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='43c82c5a95957947f3132f49400c1d30'), isatools.model.Comment(name='export', value='yes')])])], other_material=[, , , , , , , , , , , , , , , ], characteristic_categories=[isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='target repository', value='arrayexpress')], units=[]), isatools.model.Assay(measurement_type=isatools.model.OntologyAnnotation(term='copy number variation profiling', term_source=isatools.model.OntologySource(name='MSIO', file='', version='', description='Metabolomics Standards Initiative Ontology', comments=[]), term_accession='https://purl.org', comments=[]), technology_type=isatools.model.OntologyAnnotation(term='nucleotide sequencing', term_source=isatools.model.OntologySource(name='MSIO', file='', version='', description='Metabolomics Standards Initiative Ontology', comments=[]), term_accession='https://purl.org', comments=[]), 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"\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-0.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/402e3042-dc8a-4afc-8334-eab07767a01d\". name=\"extract-process-cnv-seq-1\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/7bf75dd8-c5c3-4ad1-a4f7-49ee43adf9d1\". name=\"cnv-library-name-1\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/6588e4ed-246d-439f-91d6-4360cef2947a\". name=\"assay-name-cnv-seq-1\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-1.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/5c6410c4-5d49-442d-8ff5-51ddc4a08fd9\". name=\"VCF-DT\", executes_protocol=Protocol(\n", - "\tname=CNV analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-1.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/2e4b783a-2ae3-4e08-88a2-43f1be62e9f2\". name=\"extract-process-cnv-seq-2\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/97043c3f-5ae0-4fbf-9d18-422568001f8e\". name=\"cnv-library-name-2\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/716185f3-bda4-475d-af4c-4458262c52b3\". name=\"assay-name-cnv-seq-2\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-2.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/881cacfb-0a11-422e-914d-880267d2dbee\". name=\"VCF-DT\", executes_protocol=Protocol(\n", - "\tname=CNV analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-2.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/973ee04e-ca8e-44f5-931a-de05db094802\". name=\"extract-process-cnv-seq-3\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/375dd198-8c26-4ea9-9937-a6853c1e0476\". name=\"cnv-library-name-3\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/8bda74b1-6cd0-4caf-878a-2007cc18bca7\". name=\"assay-name-cnv-seq-3\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-3.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/be6873bf-fc59-4541-8ca6-1ed63bbf7f7e\". name=\"VCF-DT\", executes_protocol=Protocol(\n", - "\tname=CNV analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-3.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/4af9e74c-2aa7-4f15-9876-152e916ec31d\". name=\"extract-process-cnv-seq-4\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/8002830e-940d-4b36-b3e2-8a268d2de9ab\". name=\"cnv-library-name-4\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/b42ea57e-6e6b-4524-a2e6-adf35dd709c9\". name=\"assay-name-cnv-seq-4\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-4.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/0fa79523-a265-4169-8fe6-8cd185e3612a\". name=\"VCF-DT\", executes_protocol=Protocol(\n", - "\tname=CNV analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-4.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/8a743b7a-6a68-4cdb-b86d-892f5778bf9b\". name=\"extract-process-cnv-seq-5\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/d91bc5f4-142b-47e7-b6de-667e13462930\". name=\"cnv-library-name-5\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/9b8ee409-8631-4a6c-b73c-398099908866\". name=\"assay-name-cnv-seq-5\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-5.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/c8ce32c9-2156-4a80-9dbc-721da691a0f1\". name=\"VCF-DT\", executes_protocol=Protocol(\n", - "\tname=CNV analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-5.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/e591cad8-79a7-4141-8c9b-47e2db130eb1\". name=\"extract-process-cnv-seq-6\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/852fe421-8b10-4e84-ac8d-656858a76c0e\". name=\"cnv-library-name-6\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/3f43510b-deef-425a-bea3-284c530ab681\". name=\"assay-name-cnv-seq-6\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-6.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/19ab987d-39b1-4d44-a161-27d84e48e04a\". name=\"VCF-DT\", executes_protocol=Protocol(\n", - "\tname=CNV analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-6.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/16f8ec30-e8f7-43cd-9b10-5c9a7844d45f\". name=\"extract-process-cnv-seq-7\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=0 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/b3c77417-ee1a-4a69-bbd8-4aafc036edcd\". name=\"cnv-library-name-7\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/6c9d8b8b-c1a8-4927-9338-f0a902fa05b3\". name=\"assay-name-cnv-seq-7\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-7.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/e9b95485-a9e4-49e5-ad34-e18f7f161fcc\". name=\"VCF-DT\", executes_protocol=Protocol(\n", - "\tname=CNV analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-7.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])])], other_material=[, , , , , , , , , , , , , , , ], characteristic_categories=[isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='target repository', value='ega')], units=[])], sources=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[]), isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], samples=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', 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comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), 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isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', 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comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), 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isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', 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comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], process_sequence=[isatools.model.process.Process(id=\"#process/9cc13ea9-45fc-49d6-88a4-4457f41fd37d\". name=\"sample-collection-process-mbx\", executes_protocol=Protocol(\n", - "\tname=cell culture and isotopic labeling\n", - "\tprotocol_type=sample collection\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/a20b676d-a33d-483d-9606-f9d95fe378f5\". name=\"sample-collection-process-gtx\", executes_protocol=Protocol(\n", - "\tname=cell culture and isotopic labeling\n", - "\tprotocol_type=sample collection\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', 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term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])])], other_material=[], characteristic_categories=[isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='EMBL Broker Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Project Name', value='OXFORD'), isatools.model.Comment(name='EMBL Lab Name', value='Oxford e-Research Centre'), isatools.model.Comment(name='EMBL Submission Action', value='ADD'), isatools.model.Comment(name='Study Funding Agency', value=''), isatools.model.Comment(name='Study Grant Number', value='')], units=[])], comments=[])" - ] + "text/plain": "isatools.model.Investigation(identifier='', filename='', title='', submission_date='', public_release_date='', ontology_source_references=[isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), isatools.model.OntologySource(name='MSIO', file='', version='', description='Metabolomics Standards Initiative Ontology', comments=[]), isatools.model.OntologySource(name='UO', file='', version='', description='Unit Ontology', comments=[])], publications=[], contacts=[], studies=[isatools.model.Study(filename='s_BH2023-study.txt', identifier='BH2023', title='[U-13C6]-D-glucose labeling experiment in MCF7 cancer cell line', description='Probing cancer pathways of MCF7 cell line using 13C stable isotope resolved metabolomics study using isotopologue distribution analysis with mass spectrometry and isotopomer analysis by 1D 1H NMR.', submission_date='2021-08-15', public_release_date='2021-08-15', contacts=[isatools.model.Person(last_name='Min', first_name='Weng', mid_initials='', email='weng.min@bim.edu.cn', phone='', fax='', address='Prospect Street, Beijing, People's Republic of China', affiliation='Beijing Institute of Metabolism', roles=[isatools.model.OntologyAnnotation(term='principal investigator role', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='SRA Inform On Status', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='SRA Inform On Error', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='Study Person REF', value='')]), isatools.model.Person(last_name='Everest', first_name='Hillary', mid_initials='', email='', phone='', fax='', address='CCM, Edinborough, United Kingdom', affiliation='Centre for Cell Metabolism', roles=[isatools.model.OntologyAnnotation(term='principal investigator role', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='Study Person REF', value='')])], design_descriptors=[isatools.model.OntologyAnnotation(term='intervention design', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='http://purl.obolibrary.org/obo/OBI_0000115', comments=[]), isatools.model.OntologyAnnotation(term='stable isotope resolved metabolomics study', term_source=isatools.model.OntologySource(name='MSIO', file='', version='', description='Metabolomics Standards Initiative Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/MSIO_0000096', comments=[])], publications=[isatools.model.Publication(pubmed_id='36007233', doi='10.1371/journal.pone.0000000', author_list='Min,W. and Everest H', title='Decyphering new cancer pathways with stable isotope resolved metabolomics in MCF7 cell lines', status=isatools.model.OntologyAnnotation(term='indexed in PubMed', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), comments=[])], factors=[isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity 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parameters=[isatools.model.ProtocolParameter(parameter_name=isatools.model.OntologyAnnotation(term='tracer molecule', term_source=None, term_accession='', comments=[]), comments=[])], components=[], comments=[]), isatools.model.Protocol(name='intracellular metabolite extraction', protocol_type=isatools.model.OntologyAnnotation(term='extraction', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='extracellular metabolite extraction', protocol_type=isatools.model.OntologyAnnotation(term='extraction', term_source=None, term_accession='', comments=[]), uri='', version='', parameters=[], components=[], comments=[]), isatools.model.Protocol(name='liquid chromatography mass spectrometry', protocol_type=isatools.model.OntologyAnnotation(term='mass spectrometry', term_source=None, term_accession='', comments=[]), uri='', version='', 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isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/68993726-e121-4c07-ae79-d025efdef7dd\". name=\"extract-process-4\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', 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isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/ee677866-1f66-4386-beff-dc01cc309f4a\". name=\"extract-process-5\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', 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generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-5.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), isatools.model.process.Process(id=\"#process/81a997d5-248e-479e-adc6-cb6e3b3baa3c\". name=\"extract-process-6\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter 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isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/3607d945-5b30-441f-90bc-e8f8ce07cbf1\". name=\"assay-name-nmr-metpro-CPMG-7\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 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isatools.model.DataFile(filename='nmr-data-metpro-CPMG-3.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-4.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-5.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[], comments=[])]), 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comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/7c2222c1-1052-42e1-b457-cba55535362f\". name=\"cnv-library-name-1\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/b8315ba9-0dba-4bc8-8d8b-e5b8dbc916fb\". name=\"assay-name-cnv-seq-1\", executes_protocol=Protocol(\n\tname=nucleic acid sequencing\n\tprotocol_type=nucleic acid sequencing\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter 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isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/79f821b2-b383-46dd-927b-c162d079ed9d\". name=\"extract-process-cnv-seq-2\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', 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description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/8d92e3c9-1a25-4ee9-8067-e357f1fd4fa2\". name=\"cnv-library-name-2\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/ec062370-3210-406a-b244-91aefce60269\". name=\"assay-name-cnv-seq-2\", executes_protocol=Protocol(\n\tname=nucleic acid sequencing\n\tprotocol_type=nucleic acid sequencing\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-2.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/2391a803-f5c0-4ed6-afef-4800bf7cb83f\". name=\"VCF-DT\", executes_protocol=Protocol(\n\tname=CNV analysis\n\tprotocol_type=data transformation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-2.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/b32470f2-f66b-4e51-b957-c71b949394ec\". name=\"extract-process-cnv-seq-3\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/cc8cab19-bc78-4702-9ad9-625295f31a8d\". name=\"cnv-library-name-3\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/d3276f10-0c48-4dda-9598-a2748336171e\". name=\"assay-name-cnv-seq-3\", executes_protocol=Protocol(\n\tname=nucleic acid sequencing\n\tprotocol_type=nucleic acid sequencing\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-3.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/234b01b9-a061-4cb6-8f08-6fbaa598cf46\". name=\"VCF-DT\", executes_protocol=Protocol(\n\tname=CNV analysis\n\tprotocol_type=data transformation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='cnv-seq-data-3.fastq', label='Raw Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])], outputs=[isatools.model.DataFile(filename='cnv-seq-derived-data.vcf', label='Derived Data File', generated_from=[], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='623e79888c6e3125283423d2df36e2fb'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/5426bf58-522e-4c38-8ad7-4db53648aaed\". name=\"extract-process-cnv-seq-4\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter 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term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/9f226150-c935-4fcd-8f07-57f9a211283c\". name=\"cnv-library-name-4\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation 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extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=0 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/8388804b-70f3-4803-bf45-2e71a78f63c4\". name=\"cnv-library-name-5\", executes_protocol=Protocol(\n\tname=gDNA library preparation\n\tprotocol_type=library construction\n\turi=\n\tversion=\n\tparameters=4 ProtocolParameter 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term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), 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comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', 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term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[]), isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), 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isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', 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term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[], comments=[])])], other_material=[], characteristic_categories=[isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='EMBL Broker Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Project Name', value='OXFORD'), isatools.model.Comment(name='EMBL Lab Name', value='Oxford e-Research Centre'), isatools.model.Comment(name='EMBL Submission Action', value='ADD'), isatools.model.Comment(name='Study Funding Agency', value=''), isatools.model.Comment(name='Study Grant Number', value='')], units=[])], comments=[])" }, - "execution_count": 20, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -2262,568 +1189,14 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 17, "metadata": {}, "outputs": [ { "data": { - "text/plain": [ - "isatools.model.Investigation(identifier='', filename='', title='', submission_date='', public_release_date='', ontology_source_references=[isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), 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comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/a1bc0959-81fe-4429-8252-4fdd8e48a1db\". name=\"process-1-intracellular metabolite extraction\", executes_protocol=Protocol(\n", - "\tname=intracellular metabolite extraction\n", - "\tprotocol_type=extraction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/18b996db-c5ef-412d-a5bb-1fc384d00e0f\". name=\"process-2-intracellular metabolite extraction\", executes_protocol=Protocol(\n", - "\tname=intracellular metabolite extraction\n", - "\tprotocol_type=extraction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/aaa4c068-adfd-4d7d-bda7-53d0f0c91e04\". name=\"process-3-intracellular metabolite extraction\", executes_protocol=Protocol(\n", - "\tname=intracellular metabolite extraction\n", - "\tprotocol_type=extraction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/982ef617-9e68-4186-9736-49ab51c47989\". name=\"process-4-intracellular metabolite extraction\", executes_protocol=Protocol(\n", - "\tname=intracellular metabolite extraction\n", - "\tprotocol_type=extraction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/508e1bf6-d610-46c9-a388-e8c909c9e6c5\". name=\"process-5-intracellular metabolite extraction\", executes_protocol=Protocol(\n", - "\tname=intracellular metabolite extraction\n", - "\tprotocol_type=extraction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/c7c4200d-2141-446c-a0a2-6d6f2a7972fc\". name=\"process-6-intracellular metabolite extraction\", executes_protocol=Protocol(\n", - "\tname=intracellular metabolite extraction\n", - "\tprotocol_type=extraction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/61ec8bb5-464d-490b-bfce-7e74f8fadbd3\". name=\"process-7-intracellular metabolite extraction\", executes_protocol=Protocol(\n", - "\tname=intracellular metabolite extraction\n", - "\tprotocol_type=extraction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/6481832b-3d85-4009-b03c-ba4fb0003a35\". name=\"assay-name-nmr-metpro-CPMG-1\", executes_protocol=Protocol(\n", - "\tname=1D 13C NMR spectroscopy for metabolite profiling\n", - "\tprotocol_type=NMR spectroscopy\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=3 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-1.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/3531cb7d-7d6c-4e07-a5af-2149318a98ea\". name=\"assay-name-nmr-metpro-CPMG-3\", executes_protocol=Protocol(\n", - "\tname=1D 13C NMR spectroscopy for metabolite profiling\n", - "\tprotocol_type=NMR spectroscopy\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=3 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-3.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/2b7cf3ed-4ca7-428b-ad6d-e92b46bafbf7\". name=\"assay-name-nmr-metpro-CPMG-5\", executes_protocol=Protocol(\n", - "\tname=1D 13C NMR spectroscopy for metabolite profiling\n", - "\tprotocol_type=NMR spectroscopy\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=3 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-5.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/416846ec-e843-4bd9-abe6-511ebed775e8\". name=\"assay-name-nmr-metpro-CPMG-7\", executes_protocol=Protocol(\n", - "\tname=1D 13C NMR spectroscopy for metabolite profiling\n", - "\tprotocol_type=NMR spectroscopy\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=3 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/52e43e4e-b37f-434b-acdf-60fc325d155f\". name=\"assay-name-nmr-metpro-CPMG-2\", executes_protocol=Protocol(\n", - "\tname=1D 13C NMR spectroscopy for metabolite profiling\n", - "\tprotocol_type=NMR spectroscopy\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=3 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-2.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/3387f54f-6e41-467a-833f-ac99981cf689\". name=\"assay-name-nmr-metpro-CPMG-4\", executes_protocol=Protocol(\n", - "\tname=1D 13C NMR spectroscopy for metabolite profiling\n", - "\tprotocol_type=NMR spectroscopy\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=3 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-4.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/f0ea64e4-0930-4841-9be3-c49856d2816a\". name=\"assay-name-nmr-metpro-CPMG-6\", executes_protocol=Protocol(\n", - "\tname=1D 13C NMR spectroscopy for metabolite profiling\n", - "\tprotocol_type=NMR spectroscopy\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=3 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/f1faa8a1-bdb7-4611-b6a5-76774faf100b\". name=\"assay-name-nmr-metpro-CPMG-8\", executes_protocol=Protocol(\n", - "\tname=1D 13C NMR spectroscopy for metabolite profiling\n", - "\tprotocol_type=NMR spectroscopy\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=3 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/b625f279-59c8-46b2-b0d9-ef07d7181894\". name=\"NMR-metpro-DT-ident\", executes_protocol=Protocol(\n", - "\tname=NMR metabolite identification\n", - "\tprotocol_type=data transformation\n", - "\turi=https://doi.org/10.1021/acs.analchem.1c01064\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-1.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', 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Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[]), isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])], outputs=[isatools.model.DataFile(filename='metpro-analysis.txt', label='Derived Spectral Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', 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term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', 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term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], process_sequence=[isatools.model.process.Process(id=\"#process/942af50f-bd71-4eb0-b78c-476f4a0d0813\". name=\"process-0-mRNA extraction\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/fa725047-c64c-47cd-a2b7-622f7a3edb76\". name=\"process-1-mRNA extraction\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/dbd6cff2-c12d-4ac5-9ed6-803714bf2a7f\". name=\"process-2-mRNA extraction\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/16567620-cc87-4028-a61e-5c40f250b96b\". name=\"process-3-mRNA extraction\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/df834344-8096-43ef-a8c3-2605d642096b\". name=\"process-4-mRNA extraction\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/1cac19b8-8283-45a5-8c69-452005e20e14\". name=\"process-5-mRNA extraction\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/e70c7b20-0552-4d78-af58-d189a7d75d89\". name=\"process-6-mRNA extraction\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/6c63d494-f38f-4ece-bd1b-030e11be2d33\". name=\"process-7-mRNA extraction\", executes_protocol=Protocol(\n", - "\tname=mRNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/7e91c752-4bbf-4152-9a74-31c7dab56d08\". name=\"process-0-mRNA library preparation\", executes_protocol=Protocol(\n", - "\tname=mRNA library 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construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/c426e1ba-08e2-47f7-81ac-1b2a75163dbd\". name=\"process-3-mRNA library preparation\", executes_protocol=Protocol(\n", - "\tname=mRNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/08af5d16-e645-468e-bb10-fbadc9884646\". name=\"process-4-mRNA library preparation\", executes_protocol=Protocol(\n", - "\tname=mRNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/b810d9f3-f730-44c6-9979-55d249c70c3a\". name=\"process-5-mRNA library preparation\", executes_protocol=Protocol(\n", - "\tname=mRNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/172a6e10-86a8-471d-b043-bc05910ded76\". name=\"process-6-mRNA library preparation\", executes_protocol=Protocol(\n", - "\tname=mRNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/a199e0e5-8dc9-4993-b27c-f6bd1eeb9f0d\". name=\"process-7-mRNA library preparation\", executes_protocol=Protocol(\n", - "\tname=mRNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/28a7e678-4263-415a-8775-51d701e247a6\". name=\"assay-name-rna-seq-0\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-0.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/378ebeb5-4022-4eca-9e9b-cceed8905c80\". name=\"assay-name-rna-seq-2\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-2.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo 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isatools.model.process.Process(id=\"#process/cbaff93b-b5f4-4d1f-a137-95ee87fbacbb\". name=\"assay-name-rna-seq-4\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-4.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/298fa11c-b0b7-4dd0-9e54-3bf67c7a853e\". name=\"assay-name-rna-seq-6\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-6.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), 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comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/0d1695ba-0c83-48e3-8953-b4c6f25d94f7\". name=\"assay-name-rna-seq-1\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-1.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/b168b2f7-4c10-415a-b292-00cc34df9c52\". name=\"assay-name-rna-seq-3\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-3.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/ff73f387-dbe8-4245-be3a-f2e49b6bb0f7\". name=\"assay-name-rna-seq-5\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-5.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/adc337e6-1630-4e73-bbbc-7a851761cc26\". name=\"assay-name-rna-seq-7\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='rna-seq-data-7.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/49253b1c-f30e-4300-955b-41c71969f317\". name=\"RNASEQ-DT\", executes_protocol=Protocol(\n", - "\tname=transcription analysis\n", - "\tprotocol_type=data transformation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.DataFile(filename='rna-seq-data-0.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), 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comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], process_sequence=[isatools.model.process.Process(id=\"#process/9af88e7d-f5a1-4bb7-8590-fba06dd0274c\". name=\"process-0-gDNA extraction\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/750a0165-23dc-454d-9dd2-82a6a1bb6662\". name=\"process-1-gDNA extraction\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/aa075807-0e4a-4846-8f03-ac3f53be8d16\". name=\"process-2-gDNA extraction\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/76626dd7-bd71-412b-95d8-9480bf216361\". name=\"process-3-gDNA extraction\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/71bcc3ea-5c35-4d3a-aa76-d4ebb2dad967\". name=\"process-4-gDNA extraction\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/b1869b25-8262-443c-a5fe-304f47457e41\". name=\"process-5-gDNA extraction\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/1dab63c0-5328-4dab-ad7c-46051e28c909\". name=\"process-6-gDNA extraction\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/79bb4fbb-ded2-437d-9dfa-be9f935d4a46\". name=\"process-7-gDNA extraction\", executes_protocol=Protocol(\n", - "\tname=gDNA extraction\n", - "\tprotocol_type=material separation\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], 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isatools.model.process.Process(id=\"#process/79559818-5cf6-478f-9948-84d1570e65bc\". name=\"process-2-gDNA library preparation\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/2f8ecdb6-d84d-41ba-b4ba-8add64e9cac2\". name=\"process-3-gDNA library preparation\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/9860f2d0-c8ff-44b1-b2ce-05bcffb781a1\". name=\"process-4-gDNA library preparation\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/0be8ea67-3566-4302-8d0c-5986dc001eb8\". name=\"process-5-gDNA library preparation\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/e25de272-9bf6-48d6-9134-939f250edac9\". name=\"process-6-gDNA library preparation\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/514cf0b9-1bc8-49f5-824f-69a1cd60dcc8\". name=\"process-7-gDNA library preparation\", executes_protocol=Protocol(\n", - "\tname=gDNA library preparation\n", - "\tprotocol_type=library construction\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=4 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[]), isatools.model.process.Process(id=\"#process/cc3a4e68-3ca7-4fd4-85d6-7815b29d1143\". name=\"assay-name-cnv-seq-0\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-0.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/1b5f0f78-0ce5-4111-ae84-41a1f76f9812\". name=\"assay-name-cnv-seq-2\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-2.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/343871f0-6600-404a-8a1c-36b4f8513795\". name=\"assay-name-cnv-seq-4\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-4.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), 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comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/d0d60175-1def-449e-b5df-0493788b2abc\". name=\"assay-name-cnv-seq-6\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-6.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/00eedc69-49f8-4360-a539-ffc84a51d3ce\". name=\"assay-name-cnv-seq-1\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-1.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/be14c4dd-207a-499d-9b5d-500477fae7c2\". name=\"assay-name-cnv-seq-3\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-3.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/fcfd2aa4-501b-40fd-a001-3aafd2d9543f\". name=\"assay-name-cnv-seq-5\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-5.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')])]), isatools.model.process.Process(id=\"#process/b4ec1275-96ad-4c4e-b263-3dd5f7454812\". name=\"assay-name-cnv-seq-7\", executes_protocol=Protocol(\n", - "\tname=nucleic acid sequencing\n", - "\tprotocol_type=nucleic acid sequencing\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='cnv-seq-data-7.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', 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comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[isatools.model.Comment(name='checksum type', value='md5'), isatools.model.Comment(name='checksum', value='d41d8cd98f00b204e9800998ecf8427e'), isatools.model.Comment(name='export', value='yes')]), isatools.model.DataFile(filename='cnv-seq-data-7.fastq', label='Raw Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-3', 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comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), 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factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', 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description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], process_sequence=[isatools.model.process.Process(id=\"#process/a18c9bb0-3c11-4be5-864c-d343b8dc5206\". name=\"process-0-cell culture and isotopic labeling\", executes_protocol=Protocol(\n", - "\tname=cell culture and isotopic labeling\n", - "\tprotocol_type=sample collection\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/344c9d09-aaab-4dcf-aebf-e6ceb48b5a9f\". name=\"process-4-cell culture and isotopic labeling\", executes_protocol=Protocol(\n", - "\tname=cell culture and isotopic labeling\n", - "\tprotocol_type=sample collection\n", - "\turi=\n", - "\tversion=\n", - "\tparameters=1 ProtocolParameter objects\n", - "\tcomponents=0 OntologyAnnotation objects\n", - "\tcomments=0 Comment objects\n", - "), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', 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term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/f8defc15-5712-4116-93d7-fa544a5a5b70\". name=\"process-1-intracellular metabolite extraction\", 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term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', 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term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/dc3441a6-f82a-48d3-b536-b2c921c75e6b\". name=\"process-3-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical 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comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/19c6eaae-bf11-42b7-89bb-b7f32dbe9a28\". name=\"process-4-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], 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term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/89ddda6c-72e6-4a02-b9a5-98b3fc9ead01\". name=\"process-5-intracellular metabolite extraction\", executes_protocol=Protocol(\n\tname=intracellular metabolite extraction\n\tprotocol_type=extraction\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', 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term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/b3e93d4c-ba70-49b0-a2c5-96a22fa53a95\". name=\"process-6-intracellular metabolite extraction\", 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version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', 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term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/44b8f636-9b99-4363-872a-79fbfac15f43\". name=\"assay-name-nmr-metpro-CPMG-1\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 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Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/99e21933-bf22-494f-aa2f-af27d77f29ce\". name=\"assay-name-nmr-metpro-CPMG-3\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-3.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/3f14e789-f458-4825-a88a-6fb5ab07e336\". name=\"assay-name-nmr-metpro-CPMG-5\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-5.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/70271b13-7b5c-4386-b981-500f19518fb3\". name=\"assay-name-nmr-metpro-CPMG-7\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-7.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/10ee62c7-e399-448a-8b03-f99662361a48\". name=\"assay-name-nmr-metpro-CPMG-2\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-2.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/9740a4c9-d09b-49a1-a15f-65d68ad8f73e\". name=\"assay-name-nmr-metpro-CPMG-4\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-4.nmrml', label='Free Induction Decay Data 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value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/626f1236-b8eb-4632-bdcb-53606323596e\". name=\"assay-name-nmr-metpro-CPMG-6\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-6.nmrml', label='Free Induction Decay Data File', generated_from=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/50172d83-1807-4e67-89c4-24e157de7f6d\". name=\"assay-name-nmr-metpro-CPMG-8\", executes_protocol=Protocol(\n\tname=1D 13C NMR spectroscopy for metabolite profiling\n\tprotocol_type=NMR spectroscopy\n\turi=\n\tversion=\n\tparameters=3 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[], outputs=[isatools.model.DataFile(filename='nmr-data-metpro-CPMG-8.nmrml', label='Free Induction 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value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', 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extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/0553e069-08ca-48d4-9fc2-b792b01bd3b3\". name=\"process-2-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/b99f9eab-cbcb-4f7d-ae54-69d09973658a\". name=\"process-3-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/48175220-5d68-4e50-823e-32b660525b27\". name=\"process-4-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/bafbe5a4-76c1-4178-aad1-01396d77a866\". name=\"process-5-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/47950561-b99f-41f9-9226-dcd71024cc93\". name=\"process-6-mRNA extraction\", executes_protocol=Protocol(\n\tname=mRNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical 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Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/554ecd56-e474-4c63-9bfa-dae28449a42b\". name=\"process-1-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/4d8eaf67-8daa-4179-9354-191b9a15a427\". name=\"process-2-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/d0d2a5fc-09a2-4f73-9bd1-9bb234cac7f9\". name=\"process-3-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/41680259-fef6-4413-ba7a-d22066acb53d\". name=\"process-4-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/44554a3e-58f7-4a72-8f31-8d44f5c7aef1\". name=\"process-5-gDNA extraction\", executes_protocol=Protocol(\n\tname=gDNA extraction\n\tprotocol_type=material separation\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/ddc57cc8-edc8-43f9-be23-4e005081c30c\". name=\"process-6-gDNA extraction\", 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comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical 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description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])], process_sequence=[isatools.model.process.Process(id=\"#process/737f363b-7c43-4e6b-956a-8a761917125b\". name=\"process-0-cell culture and isotopic labeling\", executes_protocol=Protocol(\n\tname=cell culture and isotopic labeling\n\tprotocol_type=sample collection\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-1-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-1-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='high', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])]), isatools.model.process.Process(id=\"#process/05a5ac0f-b3a7-4b1b-8aeb-225085e10d2f\". name=\"process-4-cell culture and isotopic labeling\", executes_protocol=Protocol(\n\tname=cell culture and isotopic labeling\n\tprotocol_type=sample collection\n\turi=\n\tversion=\n\tparameters=1 ProtocolParameter objects\n\tcomponents=0 OntologyAnnotation objects\n\tcomments=0 Comment objects\n), date=\"None\", performer=\"None\", inputs=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], outputs=[isatools.model.Sample(name='culture-2-sample-0', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:0', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-1', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:1', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:2', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[]), isatools.model.Sample(name='culture-2-sample-3', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SAME:3', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], factor_values=[isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='compound', factor_type=isatools.model.OntologyAnnotation(term='chemical substance', term_source=isatools.model.OntologySource(name='CHEBI', file='https://www.example.org/CHEBI', version='1.0', description='Chemical Entity of Biological Interest', comments=[]), term_accession='http://purl.obolibrary.org/obo/CHEBI_59999', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='dioxygen', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='dose', factor_type=isatools.model.OntologyAnnotation(term='dose', term_source=isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[]), term_accession='http://www.ebi.ac.uk/efo/EFO_0000428', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='normal', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None), isatools.model.FactorValue(factor_name=isatools.model.StudyFactor(name='duration', factor_type=isatools.model.OntologyAnnotation(term='time', term_source=isatools.model.OntologySource(name='PATO', file='', version='', description='Phenotype and Trait Ontology', comments=[]), term_accession='http://purl.obolibrary.org/obo/PATO_0000165', comments=[]), comments=[]), value=isatools.model.OntologyAnnotation(term='hour', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None)], derives_from=[isatools.model.Source(name='culture-2', characteristics=[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='SRC:', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='Homo sapiens', term_source=isatools.model.OntologySource(name='NCIBTaxon', file='', version='', description='NCBI Taxonomy', comments=[isatools.model.Comment(name='onto-test', value='onto-value')]), term_accession='http://purl.obolibrary.org/obo/NCBITaxon_9606', comments=[]), unit=None, comments=[]), isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='MCF-7', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/', comments=[]), unit=None, comments=[])], comments=[])], comments=[])])], other_material=[], characteristic_categories=[isatools.model.OntologyAnnotation(term='Organism', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='cell line', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:smp', term_source=None, term_accession='', comments=[]), isatools.model.OntologyAnnotation(term='namespace:biosample:src', term_source=None, term_accession='', comments=[])], comments=[isatools.model.Comment(name='EMBL Broker Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Name', value='OXFORD'), isatools.model.Comment(name='EMBL Center Project Name', value='OXFORD'), isatools.model.Comment(name='EMBL Lab Name', value='Oxford e-Research Centre'), isatools.model.Comment(name='EMBL Submission Action', value='ADD'), isatools.model.Comment(name='Study Funding Agency', value=''), isatools.model.Comment(name='Study Grant Number', value='')], units=[])], comments=[])" }, - "execution_count": 21, + "execution_count": 17, "metadata": {}, "output_type": "execute_result" } @@ -2833,10 +1206,8 @@ "with open(os.path.join(main_path,\"TAB\", \"i_investigation.txt\")) as isa_sirm_test:\n", " roundtrip = load(isa_sirm_test)\n", "\n", - "from isatools.isatab import dump\n", - "\n", "# note the use of the flag for explicit serialization on factor values on assay tables\n", - "dump(roundtrip, os.path.join(main_path,'TAB/BH23-ISATAB_FROM_TAB'), write_factor_values_in_assay_table=False) \n", + "dump(roundtrip, os.path.join(main_path,'TAB/BH23-ISATAB_FROM_TAB'), write_factor_values_in_assay_table=False)\n", " " ] }, @@ -2849,26 +1220,26 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 18, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "./output/ISA-BH2023-ALL/\n" + ] + } + ], "source": [ - "from isatools.isajson import dump\n", "from isatools.isajson.dump import ISAJSONEncoder\n", "from json import dumps, loads\n", "\n", "\n", "inv_j = dumps(investigation, cls=ISAJSONEncoder)\n", - "\n", + "print(main_path)\n", "with open(os.path.join(main_path, 'isa-bh2023-all.json'), 'w') as out_fp:\n", - " out_fp.write(inv_j)\n", - " \n", - " \n", - "# with open(os.path.join(main_path, 'isa-bh2023-all.json')) as jsin_fp:\n", - "# new_jsin = Investigation()\n", - "# new_jsin.from_dict(json.loads(jsin_fp.read()))\n", - " \n", - "# print(new_jsin.studies[0].assays[0])" + " out_fp.write(inv_j)" ] }, { @@ -2880,29 +1251,14 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 19, "metadata": {}, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "2024-03-11 15:23:42,958 [WARNING]: rules_10xx.py(check_protocol_usage:183) >> (W) Some protocols declared in the investigation file are not used neither in the study file s_BH2023-study.txt nor in any related assay file: ['MS metabolite identification', 'extracellular metabolite extraction', 'liquid chromatography mass spectrometry', '1D 13C NMR spectroscopy for isotopomer analysis', '13C SIRM MS and NMR integrative analysis']\n", - "2024-03-11 15:23:43,022 [WARNING]: rules_10xx.py(check_protocol_parameter_usage:263) >> (W) Some protocol parameters declared in the investigation file are not used in any assay file: ['mass analyzer', 'software', 'mass spectrometry instrument', 'ms software', 'chromatography column']\n", - "2024-03-11 15:23:43,039 [WARNING]: rules_40xx.py(check_protocol_fields:351) >> (W) Protocol(s) of type ['labeling'] defined in the ISA-configuration expected as a between 'Extract Name' and 'NMR Assay Name' but has not been found, in the file 'a_BH2023-metabolite-profiling-nmr-assay.txt'\n", - "2024-03-11 15:23:43,044 [WARNING]: rules_40xx.py(check_required_fields:159) >> (W) Required field 'Parameter Value[library layout]' not found in the file 'a_BH2023-rna-seq-assay.txt'\n", - "2024-03-11 15:23:43,049 [WARNING]: rules_40xx.py(check_protocol_fields:351) >> (W) Protocol(s) of type ['nucleic acid extraction'] defined in the ISA-configuration expected as a between 'Sample Name' and 'Extract Name' but has not been found, in the file 'a_BH2023-rna-seq-assay.txt'\n", - "2024-03-11 15:23:43,050 [WARNING]: rules_40xx.py(check_protocol_fields:351) >> (W) Protocol(s) of type ['sequence analysis data transformation'] defined in the ISA-configuration expected as a between 'Raw Data File' and 'Data Transformation Name' but has not been found, in the file 'a_BH2023-rna-seq-assay.txt'\n", - "2024-03-11 15:23:43,060 [WARNING]: rules_40xx.py(check_protocol_fields:351) >> (W) Protocol(s) of type ['nucleic acid extraction'] defined in the ISA-configuration expected as a between 'Sample Name' and 'Extract Name' but has not been found, in the file 'a_BH2023-cnv_seq-assay.txt'\n", - "2024-03-11 15:23:43,061 [WARNING]: rules_40xx.py(check_protocol_fields:351) >> (W) Protocol(s) of type ['sequence analysis data transformation'] defined in the ISA-configuration expected as a between 'Raw Data File' and 'Data Transformation Name' but has not been found, in the file 'a_BH2023-cnv_seq-assay.txt'\n" - ] - }, { "name": "stdout", "output_type": "stream", "text": [ - "cannot access local variable 'result' where it is not associated with a value\n", - "cannot access free variable 'spl' where it is not associated with a value in enclosing scope\n" + "free variable 'spl' referenced before assignment in enclosing scope\n" ] } ], @@ -2914,18 +1270,16 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 20, "metadata": { "scrolled": true }, "outputs": [ { "data": { - "text/plain": [ - "[]" - ] + "text/plain": "[]" }, - "execution_count": 24, + "execution_count": 20, "metadata": {}, "output_type": "execute_result" } @@ -2950,7 +1304,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 21, "metadata": { "scrolled": true }, @@ -2958,50 +1312,35 @@ "source": [ "from isatools.isatab import load\n", "with open(os.path.join(main_path,\"TAB\", \"i_investigation.txt\")) as isa_sirm_test:\n", - " roundtrip = load(isa_sirm_test)\n", - "\n", - "# print(roundtrip.studies[0].assays[0].samples[1].name)\n", - "\n", - "# print(roundtrip.studies[0].assays[0].other_material[0].name)\n", - "# print(roundtrip.studies[0].assays[0].other_material[0].type)\n", - "# print(roundtrip.studies[0].assays[0].other_material[0].characteristics[0].value)\n", - "# #NOTE: this highlights an issue with the isatab load function,\n", - "\n", - "# print(roundtrip.studies[0].assays[0].other_material[8].name)\n", - "# print(roundtrip.studies[0].assays[0].other_material[8].type)\n", - "# print(roundtrip.studies[0].assays[0].other_material[8].characteristics[0].value)\n", - "\n", - "# print(roundtrip.studies[0].assays[1].other_material[1].name)\n", - "# print(roundtrip.studies[0].assays[1].other_material[1].type)\n", - "# print(roundtrip.studies[0].assays[1].other_material[1].characteristics[0].value) " + " roundtrip = load(isa_sirm_test)" ] }, { "cell_type": "code", - "execution_count": 29, + "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "cannot access local variable 'result' where it is not associated with a value\n", - "cannot access free variable 'spl' where it is not associated with a value in enclosing scope\n", + "free variable 'spl' referenced before assignment in enclosing scope\n", "NMR spectroscopy\n", "assay-name-nmr-metpro-CPMG-5\n", - "Process(name=)\n" + "['process-0-intracellular metabolite extraction', 'process-1-intracellular metabolite extraction', 'process-2-intracellular metabolite extraction', 'process-3-intracellular metabolite extraction', 'process-4-intracellular metabolite extraction', 'process-5-intracellular metabolite extraction', 'process-6-intracellular metabolite extraction', 'process-7-intracellular metabolite extraction', 'assay-name-nmr-metpro-CPMG-1', 'assay-name-nmr-metpro-CPMG-3', 'assay-name-nmr-metpro-CPMG-5', 'assay-name-nmr-metpro-CPMG-7', 'assay-name-nmr-metpro-CPMG-2', 'assay-name-nmr-metpro-CPMG-4', 'assay-name-nmr-metpro-CPMG-6', 'assay-name-nmr-metpro-CPMG-8', 'NMR-metpro-DT-ident']\n", + "Process(name=process-0-mRNA extraction)\n" ] } ], "source": [ "from isatools.convert import isatab2json\n", - "from isatools import isajson\n", "import json\n", "\n", "isa_json = isatab2json.convert(os.path.join(main_path, \"TAB\"), validate_first=True, use_new_parser=True)\n", "\n", "print(isa_json[\"studies\"][0][\"assays\"][0][\"technologyType\"][\"annotationValue\"])\n", "print(isa_json[\"studies\"][0][\"assays\"][0][\"processSequence\"][10][\"name\"])\n", + "print([process['name'] for process in isa_json[\"studies\"][0][\"assays\"][0][\"processSequence\"]])\n", "\n", "\n", "output_path = os.path.join(main_path, 'JSON', 'isa-bh2023-t2j.json')\n", @@ -3024,15 +1363,15 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 23, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "./output/ISA-BH2023-ALL/JSON/BH23-ISATAB_FROM_JSON\n", - "CONFIG at: /Users/philippe/Documents/git/isa-api2/isa-api/isatools/isajson/../resources/config/json/default\n" + "./output/ISA-BH2023-ALL/JSON\\BH23-ISATAB_FROM_JSON\n", + "CONFIG at: F:\\Work\\isa-api\\isatools\\isajson\\..\\resources\\config\\json\\default\n" ] } ], @@ -3054,14 +1393,14 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": 24, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "CONFIG at: /Users/philippe/Documents/git/isa-api2/isa-api/isatools/isajson/../resources/config/json/default\n" + "CONFIG at: F:\\Work\\isa-api\\isatools\\isajson\\..\\resources\\config\\json\\default\n" ] } ], @@ -3086,7 +1425,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 24, "metadata": {}, "outputs": [], "source": [] @@ -3094,9 +1433,9 @@ ], "metadata": { "kernelspec": { - "display_name": "isa-py-3.11", + "display_name": "Python 3 (ipykernel)", "language": "python", - "name": "isa-py-3.11" + "name": "python3" }, "language_info": { "codemirror_mode": { @@ -3108,7 +1447,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.11.0b5" + "version": "3.10.7" } }, "nbformat": 4, diff --git a/isatools/isatab/load/core.py b/isatools/isatab/load/core.py index 1619d285..c7cbee84 100644 --- a/isatools/isatab/load/core.py +++ b/isatools/isatab/load/core.py @@ -447,7 +447,10 @@ def __set_ontology_source(self, row: Series) -> None: file=row['Term Source File'], version=row['Term Source Version'], description=row['Term Source Description']) - ontology_source.comments = self.get_comments(self.__df_dict['ontology_sources']) + for key in row.keys(): + if _RX_COMMENT.match(str(key)) and row[key]: + source_name = next(iter(_RX_COMMENT.findall(str(key)))) + ontology_source.comments.append(Comment(name=source_name, value=row[key])) self.__investigation.ontology_source_references.append(ontology_source) def __create_investigation(self) -> None: