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..78548fc3 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 @@ -2,7 +2,11 @@ "cells": [ { "cell_type": "markdown", - "metadata": {}, + "metadata": { + "pycharm": { + "name": "#%% md\n" + } + }, "source": [ "## Abstract:\n", "\n", @@ -32,163 +36,25 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "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", - 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idna<3,>=2.5 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from requests~=2.25.1->isatools==0.14.2) (2.10)\n", - "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from requests~=2.25.1->isatools==0.14.2) (1.26.6)\n", - "Requirement already satisfied: appdirs~=1.4.3 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from fs~=2.4->mzml2isa==1.1.1->isatools==0.14.2) (1.4.4)\n", - "Requirement already satisfied: zipp>=0.5 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from importlib-metadata>=3.6.0->Flask~=2.2.2->isatools==0.14.2) (3.17.0)\n", - "Requirement already satisfied: fastobo~=0.12.1 in /Users/philippe/.pyenv/versions/3.9.0/lib/python3.9/site-packages (from pronto~=2.0->mzml2isa==1.1.1->isatools==0.14.2) (0.12.2)\n", - "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" - ] - } - ], + "outputs": [], "source": [ "!pip install git+https://github.com/isa-tools/isa-api.git@issue-511" ] }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "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" - ] - } - ], + "outputs": [], "source": [ "!pip show isatools" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": { "scrolled": true }, @@ -292,7 +158,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": { "scrolled": true }, @@ -327,7 +193,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -344,7 +210,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": { "scrolled": true }, @@ -430,7 +296,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": null, "metadata": { "scrolled": true }, @@ -456,7 +322,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": null, "metadata": { "scrolled": true }, @@ -488,7 +354,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": { "scrolled": true }, @@ -677,7 +543,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": { "scrolled": true }, @@ -785,7 +651,7 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": { "scrolled": true }, @@ -839,7 +705,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -849,7 +715,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": { "scrolled": true }, @@ -969,7 +835,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1072,7 +938,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1167,7 +1033,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1308,26 +1174,11 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "[isatools.model.Characteristic(category=isatools.model.OntologyAnnotation(term='Stuff Type', term_source=None, term_accession='', comments=[]), value=isatools.model.OntologyAnnotation(term='gDNA', term_source=isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n", - 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Investigations', comments=[]), term_accession='https://purl.org/OBOfoundry/obi:123414', comments=[]), unit=None, comments=[])]\n" - ] - } - ], + "outputs": [], "source": [ "char_ext_cnv_seq = Characteristic(category=OntologyAnnotation(term=\"Stuff Type\", term_source=\"\", term_accession=\"\"),\n", " value=OntologyAnnotation(term=\"gDNA\", term_source=obi, term_accession=\"https://purl.org/OBOfoundry/obi:123414\"))\n", @@ -1458,7 +1309,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1480,7 +1331,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": { "scrolled": true }, @@ -1510,742 +1361,11 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "data": { - "text/plain": [ - "isatools.model.Investigation(identifier='', filename='', title='', submission_date='', public_release_date='', 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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/77a44af8-6c8f-46d0-bb0f-e83a877f69d3\". name=\"extract-process-3\", 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-1', 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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/b6002d9c-c0e6-4c54-9727-525f6e2482fa\". 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', 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', 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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)], derives_from=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/1d1054aa-55ee-4ff8-8b9f-93616972146b\". 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=[], comments=[])]), isatools.model.process.Process(id=\"#process/e1509bf1-f2fa-4614-85e0-eb962782bf3f\". name=\"NMR-metpro-DT-ident\", 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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', 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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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outputs=[]), isatools.model.process.Process(id=\"#process/2b193325-48ad-45dc-a2c6-86812d0259c3\". name=\"rna-library-name-0\", 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/4cb8bb43-e2d3-437c-a958-3d81fca4efd0\". 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 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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/dcc6302b-0d92-4454-8cc4-22e5daa74b9f\". name=\"rna-library-name-1\", 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/de82b8bc-1331-470e-a736-445668f775fa\". 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=[], 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/bd81cc55-b3ce-4847-a033-639f27dfbc74\". 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-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='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/4451281f-3566-4448-85d1-88ac31372c4c\". name=\"extract-process-rna-seq-2\", 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 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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/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\", 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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=[], comments=[])], outputs=[]), isatools.model.process.Process(id=\"#process/f3a0c7b2-d0e5-4155-b81c-93ecb634c1ba\". name=\"rna-library-name-3\", 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/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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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/b027d54e-49b8-4b46-bcd8-199831312a4c\". name=\"extract-process-rna-seq-5\", 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-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=[]), 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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/8dac3203-3ac3-442c-81ba-7f08994bf9d3\". name=\"rna-library-name-5\", 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/8a4f887c-cc7b-4bc8-979c-4774962d086c\". 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=[], 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/954bd5fe-2a27-48f7-beb8-9dd076418099\". 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\", 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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='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\". 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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=[]), 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=[]), 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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', 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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=[])], 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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', 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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', 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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_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.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', 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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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[ "from isatools.isatab import dump\n", "\n", @@ -2262,572 +1382,9 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "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='')]), isatools.model.OntologySource(name='EFO', file='', version='', description='Experimental Factor Ontology', comments=[isatools.model.Comment(name='onto-test', value='')]), isatools.model.OntologySource(name='OBI', file='', version='', description='Ontology for Biomedical Investigations', comments=[isatools.model.Comment(name='onto-test', value='')]), isatools.model.OntologySource(name='PATO', file='', version='', 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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/84eb04f6-f8f9-44eb-94cc-7b7a97462d83\". name=\"process-0-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-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/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', 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.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', 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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/', 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-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=[]), 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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', 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='', 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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 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/e20d891c-c6c2-4aa7-add0-0fe3a19b9c76\". name=\"process-1-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/2b550de5-aba6-46ab-bcbf-d5928b6e1ee6\". name=\"process-2-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/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 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/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=[]), 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/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='')]), 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=[])], 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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/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=[])], outputs=[]), isatools.model.process.Process(id=\"#process/f95282af-a7c7-4d73-aae5-a31a54d818fb\". name=\"process-0-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/889a400d-c211-467a-8d85-5d9581a62005\". name=\"process-1-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/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=[]), 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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', 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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', 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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', 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/0f8b9b08-b7fc-45b0-9bcc-ef4945d4757d\". 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-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=[]), 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isatools.model.Comment(name='export', value='yes')]), 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 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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), 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)], 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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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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=[]), 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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/', 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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/', 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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', 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', 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=[])])], 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, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "from isatools.isatab import load\n", "with open(os.path.join(main_path,\"TAB\", \"i_investigation.txt\")) as isa_sirm_test:\n", @@ -2849,7 +1406,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -2880,32 +1437,9 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "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" - ] - } - ], + "outputs": [], "source": [ "from isatools import isatab\n", "\n", @@ -2914,22 +1448,11 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": null, "metadata": { "scrolled": true }, - "outputs": [ - { - "data": { - "text/plain": [ - "[]" - ] - }, - "execution_count": 24, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "my_json_report_isa_flux[\"errors\"]" ] @@ -2950,7 +1473,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": null, "metadata": { "scrolled": true }, @@ -2960,7 +1483,7 @@ "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", + "#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", @@ -2978,27 +1501,15 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": null, "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", - "NMR spectroscopy\n", - "assay-name-nmr-metpro-CPMG-5\n", - "Process(name=)\n" - ] - } - ], + "outputs": [], "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", + "isa_json = isatab2json.convert(os.path.join(main_path, \"TAB\"), validate_first=False, 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", @@ -3024,18 +1535,9 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": null, "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" - ] - } - ], + "outputs": [], "source": [ "from isatools.convert import json2isatab\n", "with open(os.path.join(main_path,'JSON','isa-bh2023-t2j.json')) as in_fp:\n", @@ -3054,17 +1556,9 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": null, "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" - ] - } - ], + "outputs": [], "source": [ "from isatools.convert import json2isatab\n", "with open(os.path.join(main_path, 'isa-v2.json')) as in_fp:\n", @@ -3113,4 +1607,4 @@ }, "nbformat": 4, "nbformat_minor": 4 -} +} \ No newline at end of file diff --git a/isatools/isatab/validate/rules/rules_40xx.py b/isatools/isatab/validate/rules/rules_40xx.py index ef87ec63..35f5c146 100644 --- a/isatools/isatab/validate/rules/rules_40xx.py +++ b/isatools/isatab/validate/rules/rules_40xx.py @@ -26,18 +26,6 @@ def check_investigation_against_config(i_df_dict, configs): code = 4003 message = "A required property is missing" - # def add_warning(index, column, value_index): - # if index > 0: - # spl = "A property value in {}.{} of investigation file at column {} is required" - # spl = spl.format(column, index + 1, value_index + 1) - # validator.add_warning(message=message, supplemental=spl, code=code) - # log.warning("(W) {}".format(spl)) - # else: - # spl = "A property value in {} of investigation file at column {} is required" - # spl = spl.format(column, value_index + 1) - # validator.add_warning(message=message, supplemental=spl, code=code) - # log.warning("(W) {}".format(spl)) - def add_error(index, column, value_index): if index > 0: spl = "A property value in {}.{} of investigation file at column {} is required" @@ -333,43 +321,6 @@ def load_table_checks(df, filename): for x, column in enumerate(columns): # check if columns have valid labels if _RX_INDEXED_COL.match(column): column = column[:column.rfind('.')] - # [ - # 'Source Name', - # 'Sample Name', - # 'Extract Name', - # 'Material Type', - # 'Labeled Extract Name', - # 'Label', - # 'Protocol REF', - # 'Performer', - # 'Date', - # 'Term Source REF', - # 'Term Accession Number', - # 'Unit', - # 'Assay Name', - # 'Hybridization Assay Name', - # 'Scan Name', - # 'Array Design REF', - # 'MS Assay Name', - # 'NMR Assay Name', - # 'Image File', - # 'Raw Data File', - # 'Free Induction Decay Data File', - # 'Raw Spectral Data File', - # 'Array Data File', - # 'Normalization Name', - # 'Data Transformation Name', - # 'Derived Data File', - # 'Derived Spectral Data File', - # 'Protein Assignment File', - # 'Peptide Assignment File', - # 'Post Translational Modification Assignment File', - # 'Metabolite Assignment File', - # 'Derived Array Data File', - # 'Array Data Matrix File', - # 'Derived Array Data Matrix File', - # 'Acquisition Parameter Data File' - # # ] if (column not in ALL_LABELS) \ and not _RX_CHARACTERISTICS.match(column) \ and not _RX_PARAMETER_VALUE.match(column) \ diff --git a/isatools/resources/config/xml/investigation.xml b/isatools/resources/config/xml/investigation.xml index 012e7b52..3f046276 100644 --- a/isatools/resources/config/xml/investigation.xml +++ b/isatools/resources/config/xml/investigation.xml @@ -9,13 +9,13 @@ diff --git a/tests/convert/test_mzml2isa.py b/tests/convert/test_mzml2isa.py index caaeb7f8..d7c41b03 100644 --- a/tests/convert/test_mzml2isa.py +++ b/tests/convert/test_mzml2isa.py @@ -24,7 +24,7 @@ def test_mzml2isa_convert_investigation(self): validate_output=True) # self.assertTrue(report['validation_finished']) self.assertEqual(len(report['warnings']), 8) - self.assertEqual(len(report['errors']), 5) + self.assertEqual(len(report['errors']), 3) # Strip out the line with Comment[Created With Tool] to avoid changes in version number generated by mzml2isa with open(os.path.join(self._tmp_dir, 'i_Investigation.txt')) as in_fp, StringIO() as stripped_actual_file: @@ -45,7 +45,7 @@ def test_mzml2isa_convert_study_table(self): validate_output=True) # self.assertTrue(report['validation_finished']) self.assertEqual(len(report['warnings']), 8) - self.assertEqual(len(report['errors']), 5) + self.assertEqual(len(report['errors']), 3) with open(os.path.join(self._tmp_dir, 's_{}.txt'.format(study_id))) as out_fp: with open(os.path.join(self._tab_data_dir, study_id + '-partial', 's_{}.txt'.format(study_id))) as reference_fp: self.assertTrue(assert_tab_content_equal(out_fp, reference_fp)) @@ -56,7 +56,7 @@ def test_mzml2isa_convert_assay_table(self): validate_output=True) self.assertTrue(report['validation_finished']) self.assertEqual(len(report['warnings']), 8) - self.assertEqual(len(report['errors']), 5) + self.assertEqual(len(report['errors']), 3) with open(os.path.join(self._tmp_dir, 'a_{}_metabolite_profiling_mass_spectrometry.txt'.format(study_id))) as out_fp: with open(os.path.join(self._tab_data_dir, study_id + '-partial', 'a_{}_metabolite_profiling_mass_spectrometry.txt'.format(study_id))) as reference_fp: self.assertTrue(assert_tab_content_equal(out_fp, reference_fp)) diff --git a/tests/isatab/validate/test_core.py b/tests/isatab/validate/test_core.py index 401385c0..fbe170ad 100644 --- a/tests/isatab/validate/test_core.py +++ b/tests/isatab/validate/test_core.py @@ -25,13 +25,13 @@ def test_mtbls267(self): with open(path.join(data_path, 'i_Investigation.txt'), 'r') as data_file: r = validate(fp=data_file, config_dir=self.default_conf, origin="mzml2isa") print(r['warnings']) - self.assertEqual(len(r['errors']), 5) + self.assertEqual(len(r['errors']), 4) def test_mtbls_1846(self): data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'mtbls', 'MTBLS1846') with open(path.join(data_path, 'i_Investigation.txt'), 'r') as data_file: r = validate(fp=data_file, config_dir=self.default_conf) - self.assertEqual(len(r['errors']), 33) + self.assertEqual(len(r['errors']), 20) def test_bii_i_1(self): data_path = path.join(path.dirname(path.abspath(__file__)), '..', '..', 'data', 'tab', 'BII-I-1')