diff --git a/docs/search-indices/assay-type-schemas/af.md b/docs/search-indices/assay-type-schemas/af.md new file mode 100644 index 0000000..15ada13 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/af.md @@ -0,0 +1,42 @@ +--- +layout: page +--- +# AF + +## Overview: +This schema is for autofluorescence (AF). For an example of an AF dataset & directory, see this example autofluorescence dataset and click the Globus link. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | AF | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. Leave blank if not applicable. | Shared by all types | | False | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| resolution_x_value | The width of a pixel. | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. | Unique to this type | | True | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices. Leave blank if not applicable. | Unique to this type | mm, um, or nm | False | | resolution_z_value present | | | | +| number_of_channels | Number of channels capturing the emission spectrum from natural fluorophores in the sample. | Unique to this type | | True | | | integer | | | +| overall_protocols_io_doi | DOI for protocols.io referring to the overall protocol for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/antibodies.md b/docs/search-indices/assay-type-schemas/antibodies.md new file mode 100644 index 0000000..9977242 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/antibodies.md @@ -0,0 +1,16 @@ +--- +layout: page +--- +# antibodies + +## Overview: +Changes: + +### Last Updated: 2023-04-25 + +### Version 2 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| diff --git a/docs/search-indices/assay-type-schemas/bodyct.md b/docs/search-indices/assay-type-schemas/bodyct.md new file mode 100644 index 0000000..d772f09 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/bodyct.md @@ -0,0 +1,48 @@ +--- +layout: page +--- +# Body CT + +## Overview: +This schema is for clinical imaging using body computed tomography (Body CT). + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | clinical_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | Body CT | True | | | | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| single_file_export_format | The format in which each single imaging file will be exported. (Example: DICOM, tiff, avi, etc.) | Shared by all clinical imaging assays | | True | | | | | | +| max_x_width_value | Image width value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_x_width_value present | | | | +| max_y_height_value | Image height value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_y_height_value present | | | | +| roi_description | A description of the region of interest (ROI) captured in the image. | Shared by all clinical imaging assays | | True | | | | | | +| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | integer | | | +| resolution_x_value | The width of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices.(um) Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_z_value present | | | | +| pixel_size_z_value | Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value). Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| pixel_size_z_unit | Depth unit of the pixel or voxel measurement. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | pixel_size_z_value present | | | | +| number_of_images | The total number of images in the dataset. | Shared by all clinical imaging assays | | True | | | integer | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/bulkatacseq.md b/docs/search-indices/assay-type-schemas/bulkatacseq.md new file mode 100644 index 0000000..6a990ab --- /dev/null +++ b/docs/search-indices/assay-type-schemas/bulkatacseq.md @@ -0,0 +1,57 @@ +--- +layout: page +--- +# bulkATACseq + +## Overview: +This schema is for Assay for Transposase-Accessible Chromatin by sequencing (ATACseq)of bulk sample. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | sequence | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | bulkATACseq | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | DNA | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| bulk_transposition_input_number_nuclei | A number (no comma separators) | Unique to this type | | True | | | | | | +| bulk_atac_cell_isolation_protocols_io_doi | Link to a protocols document answering the question: How was tissue stored and processed for cell/nuclei isolation. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| is_technical_replicate | Is this a sequencing replicate? | Unique to this type | | True | | | boolean | | | +| library_adapter_sequence | Adapter sequence to be used for adapter trimming. | Unique to this type | | True | | | | | | +| library_average_fragment_size | Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. | Unique to this type | | True | | | integer | | | +| library_concentration_value | The concentration value of the pooled library samples submitted for sequencing. | Unique to this type | | True | | | number | | | +| library_concentration_unit | Unit of library_concentration_value. Leave blank if not applicable. | Unique to this type | nM | False | | library_concentration_value present | | | | +| library_construction_protocols_io_doi | A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| library_creation_date | date and time of library creation. YYYY-MM-DD, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s. Leave blank if not applicable. | Unique to this type | | False | %Y-%m-%d | | datetime | | | +| library_final_yield_value | Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul) | Unique to this type | | True | | | number | | | +| library_final_yield_unit | Units of final library yield. Leave blank if not applicable. | Unique to this type | ng | False | | library_final_yield_value present | | | | +| library_id | A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked. | Unique to this type | | True | | | | | | +| library_layout | State whether the library was generated for single-end or paired end sequencing. | Unique to this type | single-end or paired-end | True | | | | | | +| library_pcr_cycles | Number of PCR cycles performed in order to add adapters and amplify the library. Usually, this includes 5 pre-amplificationn cycles followed by 0-5 additional cycles determined by qPCR. | Unique to this type | | True | | | integer | | | +| library_preparation_kit | Reagent kit used for library preparation. | Unique to this type | | True | | | | | | +| sample_quality_metric | This is a quality metric by visual inspection. This should answer the question: Are the nuclei intact and are the nuclei free of significant amounts of debris? This can be captured at a high level, “OK” or “not OK”. | Unique to this type | | True | | | | | | +| sequencing_phix_percent | Percent PhiX loaded to the run. | Unique to this type | | True | | | number | | | +| sequencing_read_format | Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56. | Unique to this type | | True | | | | \d+(/\d+)+ | | +| sequencing_read_percent_q30 | Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …) | Unique to this type | | True | | | number | | | +| sequencing_reagent_kit | Reagent kit used for sequencing. | Unique to this type | | True | | | | | | +| transposition_kit_number | If Tn5 came from a kit, provide the catalog number. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| transposition_method | Modality of capturing accessible chromatin molecules. The kit used, for example. | Unique to this type | | True | | | | | | +| transposition_transposase_source | The source of the Tn5 transposase and transposon used for capturing accessible chromatin. | Unique to this type | | True | | | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/bulkrnaseq.md b/docs/search-indices/assay-type-schemas/bulkrnaseq.md new file mode 100644 index 0000000..36ef4ee --- /dev/null +++ b/docs/search-indices/assay-type-schemas/bulkrnaseq.md @@ -0,0 +1,52 @@ +--- +layout: page +--- +# bulk RNA + +## Overview: +Directory schemas + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | sequence | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | bulk RNA | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | RNA | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| bulk_rna_isolation_protocols_io_doi | Link to a protocols document answering the question: How was tissue stored and processed for RNA isolation RNA_isolation_protocols_io_doi. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| bulk_rna_yield_value | RNA (ng) per Weight of Tissue (mg). Answer the question: How much RNA in ng was isolated? How much tissue in mg was initially used for isolating RNA? Calculate the yield by dividing total RNA isolated by amount of tissue used to isolate RNA from (ng/mg). | Unique to this type | | True | | | number | | | +| bulk_rna_yield_units_per_tissue_unit | RNA amount per Tissue input amount. Valid values should be weight/weight (ng/mg). | Unique to this type | ng/mg | True | | | | | | +| bulk_rna_isolation_quality_metric_value | RIN value. | Unique to this type | | True | | | number | | | +| rnaseq_assay_input_value | RNA input amount value to the assay. | Unique to this type | | True | | | number | | | +| rnaseq_assay_input_unit | Units of RNA input amount to the assay. Leave blank if not applicable. | Unique to this type | ug | False | | rnaseq_assay_input_value present | | | | +| rnaseq_assay_method | The kit used for the RNA sequencing assay. | Unique to this type | | True | | | | | | +| library_construction_protocols_io_doi | A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| library_layout | State whether the library was generated for single-end or paired end sequencing. | Unique to this type | single-end or paired-end | True | | | | | | +| library_adapter_sequence | Adapter sequence to be used for adapter trimming. Example: 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. | Unique to this type | | True | | | | 5-[GATCU]+ | | +| library_pcr_cycles_for_sample_index | Number of PCR cycles performed for library indexing. | Unique to this type | | True | | | integer | | | +| library_final_yield_value | Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul) | Unique to this type | | True | | | number | | | +| library_final_yield_unit | Units of final library yield. Leave blank if not applicable. | Unique to this type | ng | False | | library_final_yield_value present | | | | +| library_average_fragment_size | Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. | Unique to this type | | True | | | integer | | | +| sequencing_reagent_kit | Reagent kit used for sequencing. | Unique to this type | | True | | | | | | +| sequencing_read_format | Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56. | Unique to this type | | True | | | | \d+(/\d+)+ | | +| sequencing_read_percent_q30 | Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …) | Unique to this type | | True | | | number | | | +| sequencing_phix_percent | Percent PhiX loaded to the run. | Unique to this type | | True | | | number | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/celldive.md b/docs/search-indices/assay-type-schemas/celldive.md new file mode 100644 index 0000000..a0e2c60 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/celldive.md @@ -0,0 +1,46 @@ +--- +layout: page +--- +# Cell DIVE / cell-dive + +## Overview: +CellDIVE uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For CellDIVE, the channel_id is represented as a cycle#/channel# combination (of the form Cycle[0-9]_CH[0-9]) linked to a given image file in the directory. +The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | Cell DIVE or cell-dive | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| number_of_antibodies | Number of antibodies. | Unique to this type | | True | | | integer | | | +| number_of_channels | Number of fluorescent channels imaged during each cycle. | Unique to this type | | True | | | integer | | | +| number_of_cycles | Number of cycles of 1. oligo application, 2. fluor application, 3. dye inactivation. | Unique to this type | | True | | | integer | | | +| number_of_imaging_rounds | the total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal. | Unique to this type | | True | | | integer | | | +| resolution_x_value | The width of a pixel. | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| processing_protocols_io_doi | DOI for analysis protocols.io for this assay. Leave blank if not applicable. | Unique to this type | | False | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| overall_protocols_io_doi | DOI for protocols.io for the overall process. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| antibodies_path | Relative path to file with antibody information for this dataset. | Unique to this type | | True | | | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/cems.md b/docs/search-indices/assay-type-schemas/cems.md new file mode 100644 index 0000000..02bd39c --- /dev/null +++ b/docs/search-indices/assay-type-schemas/cems.md @@ -0,0 +1,61 @@ +--- +layout: page +--- +# CE-MS + +## Overview: +Directory schemas + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | mass_spectrometry | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | CE-MS | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein, metabolites, lipids, peptides, phosphopeptides, or glycans | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| ms_source | The technique used for sampling and ionization of the sample. | Unique to this type | nanoflex or ESI | True | | | | | | +| polarity | The polarity of the mass analysis (positive or negative ion modes) | Unique to this type | negative ion mode, positive ion mode, or negative and positive ion mode | True | | | | | | +| mz_range_low_value | The low value of the scanned mass range for MS1. (unitless) | Unique to this type | | True | | | number | | | +| mz_range_high_value | The high value of the scanned mass range for MS1. (unitless) | Unique to this type | | True | | | number | | | +| mass_resolving_power | The MS1 resolving power defined as m/∆m where ∆m is the FWHM for a given peak with a specified m/z (m). (unitless) Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| mz_resolving_power | The peak (m/z) used to calculate the resolving power. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| ion_mobility | Specifies whether or not ion mobility spectrometry was performed and which technology was used. Technologies for measuring ion mobility: Traveling Wave Ion Mobility Spectrometry (TWIMS), Trapped Ion Mobility Spectrometry (TIMS), High Field Asymmetric waveform ion Mobility Spectrometry (FAIMS), Drift Tube Ion Mobility Spectrometry (DTIMS, Structures for Lossless Ion Manipulations (SLIM). Leave blank if not applicable. | Unique to this type | TIMS, TWIMS, FAIMS, DTIMS, or SLIMS | False | | | | | | +| data_collection_mode | Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring), or PRM (parallel reaction monitoring). | Unique to this type | DDA, DIA, MRM, or PRM | True | | | | | | +| ms_scan_mode | Indicates whether the data were generated using MS, MS/MS or MS3. | Unique to this type | MS, MS/MS, or MS3 | True | | | | | | +| labeling | Indicates whether samples were labeled prior to MS analysis (e.g., TMT). | Unique to this type | | True | | | | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| ce_interface | Method by which the separation capillary interfaces with mass spectrometer and enables electrospray ionization while completing the separation circuit. The two most prevalent commercial interfaces are sheathless and sheath-flow. | Unique to this type | sheath-flow or sheathless | True | | | | | | +| ce_capillary_coating | Treatment of surface of separation capillary. Capillary coating affects the absorption of analytes on capillary inner walls and regulates electroosmotic flow. Entries should indicate the charge of the coating and chemical composition (e.g. “Neutral; Polyacrylamide” or “Positive; Polyethyleneimine” or “Uncoated”). | Unique to this type | | True | | | | | | +| ce_background_electrolyte | Chemical composition of the background electrolyte that fills the separation capillary (e.g. “3% acetic acid”). | Unique to this type | | True | | | | | | +| ce_instrument_vendor | The manufacturer of the instrument used for capillary zone electrophoresis. Capillary electrophoresis is used to separate complex biological mixtures prior to performing MS-based analyses. Separations are performed based the analytes migrate through an electrolyte solution in the presence of an electric field. | Unique to this type | | True | | | | | | +| ce_instrument_model | The model name of the instrument used for capillary zone electrophoresis. | Unique to this type | | True | | | | | | +| ce_electroosmotic_flow | Properties of the electroosmotic flow (EOF). Normal EOF is defined as flow towards the cathode, reversed EOF is defined as flow towards the anode, and suppressed EOF involves marginal to almost no flow (e.g. when a neutral coating is used). | Unique to this type | suppressed, normal, or reversed | True | | | | | | +| spatial_type | Specifies whether or not the analysis was performed in a spatialy targeted manner and the technique used for spatial sampling. For example, Laser-capture microdissection (LCM), Liquid Extraction Surface Analysis (LESA), Nanodroplet Processing in One pot for Trace Samples (nanoPOTS). Leave blank if not applicable. | Unique to this type | LCM, LESA, nanoPOTS, or microLESA | False | | | | | | +| spatial_sampling_type | Specifies whether or not the analysis was performed in a spatially targeted manner. Spatial profiling experiments target specific tissue foci but do not necessarily generate images. Spatial imaging expriments collect data from a regular array (pixels) that can be visualized as heat maps of ion intensity at each location (molecular images). Leave blank if data are derived from bulk analysis. Leave blank if not applicable. | Unique to this type | profiling or imaging | False | | | | | | +| spatial_target | Specifies the cell-type or functional tissue unit (FTU) that is targeted in the spatial profiling experiment. Leave blank if data are generated in imaging mode without a specific target structure. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| resolution_x_value | The width of a pixel. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| processing_search | Software for analyzing and searching LC-MS/MS omics data. | Unique to this type | | True | | | | | | +| processing_protocols_io_doi | DOI for analysis protocols.io for this assay. Leave blank if not applicable. | Unique to this type | | False | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| overall_protocols_io_doi | DOI for protocols.io for the overall process. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/codex.md b/docs/search-indices/assay-type-schemas/codex.md new file mode 100644 index 0000000..d1fdbb6 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/codex.md @@ -0,0 +1,49 @@ +--- +layout: page +--- +# CODEX / CODEX2 + +## Overview: +This schema is for CO-Detection by indEXing (CODEX). CODEX uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For CODEX, in that TSV, the channel_id is a cycle#/channel# combination linked to a given image file (of the form Cycle[0-9]_CH[0-9]). Each TIF file in a CODEX dataset contains image data captured from a single channel in a single cycle, identified and connected to the channel_id by its location in the upload directory (of the form src_*/cyc*_reg*_*/*_*_Z*_CH*.tif). For an example of a CODEX dataset & directory, see this example CODEX dataset and click the Globus link. +The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | CODEX or CODEX2 | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition_instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing molecular mass. | Shared by all types | Keyence or Zeiss | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | BZ-X800, BZ-X710, or Axio Observer Z1 | True | | | | | | +| resolution_x_value | The width of a pixel. (Akoya pixel is 377nm square) | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of width of a pixel.(nm) Leave blank if not applicable. | Unique to this type | mm, um, or nm | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. (Akoya pixel is 377nm square) | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of height of a pixel. (nm) Leave blank if not applicable. | Unique to this type | mm, um, or nm | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices (for Akoya, z-pitch=1.5um) ie. the microscope stage is moved up or down in increments of 1.5um to capture images of several focal planes. The best one will be used & the rest discarded. The thickness of the sample itself is sample metadata. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices. Leave blank if not applicable. | Unique to this type | mm, um, or nm | False | | resolution_z_value present | | | | +| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | Unique to this type | CODEX | True | | | | | | +| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay. | Unique to this type | version 1 robot or prototype robot - Stanford/Nolan Lab | True | | | | | | +| number_of_antibodies | Number of antibodies. | Unique to this type | | True | | | integer | | | +| number_of_channels | Number of fluorescent channels imaged during each cycle. | Unique to this type | | True | | | integer | | | +| number_of_cycles | Number of cycles of 1. oligo application, 2. fluor application, 3. washes. | Unique to this type | | True | | | integer | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| antibodies_path | Relative path to file with antibody information for this dataset. | Unique to this type | | True | | | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/contributors.md b/docs/search-indices/assay-type-schemas/contributors.md new file mode 100644 index 0000000..5ca472f --- /dev/null +++ b/docs/search-indices/assay-type-schemas/contributors.md @@ -0,0 +1,16 @@ +--- +layout: page +--- +# contributors + +## Overview: +Metadata schema + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| diff --git a/docs/search-indices/assay-type-schemas/gcms.md b/docs/search-indices/assay-type-schemas/gcms.md new file mode 100644 index 0000000..3b4d879 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/gcms.md @@ -0,0 +1,63 @@ +--- +layout: page +--- +# GC-MS + +## Overview: +This schema is for gas chromatography - mass spectrophotometry (GCMS). + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | mass_spectrometry | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | GC-MS | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | metabolites or lipids | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| ms_source | The ion source type used for surface sampling. | Unique to this type | MALDI, MALDI-2, DESI, SIMS, nESI, or EI | True | | | | | | +| polarity | The polarity of the mass analysis (positive or negative ion modes) | Unique to this type | negative ion mode, positive ion mode, or negative and positive ion mode | True | | | | | | +| mz_range_low_value | The low value of the scanned mass range for MS1. (unitless) | Unique to this type | | True | | | number | | | +| mz_range_high_value | The high value of the scanned mass range for MS1. (unitless) | Unique to this type | | True | | | number | | | +| mass_resolving_power | The MS1 resolving power defined as m/∆m where ∆m is the FWHM for a given peak with a specified m/z (m). (unitless) Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| mz_resolving_power | The peak (m/z) used to calculate the resolving power. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| ion_mobility | Specifies whether or not ion mobility spectrometry was performed and which technology was used. Technologies for measuring ion mobility: Traveling Wave Ion Mobility Spectrometry (TWIMS), Trapped Ion Mobility Spectrometry (TIMS), High Field Asymmetric waveform ion Mobility Spectrometry (FAIMS), Drift Tube Ion Mobility Spectrometry (DTIMS, Structures for Lossless Ion Manipulations (SLIM). Leave blank if not applicable. | Unique to this type | TIMS, TWIMS, FAIMS, DTIMS, or SLIMS | False | | | | | | +| data_collection_mode | Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring), or PRM (parallel reaction monitoring). | Unique to this type | DDA, DIA, MRM, or PRM | True | | | | | | +| ms_scan_mode | Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT) | Unique to this type | | True | | | | | | +| labeling | Indicates whether samples were labeled prior to MS analysis (e.g., TMT) | Unique to this type | | True | | | | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| column_vendor | The manufacturer of the GC column. | Unique to this type | | True | | | | | | +| column_model | The model of the GC column used. | Unique to this type | | True | | | | | | +| column_length_value | GC column length. | Unique to this type | | True | | | number | | | +| column_length_unit | Unit for GC column length. Leave blank if not applicable. | Unique to this type | cm | False | | column_length_value present | | | | +| column_temp_value | GC column temperature. | Unique to this type | | True | | | number | | | +| column_temp_unit | Units for GC column temperature. Leave blank if not applicable. | Unique to this type | C | False | | column_temp_value present | | | | +| internal_standard | Specifies if internal standard was utilized and designates what standard was used. Leave blank if not applicable. | Unique to this type | | True | | | | | | +| ion_source | Specifies the ion source used. | Unique to this type | | True | | | | | | +| guard_column | Specifies if guard column was used. | Unique to this type | | True | | | | | | +| spatial_type | Specifies whether or not the analysis was performed in a spatialy targeted manner and the technique used for spatial sampling. For example, Laser-capture microdissection (LCM), Liquid Extraction Surface Analysis (LESA), Nanodroplet Processing in One pot for Trace Samples (nanoPOTS). Leave blank if not applicable. | Unique to this type | LCM, LESA, nanoPOTS, or microLESA | False | | | | | | +| spatial_sampling_type | Specifies whether or not the analysis was performed in a spatially targeted manner. Spatial profiling experiments target specific tissue foci but do not necessarily generate images. Spatial imaging expriments collect data from a regular array (pixels) that can be visualized as heat maps of ion intensity at each location (molecular images). Leave blank if data are derived from bulk analysis. Leave blank if not applicable. | Unique to this type | profiling or imaging | False | | | | | | +| spatial_target | Specifies the cell-type or functional tissue unit (FTU) that is targeted in the spatial profiling experiment. Leave blank if data are generated in imaging mode without a specific target structure. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| resolution_x_value | The width of a pixel. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| processing_search | Software for analyzing and searching LC-MS/MS omics data. | Unique to this type | | True | | | | | | +| overall_protocols_io_doi | DOI for protocols.io for the overall process. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/imc.md b/docs/search-indices/assay-type-schemas/imc.md new file mode 100644 index 0000000..2ea1b05 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/imc.md @@ -0,0 +1,58 @@ +--- +layout: page +--- +# Imaging Mass Cytometry + +## Overview: +This schema is for imaging mass cytometry (IMC). IMC uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For IMC, the channel_id is the name of the metal tag on the corresponding antibody. +The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | mass_spectrometry_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | Imaging Mass Cytometry | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | Unique to this type | | True | | | | | | +| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay. | Unique to this type | | True | | | | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| number_of_channels | Number of mass channels measured. | Unique to this type | | True | | | integer | | | +| ablation_distance_between_shots_x_value | x resolution. Distance between laser ablation shots in the X-dimension. | Unique to this type | | True | | | number | | | +| ablation_distance_between_shots_x_units | Units of x resolution distance between laser ablation shots. | Unique to this type | um or nm | True | | | | | | +| ablation_distance_between_shots_y_value | y resolution. Distance between laser ablation shots in the Y-dimension. | Unique to this type | | True | | | number | | | +| ablation_distance_between_shots_y_units | Units of y resolution distance between laser ablation shots. | Unique to this type | um or nm | True | | | | | | +| ablation_frequency_value | Frequency value of laser ablation (in Hz) | Unique to this type | | True | | | number | | | +| ablation_frequency_unit | Frequency unit of laser ablation. Leave blank if not applicable. | Unique to this type | Hz | False | | ablation_frequency_value present | | | | +| roi_description | A description of the region of interest (ROI) captured in the image. | Unique to this type | | True | | | | | | +| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. | Unique to this type | | True | | | integer | | | +| acquisition_id | The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image. | Unique to this type | | True | | | | | | +| dual_count_start | Threshold for dual counting. | Unique to this type | | True | | | number | | | +| max_x_width_value | Image width value of the ROI acquisition. | Unique to this type | | True | | | number | | | +| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Unique to this type | um | False | | max_x_width_value present | | | | +| max_y_height_value | Image height value of the ROI acquisition. | Unique to this type | | True | | | number | | | +| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Unique to this type | um | False | | max_y_height_value present | | | | +| segment_data_format | This refers to the data type, which is a “float” for the IMC counts. | Unique to this type | float, integer, or string | True | | | | | | +| signal_type | Type of signal measured per channel (usually dual counts) | Unique to this type | dual count, pulse count, or intensity value | True | | | | | | +| data_precision_bytes | Numerical data precision in bytes. | Unique to this type | | True | | | number | | | +| antibodies_path | Relative path to file with antibody information for this dataset. | Unique to this type | | True | | | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/imc3d.md b/docs/search-indices/assay-type-schemas/imc3d.md new file mode 100644 index 0000000..53f6e8d --- /dev/null +++ b/docs/search-indices/assay-type-schemas/imc3d.md @@ -0,0 +1,57 @@ +--- +layout: page +--- +# 3D Imaging Mass Cytometry + +## Overview: +This schema is for 3 dimensional imaging mass cytometry (IMC 3D). 3D IMC uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For 3D IMC, the channel_id is the name of the metal tag on the corresponding antibody. +The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | mass_spectrometry_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | 3D Imaging Mass Cytometry | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | Unique to this type | | True | | | | | | +| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay. | Unique to this type | | True | | | | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| number_of_channels | Number of mass channels measured. | Unique to this type | | True | | | integer | | | +| number_of_sections | Number of sections. | Unique to this type | | True | | | integer | | | +| ablation_distance_between_shots_x_value | x resolution. Distance between laser ablation shots in the X-dimension. | Unique to this type | | True | | | number | | | +| ablation_distance_between_shots_x_units | Units of x resolution distance between laser ablation shots. | Unique to this type | um or nm | True | | | | | | +| ablation_distance_between_shots_y_value | y resolution. Distance between laser ablation shots in the Y-dimension. | Unique to this type | | True | | | number | | | +| ablation_distance_between_shots_y_units | Units of y resolution distance between laser ablation shots. | Unique to this type | um or nm | True | | | | | | +| ablation_frequency_value | Frequency value of laser ablation (in Hz) | Unique to this type | | True | | | number | | | +| ablation_frequency_unit | Frequency unit of laser ablation. Leave blank if not applicable. | Unique to this type | Hz | False | | ablation_frequency_value present | | | | +| roi_description | A description of the region of interest (ROI) captured in the image. | Unique to this type | | True | | | | | | +| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. | Unique to this type | | True | | | integer | | | +| acquisition_id | The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image. | Unique to this type | | True | | | | | | +| max_x_width_value | Image width value of the ROI acquisition. | Unique to this type | | True | | | number | | | +| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Unique to this type | um | False | | max_x_width_value present | | | | +| max_y_height_value | Image height value of the ROI acquisition. | Unique to this type | | True | | | number | | | +| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Unique to this type | um | False | | max_y_height_value present | | | | +| segment_data_format | This refers to the data type, which is a “float” for the IMC counts. | Unique to this type | float, integer, or string | True | | | | | | +| signal_type | Type of signal measured per channel (usually dual counts) | Unique to this type | dual count, pulse count, or intensity value | True | | | | | | +| antibodies_path | Relative path to file with antibody information for this dataset. | Unique to this type | | True | | | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/ims.md b/docs/search-indices/assay-type-schemas/ims.md new file mode 100644 index 0000000..ef00093 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/ims.md @@ -0,0 +1,56 @@ +--- +layout: page +--- +# MALDI-IMS / SIMS-IMS / NanoDESI / DESI + +## Overview: +This schema is for imaging mass spectrometry (IMS). + +### Last Updated: 2023-04-25 + +### Version 2 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 2 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | mass_spectrometry_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | MALDI-IMS, SIMS-IMS, NanoDESI, or DESI | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein, metabolites, lipids, peptides, phosphopeptides, or glycans | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| ms_source | The ion source type used for surface sampling (MALDI, MALDI-2, DESI, nanoDESI or SIMS). | Unique to this type | MALDI, MALDI-2, LDI, LA, SIMS-C60, SIMS-H2O, DESI, or nanoDESI | True | | | | | | +| polarity | The polarity of the mass analysis (positive or negative ion modes) | Unique to this type | negative ion mode, positive ion mode, or negative and positive ion mode | True | | | | | | +| mz_range_low_value | The low value of the scanned mass range for MS1. (unitless) | Unique to this type | | True | | | number | | | +| mz_range_high_value | The high value of the scanned mass range for MS1. (unitless) | Unique to this type | | True | | | number | | | +| mass_resolving_power | The MS1 resolving power defined as m/∆m where ∆m is the FWHM for a given peak with a specified m/z (m). (unitless) | Unique to this type | | True | | | number | | | +| mz_resolving_power | The peak (m/z) used to calculate the resolving power. | Unique to this type | | True | | | number | | | +| ion_mobility | Specifies whether or not ion mobility spectrometry was performed and which technology was used. Technologies for measuring ion mobility: Traveling Wave Ion Mobility Spectrometry (TWIMS), Trapped Ion Mobility Spectrometry (TIMS), High Field Asymmetric waveform ion Mobility Spectrometry (FAIMS), Drift Tube Ion Mobility Spectrometry (DTIMS, Structures for Lossless Ion Manipulations (SLIM). Leave blank if not applicable. | Unique to this type | TIMS, TWIMS, FAIMS, DTIMS, or SLIMS | False | | | | | | +| ms_scan_mode | Scan mode refers to the number of steps in the separation of fragments. | Unique to this type | MS, MS/MS, or MS3 | True | | | | | | +| resolution_x_value | The width of a pixel. | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| preparation_type | Common methods of depositing matrix for MALDI imaging include robotic spotting, electrospray deposition, and spray-coating with an airbrush. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| preparation_maldi_matrix | The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the laser. It also helps ionize the sample, carrying it along the flight tube so it can be detected. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| desi_solvent | Solvent composition for conducting nanospray desorption electrospray ionization (nanoDESI) or desorption electrospray ionization (DESI). Leave blank if not applicable. | Unique to this type | | False | | | | | | +| desi_solvent_flow_rate | The rate of flow of the solvent into a spray. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| desi_solvent_flow_rate_unit | Units of the rate of solvent flow. Leave blank if not applicable. | Unique to this type | uL/minute | False | | desi_solvent_flow_rate present | | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| processing_protocols_io_doi | DOI for analysis protocols.io for this assay. Leave blank if not applicable. | Unique to this type | | False | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| overall_protocols_io_doi | DOI for protocols.io for the overall process. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/lcms.md b/docs/search-indices/assay-type-schemas/lcms.md new file mode 100644 index 0000000..ae44408 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/lcms.md @@ -0,0 +1,75 @@ +--- +layout: page +--- +# LC-MS / MS / LC-MS Bottom-Up / MS Bottom-Up / LC-MS Top-Down / MS Top-Down + +## Overview: +This schema is for liquid chromatography mass spectrometry (LCMS). +v2 adds mass_resolving_power, mz_resolving_power, ion_mobility, spatial_type, spatial_sampling_type, spatial_target, and resolution_{x/y}_{value/unit}. In the case of datasets in which more than one analyte_type was interrogated (e.g. lipids plus metabolytes), those datasets should be split into one dataset per analyte. +v3 adds dms and label_name fields, and negative and positive ion mode as a polarity option. + +### Last Updated: 2023-04-25 + +### Version 3 (current, release date 2021-12-06) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 3 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | mass_spectrometry | True | | | | | | +| assay_type | Bottom-up refers to analyzing proteins in a sample by digesting them to peptides. Top-down refers to analyzing whole proteins without digestion. LC-MS and MS are for lipids/metabolites. LC-MS Bottom-Up and MS Bottom-Up are for peptides. LC-MS Top-Down and MS Top-Down are for proteins. | Shared by all types | LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. Leave blank if not applicable. | Shared by all types | protein, metabolites, lipids, peptides, phosphopeptides, or glycans | False | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| dms | Was differential mobility spectrometry used in this assay? | Unique to this type | | True | | | boolean | | | +| ms_source | The ion source type used for surface sampling. | Unique to this type | ESI | True | | | | | | +| polarity | The polarity of the mass analysis (positive or negative ion modes) | Unique to this type | negative ion mode, positive ion mode, or negative and positive ion mode | True | | | | | | +| mz_range_low_value | The low value of the scanned mass range for MS1. (unitless) | Unique to this type | | True | | | number | | | +| mz_range_high_value | The high value of the scanned mass range for MS1. (unitless) | Unique to this type | | True | | | number | | | +| mass_resolving_power | The MS1 resolving power defined as m/∆m where ∆m is the FWHM for a given peak with a specified m/z (m). (unitless) Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| mz_resolving_power | The peak (m/z) used to calculate the resolving power. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| ion_mobility | Specifies whether or not ion mobility spectrometry was performed and which technology was used. Technologies for measuring ion mobility: Traveling Wave Ion Mobility Spectrometry (TWIMS), Trapped Ion Mobility Spectrometry (TIMS), High Field Asymmetric waveform ion Mobility Spectrometry (FAIMS), Drift Tube Ion Mobility Spectrometry (DTIMS, Structures for Lossless Ion Manipulations (SLIM). Leave blank if not applicable. | Unique to this type | TIMS, TWIMS, FAIMS, DTIMS, or SLIMS | False | | | | | | +| data_collection_mode | Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring), or PRM (parallel reaction monitoring). | Unique to this type | DDA, DIA, MRM, or PRM | True | | | | | | +| ms_scan_mode | Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT) | Unique to this type | | True | | | | | | +| labeling | Indicates whether samples were labeled prior to MS analysis (e.g., TMT) | Unique to this type | | True | | | | | | +| label_name | If the samples were labeled (e.g. TMT), provide the name/ID of the label on this sample. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| lc_instrument_vendor | The manufacturer of the instrument used for LC. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| lc_instrument_model | The model number/name of the instrument used for LC. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| lc_column_vendor | OPTIONAL: The manufacturer of the LC Column unless self-packed, pulled tip capilary is used. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| lc_column_model | The model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter “Pulled tip capilary”. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| lc_resin | Details of the resin used for lc, including vendor, particle size, pore size. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| lc_length_value | LC column length. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| lc_length_unit | units for LC column length (typically cm) Leave blank if not applicable. | Unique to this type | um, mm, or cm | False | | lc_length_value present | | | | +| lc_temp_value | LC temperature. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| lc_temp_unit | units for LC temperature. Leave blank if not applicable. | Unique to this type | C | False | | lc_temp_value present | | | | +| lc_id_value | LC column inner diameter (microns) Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| lc_id_unit | units of LC column inner diameter (typically microns) Leave blank if not applicable. | Unique to this type | um, mm, or cm | False | | lc_id_value present | | | | +| lc_flow_rate_value | Value of flow rate. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| lc_flow_rate_unit | Units of flow rate. Leave blank if not applicable. | Unique to this type | nL/min or mL/min | False | | lc_flow_rate_value present | | | | +| lc_gradient | LC gradient. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| lc_mobile_phase_a | Composition of mobile phase A. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| lc_mobile_phase_b | Composition of mobile phase B. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| spatial_type | Specifies whether or not the analysis was performed in a spatialy targeted manner and the technique used for spatial sampling. For example, Laser-capture microdissection (LCM), Liquid Extraction Surface Analysis (LESA), Nanodroplet Processing in One pot for Trace Samples (nanoPOTS). Leave blank if not applicable. | Unique to this type | LCM, LESA, nanoPOTS, or microLESA | False | | | | | | +| spatial_sampling_type | Specifies whether or not the analysis was performed in a spatially targeted manner. Spatial profiling experiments target specific tissue foci but do not necessarily generate images. Spatial imaging expriments collect data from a regular array (pixels) that can be visualized as heat maps of ion intensity at each location (molecular images). Leave blank if data are derived from bulk analysis. Leave blank if not applicable. | Unique to this type | profiling or imaging | False | | | | | | +| spatial_target | Specifies the cell-type or functional tissue unit (FTU) that is targeted in the spatial profiling experiment. Leave blank if data are generated in imaging mode without a specific target structure. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| resolution_x_value | The width of a pixel. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| processing_search | Software for analyzing and searching LC-MS/MS omics data. | Unique to this type | | True | | | | | | +| processing_protocols_io_doi | DOI for analysis protocols.io for this assay. Leave blank if not applicable. | Unique to this type | | False | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| overall_protocols_io_doi | DOI for protocols.io for the overall process for this assay. Leave blank if not applicable. | Unique to this type | | False | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/lightsheet.md b/docs/search-indices/assay-type-schemas/lightsheet.md new file mode 100644 index 0000000..ce5a4a6 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/lightsheet.md @@ -0,0 +1,48 @@ +--- +layout: page +--- +# Light Sheet + +## Overview: +Lightsheet uploads require metadata on the antibodies used in the assay to be provided in an Antibodies TSV. For Lightsheet, the channel_id is the name of the fluorophore tag on the antibody. For an example of a lightsheet dataset & directory, see this example lightsheet dataset and click the Globus link. +Version 2 has 5 new fields for metadata describing the Z-dimension specifically relevant to lightsheet. These values provide the total number of image sections captured, the incremental value and unit of distance between the sections and the value and unit of the total distance captured. +The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation. + +### Last Updated: 2023-04-25 + +### Version 2 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 2 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | Light Sheet | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| resolution_x_value | The width of a pixel. | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| range_z_value | The total range of the z axis. | Unique to this type | | True | | | number | | | +| range_z_unit | The unit of range_z_value. Leave blank if not applicable. | Unique to this type | nm or um | False | | range_z_value present | | | | +| step_z_value | The number of optical sections in z axis range. | Unique to this type | | True | | | number | | | +| increment_z_value | The distance between sequential optical sections. | Unique to this type | | True | | | number | | | +| increment_z_unit | The units of increment z value. Leave blank if not applicable. | Unique to this type | nm or um | False | | increment_z_value present | | | | +| number_of_antibodies | Number of antibodies. | Unique to this type | | True | | | integer | | | +| number_of_channels | Number of fluorescent channels imaged during each cycle. | Unique to this type | | True | | | integer | | | +| antibodies_path | Relative path to file with antibody information for this dataset. | Unique to this type | | True | | | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/mibi.md b/docs/search-indices/assay-type-schemas/mibi.md new file mode 100644 index 0000000..f29df5d --- /dev/null +++ b/docs/search-indices/assay-type-schemas/mibi.md @@ -0,0 +1,69 @@ +--- +layout: page +--- +# MIBI + +## Overview: +This schema is for Multiplex Ion Beam Imaging (MIBI). For MIBI, the channel_id (in the Antibodies TSV) is the name of the metal tag on the corresponding antibody. The other fields function the same way for all assays using antibodies. For more information, see the Antibodies TSV documentation. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | mass_spectrometry_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | MIBI | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| number_of_antibodies | Number of antibodies. | Unique to this type | | True | | | integer | | | +| number_of_channels | Number of fluorescent channels imaged during each cycle. | Unique to this type | | True | | | integer | | | +| resolution_x_value | The width of a pixel. (Akoya pixel is 377nm square) | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of width of a pixel.(nm) Leave blank if not applicable. | Unique to this type | mm, um, or nm | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. (Akoya pixel is 377nm square) | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of height of a pixel. (nm) Leave blank if not applicable. | Unique to this type | mm, um, or nm | False | | resolution_y_value present | | | | +| max_x_width_value | Image width value of the ROI acquisition. | Unique to this type | | True | | | number | | | +| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Unique to this type | um | False | | max_x_width_value present | | | | +| max_y_height_value | Image height value of the ROI acquisition. | Unique to this type | | True | | | number | | | +| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Unique to this type | um | False | | max_y_height_value present | | | | +| roi_description | A description of the region of interest (ROI) captured in the image. | Unique to this type | | True | | | | | | +| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. | Unique to this type | | True | | | integer | | | +| acquisition_id | The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image. | Unique to this type | | True | | | | | | +| area_normalized_ion_dose_unit | Area normalized ion dose unit. Leave blank if not applicable. | Unique to this type | nA*hr/mm2 | False | | area_normalized_ion_dose_value present | | | | +| area_normalized_ion_dose_value | Number of primary ions delivered to the sample per unit area. | Unique to this type | | True | | | number | | | +| data_precision_bytes | Numerical data precision in bytes. | Unique to this type | | True | | | number | | | +| dual_count_start | Threshold for dual counting. | Unique to this type | | True | | | number | | | +| end_datetime | Time stamp indicating end of ablation for ROI. | Unique to this type | | True | %Y-%m-%d %H:%M | | datetime | | | +| pixel_dwell_time_value | Resident time of primary ion beam on each pixel. | Unique to this type | | True | | | number | | | +| pixel_dwell_time_unit | Pixel dwell time unit. Leave blank if not applicable. | Unique to this type | ms | False | | pixel_dwell_time_value present | | | | +| pixel_size_x_value | Width value of the pixel or voxel measurement (distinct from the image resolution_x_value). | Unique to this type | | True | | | number | | | +| pixel_size_x_unit | Width unit of the pixel or voxel measurement. Leave blank if not applicable. | Unique to this type | nm | False | | pixel_size_x_value present | | | | +| pixel_size_y_value | Length value of the pixel or voxel measurement (distinct from the image resolution_y_value). | Unique to this type | | True | | | number | | | +| pixel_size_y_unit | Length unit of the pixel or voxel measurement. Leave blank if not applicable. | Unique to this type | nm | False | | pixel_size_y_value present | | | | +| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | Unique to this type | Custom or Ionpath | True | | | | | | +| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay. | Unique to this type | Custom, MIBIscope 1, or MIBIscope 2 | True | | | | | | +| primary_ion | Primary ion. | Unique to this type | Xe | True | | | | | | +| primary_ion_current_value | Primary ion current value. | Unique to this type | | True | | | number | | | +| primary_ion_current_unit | Primary ion current unit, typically nA or pA. Leave blank if not applicable. | Unique to this type | nA or pA | False | | primary_ion_current_value present | | | | +| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| segment_data_format | This refers to the data type, which is a “float” for the IMC counts. | Unique to this type | float, integer, or string | True | | | | | | +| signal_type | Type of signal measured per channel (usually dual counts) | Unique to this type | dual count, pulse count, or intensity value | True | | | | | | +| start_datetime | Time stamp indicating start of ablation for ROI. | Unique to this type | | True | %Y-%m-%d %H:%M | | datetime | | | +| antibodies_path | Relative path to file with antibody information for this dataset. | Unique to this type | | True | | | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/microct.md b/docs/search-indices/assay-type-schemas/microct.md new file mode 100644 index 0000000..77bc54b --- /dev/null +++ b/docs/search-indices/assay-type-schemas/microct.md @@ -0,0 +1,56 @@ +--- +layout: page +--- +# Micro CT + +## Overview: +This schema is for clinical imaging using micro computed tomography (Micro CT). + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | clinical_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | Micro CT | True | | | | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| single_file_export_format | The format in which each single imaging file will be exported. (Example: DICOM, tiff, avi, etc.) | Shared by all clinical imaging assays | | True | | | | | | +| max_x_width_value | Image width value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_x_width_value present | | | | +| max_y_height_value | Image height value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_y_height_value present | | | | +| roi_description | A description of the region of interest (ROI) captured in the image. | Shared by all clinical imaging assays | | True | | | | | | +| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | integer | | | +| resolution_x_value | The width of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices.(um) Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_z_value present | | | | +| pixel_size_z_value | Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value). Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| pixel_size_z_unit | Depth unit of the pixel or voxel measurement. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | pixel_size_z_value present | | | | +| number_of_images | The total number of images in the dataset. | Shared by all clinical imaging assays | | True | | | integer | | | +| voltage_value | The voltage used to acquire images. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| voltage_unit | The unit of the voltage used to acquire microCT images. Example: V. Leave blank if not applicable. | Unique to this type | V or kV | False | | voltage_value present | | | | +| current_value | The current used to acquire microCT images. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| current_unit | The unit of the current used to acquire microCT images. Example: mA. Leave blank if not applicable. | Unique to this type | mA, microA, or A | False | | current_value present | | | | +| filter | The filter used to acquire microCT images. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| imaging_threshold_value | The threshold used for analyzing microCT images. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| imaging_threshold_unit_value | The threshold unit used for analyzing microCT images (unitless) Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| total_sections_analyzed | The number of sections used for analyzing microCT or OCT images. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/mri.md b/docs/search-indices/assay-type-schemas/mri.md new file mode 100644 index 0000000..63eabcf --- /dev/null +++ b/docs/search-indices/assay-type-schemas/mri.md @@ -0,0 +1,64 @@ +--- +layout: page +--- +# MRI + +## Overview: +This schema is for clinical imaging using magnetic resonance imaging (MRI). + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | clinical_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | MRI | True | | | | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| single_file_export_format | The format in which each single imaging file will be exported. (Example: DICOM, tiff, avi, etc.) | Shared by all clinical imaging assays | | True | | | | | | +| max_x_width_value | Image width value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_x_width_value present | | | | +| max_y_height_value | Image height value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_y_height_value present | | | | +| roi_description | A description of the region of interest (ROI) captured in the image. | Shared by all clinical imaging assays | | True | | | | | | +| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | integer | | | +| resolution_x_value | The width of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices.(um) Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_z_value present | | | | +| pixel_size_z_value | Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value). Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| pixel_size_z_unit | Depth unit of the pixel or voxel measurement. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | pixel_size_z_value present | | | | +| number_of_images | The total number of images in the dataset. | Shared by all clinical imaging assays | | True | | | integer | | | +| frequency_value | Frequency at which the imaging device is operating. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| frequency_unit | Unit of frequency at which the imaging device is operating. Example: Hz, kHz, MHz. Leave blank if not applicable. | Unique to this type | Hz, kHz, or MHz | False | | frequency_value present | | | | +| coil | Receiver coil name used to collect MRI data. Example: 32 channel body coil. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| field_strength_value | MRI scanner magnetic field strength value. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| field_strength_unit | MRI scanner magnetic field strength in units of Tesla [T]. Leave blank if not applicable. | Unique to this type | Tesla | False | | field_strength_value present | | | | +| scanning_sequence | Pulse sequence used to collect MRI data. Leave blank if not applicable. | Unique to this type | spin echo, inversion recovery, gradient echo, echo planar, or research mode | False | | | | | | +| sequence_variant | Variant of the Scanning Sequence. Leave blank if not applicable. | Unique to this type | segmented k-space, magnetization transfer contrast, steady state, time reversed steady state, spoiled, magnetization prepared, oversampling phase, or no sequence variant | False | | | | | | +| echo_time | Time in msec between the middle of the excitation pulse and the peak of the echo produced (kx=0). In the case of segmented k-space, the TE(eff) is the time between the middle of the excitation pulse to the peak of the echo that is used to cover the center of k-space (i.e., -kx=0, ky=0). Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| repetition_time | The period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| flip_angle | Steady state angle in degrees to which the magnetic vector is flipped from the magnetic vector of the primary field. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| echo_train_length | Number of lines in k-space acquired per excitation per image. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| acquisition_matrix_size_in_frequency_encoding_direction | Dimensions of the acquired frequency data before reconstruction. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| acquisition_matrix_size_in_phase_encoding_direction | Dimensions of the acquired phase data before reconstruction, per image. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| number_of_image_rows | Number of rows of the reconstructed data, per image. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| number_of_image_columns | Number of columns of the reconstructed data. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| number_of_averages | Number of times a given pulse sequence is repeated in the collection of a single image or volume. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/mxif.md b/docs/search-indices/assay-type-schemas/mxif.md new file mode 100644 index 0000000..40660cf --- /dev/null +++ b/docs/search-indices/assay-type-schemas/mxif.md @@ -0,0 +1,44 @@ +--- +layout: page +--- +# MxIF + +## Overview: +This schema is for multiplex immunofluorescence microscopy (MxIF). + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | MxIF | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | protein | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| resolution_x_value | The width of a pixel. | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| number_of_channels | Number of fluorescent channels imaged during each cycle. | Unique to this type | | True | | | integer | | | +| number_of_cycles | Number of cycles of 1. antibody application, 2. image capture, 3. antibody stripping. | Unique to this type | | True | | | integer | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| overall_protocols_io_doi | DOI for protocols.io for the overall process. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| antibodies_path | Relative path to file with antibody information for this dataset. | Unique to this type | | True | | | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/oct.md b/docs/search-indices/assay-type-schemas/oct.md new file mode 100644 index 0000000..1b13322 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/oct.md @@ -0,0 +1,54 @@ +--- +layout: page +--- +# OCT + +## Overview: +This schema is for clinical imaging using optical coherence tomography (OCT). + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | clinical_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | OCT | True | | | | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| single_file_export_format | The format in which each single imaging file will be exported. (Example: DICOM, tiff, avi, etc.) | Shared by all clinical imaging assays | | True | | | | | | +| max_x_width_value | Image width value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_x_width_value present | | | | +| max_y_height_value | Image height value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_y_height_value present | | | | +| roi_description | A description of the region of interest (ROI) captured in the image. | Shared by all clinical imaging assays | | True | | | | | | +| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | integer | | | +| resolution_x_value | The width of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices.(um) Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_z_value present | | | | +| pixel_size_z_value | Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value). Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| pixel_size_z_unit | Depth unit of the pixel or voxel measurement. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | pixel_size_z_value present | | | | +| number_of_images | The total number of images in the dataset. | Shared by all clinical imaging assays | | True | | | integer | | | +| total_sections_analyzed | The number of sections used for analyzing microCT or OCT images. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| wavelength_value | The value of the wavelength used to acquire OCT images (Example: 787) Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| wavelength_unit | The unit of the wavelength value used to acquire OCT images (nm) Leave blank if not applicable. | Unique to this type | nm | False | | wavelength_value present | | | | +| volume_export_format | The format of the volume export of OCT images (Example: tiff) Leave blank if not applicable. | Unique to this type | tiff or avi | False | | | | | | +| sn_quality | An integer describing the signal to noise quality of an OCT image (Example: 30) Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| sn_quality_unit | The unit of the integer describing the signal to noise quality of an OCT image (Example: dB) Leave blank if not applicable. | Unique to this type | dB | False | | sn_quality present | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/sample-block.md b/docs/search-indices/assay-type-schemas/sample-block.md new file mode 100644 index 0000000..dcf3684 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/sample-block.md @@ -0,0 +1,16 @@ +--- +layout: page +--- +# sample-block + +## Overview: +Metadata schema + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| diff --git a/docs/search-indices/assay-type-schemas/sample-section.md b/docs/search-indices/assay-type-schemas/sample-section.md new file mode 100644 index 0000000..caddba7 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/sample-section.md @@ -0,0 +1,16 @@ +--- +layout: page +--- +# sample-section + +## Overview: +Metadata schema + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| diff --git a/docs/search-indices/assay-type-schemas/sample-suspension.md b/docs/search-indices/assay-type-schemas/sample-suspension.md new file mode 100644 index 0000000..3b2e0bb --- /dev/null +++ b/docs/search-indices/assay-type-schemas/sample-suspension.md @@ -0,0 +1,16 @@ +--- +layout: page +--- +# sample-suspension + +## Overview: +Metadata schema + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| diff --git a/docs/search-indices/assay-type-schemas/sample.md b/docs/search-indices/assay-type-schemas/sample.md new file mode 100644 index 0000000..8a7ba70 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/sample.md @@ -0,0 +1,31 @@ +--- +layout: page +--- +# sample + +## Overview: +Metadata schema + +### Last Updated: 2023-04-25 + +### Version 0 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| sample_id | (No description for this field was supplied.) Example: VAN0010-LK-152-162. | IDs | | True | | | | ([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)? | | +| vital_state | Identify the vital state of the donor. | Donor | living or deceased | True | | | | | | +| health_status | Patient’s baseline physical condition prior to immediate event leading to organ/tissue acquisition. For example, if a relatively healthy patient suffers trauma, and as a result of reparative surgery, a tissue sample is collected, the subject will be deemed “relatively healthy”. Likewise, a relatively healthy subject may have experienced trauma leading to brain death. As a result of organ donation, a sample is collected. In this scenario, the subject is deemed “relatively healthy.”. | Donor | cancer, relatively healthy, or chronic illness | True | | | | | | +| organ_condition | Health status of the organ at the time of sample recovery. | Medical Procedure | healthy or diseased | True | | | | | | +| procedure_date | Date of procedure to procure organ. | Medical Procedure | | True | %Y-%m-%d | | date | | | +| perfusion_solution | Type of solution that was used to perfuse the organ. | Medical Procedure | UWS, HTK, Belzer MPS/KPS, Formalin, Perfadex, Unknown, or None | True | | | | | | +| pathologist_report | Further details on organ level QC checks. | Medical Procedure | | True | | | | | | +| warm_ischemia_time_value | Time interval between cessation of blood flow and cooling to 4C. Leave blank if not applicable. | Medical Procedure | | False | | | number | | | +| warm_ischemia_time_unit | Time unit. Leave blank if not applicable. | Medical Procedure | minutes | False | | warm_ischemia_time_value present | | | | +| cold_ischemia_time_value | Time interval on ice to the start of preservation protocol. Leave blank if not applicable. | Medical Procedure | | False | | | number | | | +| cold_ischemia_time_unit | Time unit. Leave blank if not applicable. | Medical Procedure | minutes | False | | cold_ischemia_time_value present | | | | +| specimen_preservation_temperature | The temperature of the medium during the preservation process. | Biospecimen | Liquid Nitrogen, Liquid Nitrogen Vapor, Freezer (-80 Celsius), Freezer (-20 Celsius), Refrigerator (4 Celsius), or Room Temperature | True | | | | | | +| specimen_quality_criteria | For example, RIN: 8.7. Leave blank if not applicable. | Biospecimen | | False | | | | | | +| specimen_tumor_distance_value | If surgical sample, how far from the tumor was the sample obtained from. Typically a number of centimeters. Leave blank if not applicable or unknown. Leave blank if not applicable. | Biospecimen | | False | | | number | | | +| specimen_tumor_distance_unit | Distance unit. Leave blank if not applicable. | Biospecimen | cm | False | | specimen_tumor_distance_value present | | | | diff --git a/docs/search-indices/assay-type-schemas/scatacseq.md b/docs/search-indices/assay-type-schemas/scatacseq.md new file mode 100644 index 0000000..e65a4e5 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/scatacseq.md @@ -0,0 +1,61 @@ +--- +layout: page +--- +# SNARE-seq2 / sciATACseq / snATACseq + +## Overview: +This schema is for the single nucleus Assay for Transposase Accessible Chromatin by sequencing (snATACseq). + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | sequence | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | SNARE-seq2, sciATACseq, or snATACseq | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | DNA | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| is_technical_replicate | If TRUE, fastq files in dataset need to be merged. | Unique to this type | | True | | | boolean | | | +| library_id | A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked. | Unique to this type | | True | | | | | | +| sc_isolation_protocols_io_doi | Link to a protocols document answering the question: How were single cells separated into a single-cell suspension? | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| sc_isolation_entity | The type of single cell entity derived from isolation protocol. | Unique to this type | whole cell, nucleus, cell-cell multimer, or spatially encoded cell barcoding | True | | | | | | +| sc_isolation_tissue_dissociation | The method by which tissues are dissociated into single cells in suspension. | Unique to this type | | True | | | | | | +| sc_isolation_enrichment | The method by which specific cell populations are sorted or enriched. | Unique to this type | none or FACS | True | | | | | | +| sc_isolation_quality_metric | A quality metric by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level. “OK” or “not OK”, or with more specificity such as “debris”, “clump”, “low clump”. | Unique to this type | | True | | | | | | +| sc_isolation_cell_number | Total number of cell/nuclei yielded post dissociation and enrichment. | Unique to this type | | True | | | integer | | | +| transposition_input | Number of cell/nuclei input to the assay. | Unique to this type | | True | | | number | | | +| transposition_method | Modality of capturing accessible chromatin molecules. | Unique to this type | SNARE-Seq2-AC, bulkATACseq, snATACseq, or sciATACseq | True | | | | | | +| transposition_transposase_source | The source of the Tn5 transposase and transposon used for capturing accessible chromatin. | Unique to this type | 10X snATAC, In-house, Nextera, or 10X multiome | True | | | | | | +| transposition_kit_number | If Tn5 came from a kit, provide the catalog number. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| library_construction_protocols_io_doi | A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”. DOI for protocols.io referring to the protocol for this assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| library_layout | State whether the library was generated for single-end or paired end sequencing. | Unique to this type | single-end or paired-end | True | | | | | | +| library_adapter_sequence | Adapter sequence to be used for adapter trimming. Example: CTGTCTCTTATACACATCT. | Unique to this type | | True | | | | [ATCG]+(\+[ATCG]+)? | | +| cell_barcode_read | Which read file(s) contains the cell barcode. Multiple cell_barcode_read files must be provided as a comma-delimited list (e.g. file1,file2,file3). This field is not required for barcoding by single-cell combinatorial indexing. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| cell_barcode_offset | Positions in the read at which the cell barcodes start. Cell barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences (the offsets). First barcode at position 0, then 38, then 76. (Does not apply to sciATACseq, SNARE-seq and BulkATAC.) Leave blank if not applicable. Example: 0,0,38,76. | Unique to this type | | False | | | | \d+(,\d+)* | | +| cell_barcode_size | Length of the cell barcode in base pairs. Cell barcodes are, for example, 3 x 8 bp sequences that are spaced by constant sequences, the offsets. (Does not apply to sciATACseq, SNARE-seq and BulkATAC.) Leave blank if not applicable. Example: 16,8,8,8. | Unique to this type | | False | | | | \d+(,\d+)* | | +| library_pcr_cycles | Number of PCR cycles to enrich for accessible chromatin fragments. | Unique to this type | | True | | | integer | | | +| library_pcr_cycles_for_sample_index | Number of PCR cycles performed for library generation (figure in Descriptions section) | Unique to this type | | True | | | integer | | | +| library_final_yield | Total ng of library after final pcr amplification step. | Unique to this type | | True | | | number | | | +| library_final_yield_unit | Units for library_final_yield. Leave blank if not applicable. | Unique to this type | ng | False | | library_final_yield present | | | | +| library_average_fragment_size | Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. | Unique to this type | | True | | | integer | | | +| sequencing_reagent_kit | Reagent kit used for sequencing. | Unique to this type | | True | | | | | | +| sequencing_read_format | Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56. | Unique to this type | | True | | | | \d+(/\d+)+ | | +| sequencing_read_percent_q30 | Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …) | Unique to this type | | True | | | number | | | +| sequencing_phix_percent | Percent PhiX loaded to the run. | Unique to this type | | True | | | number | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/scrnaseq.md b/docs/search-indices/assay-type-schemas/scrnaseq.md new file mode 100644 index 0000000..0950074 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/scrnaseq.md @@ -0,0 +1,63 @@ +--- +layout: page +--- +# scRNAseq-10xGenomics-v2 / scRNAseq-10xGenomics-v3 / snRNAseq-10xGenomics-v2 / snRNAseq-10xGenomics-v3 / scRNAseq / sciRNAseq / snRNAseq / SNARE2-RNAseq + +## Overview: +This schema is for single cell RNA sequencing (scRNAseq). v3 adds umi_* fields. + +### Last Updated: 2023-04-25 + +### Version 3 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 3 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | sequence | True | | | | | | +| assay_type | The UMI sequence length in the 10xGenomics-v2 kit is 10 base pairs and the length in the 10xGenomics-v3 kit is 12 base pairs. | Shared by all types | scRNAseq-10xGenomics-v2, scRNAseq-10xGenomics-v3, snRNAseq-10xGenomics-v2, snRNAseq-10xGenomics-v3, scRNAseq, sciRNAseq, snRNAseq, or SNARE2-RNAseq | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | RNA | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| sc_isolation_protocols_io_doi | Link to a protocols document answering the question: How were single cells separated into a single-cell suspension? | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| sc_isolation_entity | The type of single cell entity derived from isolation protocol. | Unique to this type | whole cell, nucleus, cell-cell multimer, or spatially encoded cell barcoding | True | | | | | | +| sc_isolation_tissue_dissociation | The method by which tissues are dissociated into single cells in suspension. | Unique to this type | | True | | | | | | +| sc_isolation_enrichment | The method by which specific cell populations are sorted or enriched. | Unique to this type | none or FACS | True | | | | | | +| sc_isolation_quality_metric | A quality metric by visual inspection prior to cell lysis or defined by known parameters such as wells with several cells or no cells. This can be captured at a high level. | Unique to this type | | True | | | | | | +| sc_isolation_cell_number | Total number of cell/nuclei yielded post dissociation and enrichment. | Unique to this type | | True | | | integer | | | +| rnaseq_assay_input | Number of cell/nuclei input to the assay. | Unique to this type | | True | | | integer | | | +| rnaseq_assay_method | The kit used for the RNA sequencing assay. | Unique to this type | | True | | | | | | +| library_construction_protocols_io_doi | A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| library_layout | State whether the library was generated for single-end or paired end sequencing. | Unique to this type | single-end or paired-end | True | | | | | | +| library_adapter_sequence | Adapter sequence to be used for adapter trimming. Example: CTGTCTCTTATACACATCT. | Unique to this type | | True | | | | [ATCG]+(\+[ATCG]+)? | | +| library_id | A library ID, unique within a TMC, which allows corresponding RNA and chromatin accessibility datasets to be linked. | Unique to this type | | True | | | | | | +| is_technical_replicate | Is the sequencing reaction run in replicate, TRUE or FALSE. | Unique to this type | | True | | | boolean | | | +| cell_barcode_read | Which read file(s) contains the cell barcode. Multiple cell_barcode_read files must be provided as a comma-delimited list (e.g. file1,file2,file3). Leave blank if not applicable. | Unique to this type | | False | | | | | | +| umi_read | Which read file(s) contains the UMI (unique molecular identifier) barcode. Example: R1. | Unique to this type | | True | | | | [^/]+ | | +| umi_offset | Position in the read at which the umi barcode starts. | Unique to this type | | True | | | integer | | | +| umi_size | Length of the umi barcode in base pairs. | Unique to this type | | True | | | integer | | | +| cell_barcode_offset | Position(s) in the read at which the cell barcode starts. Leave blank if not applicable. Example: 0,0,38,76. | Unique to this type | | False | | | | \d+(,\d+)* | | +| cell_barcode_size | Length of the cell barcode in base pairs. Leave blank if not applicable. Example: 16,8,8,8. | Unique to this type | | False | | | | \d+(,\d+)* | | +| expected_cell_count | How many cells are expected? This may be used in downstream pipelines to guide selection of cell barcodes or segmentation parameters. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| library_pcr_cycles | Number of PCR cycles to amplify cDNA. | Unique to this type | | True | | | integer | | | +| library_pcr_cycles_for_sample_index | Number of PCR cycles performed for library indexing. | Unique to this type | | True | | | integer | | | +| library_final_yield_value | Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul) | Unique to this type | | True | | | number | | | +| library_final_yield_unit | Units of final library yield. Leave blank if not applicable. | Unique to this type | ng | False | | library_final_yield_value present | | | | +| library_average_fragment_size | Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. | Unique to this type | | True | | | integer | | | +| sequencing_reagent_kit | Reagent kit used for sequencing. | Unique to this type | | True | | | | | | +| sequencing_read_format | Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56. | Unique to this type | | True | | | | \d+(/\d+)+ | | +| sequencing_read_percent_q30 | Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …) | Unique to this type | | True | | | number | | | +| sequencing_phix_percent | Percent PhiX loaded to the run. | Unique to this type | | True | | | number | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/seqfish.md b/docs/search-indices/assay-type-schemas/seqfish.md new file mode 100644 index 0000000..b98ebfa --- /dev/null +++ b/docs/search-indices/assay-type-schemas/seqfish.md @@ -0,0 +1,50 @@ +--- +layout: page +--- +# seqFISH + +## Overview: +This schema is for spatial sequencing by fluorescence in situ hybridization (seqFISH). + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | seqFISH | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | RNA | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| resolution_x_value | The width of a pixel. | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices (for Akoya, z-pitch=1.5um) ie. the microscope stage is moved up or down in increments of 1.5um to capture images of several focal planes. The best one will be used & the rest discarded. The thickness of the sample itself is sample metadata. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices. Leave blank if not applicable. | Unique to this type | mm, um, or nm | False | | resolution_z_value present | | | | +| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | Unique to this type | | True | | | | | | +| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay. | Unique to this type | | True | | | | | | +| number_of_barcode_probes | Number of barcode probes targeting mRNAs (eg. 24,000 barcode probes = 24,000 mRNAs - 1 per mRNA of interest) | Unique to this type | | True | | | integer | | | +| number_of_barcode_regions_per_barcode_probe | Number of barcode regions on each mRNA barcode probe (the paper describes mRNA probes with 4 barcoded regions) | Unique to this type | | True | | | integer | | | +| number_of_readout_probes_per_channel | Number of readout probes that can be interrogated per channel per cycle (the paper describes 20 readout probes per channel (x 3 channels -> total = 60)) | Unique to this type | | True | | | integer | | | +| number_of_pseudocolors_per_channel | Number of pseudocolors that can be assigned to each fluorescent channel (the paper describes 20 pseudocolors per channel (x 3 channels -> total = 60) | Unique to this type | | True | | | integer | | | +| number_of_channels | Number of fluorescent channels (the paper describes 3 channels - for 3 fluorescent dyes) | Unique to this type | | True | | | integer | | | +| number_of_cycles | For each barcode region being interrogated, the number of cycles of 1. Hybridization of readout probes, 2. imaging, 3. Washes (the paper describes 1 readout probe per hyb cycle -> 20 readout probes = 20 hyb cycles) | Unique to this type | | True | | | integer | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/slideseq.md b/docs/search-indices/assay-type-schemas/slideseq.md new file mode 100644 index 0000000..fcc4d4b --- /dev/null +++ b/docs/search-indices/assay-type-schemas/slideseq.md @@ -0,0 +1,52 @@ +--- +layout: page +--- +# Slide-seq + +## Overview: +Directory schemas + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | sequence | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | Slide-seq | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | RNA | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| rnaseq_assay_method | The kit used for the RNA sequencing assay. | Unique to this type | | True | | | | | | +| library_construction_protocols_io_doi | A link to the protocol document containing the library construction method (including version) that was used, e.g. “Smart-Seq2”, “Drop-Seq”, “10X v3”. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| library_layout | State whether the library was generated for single-end or paired end sequencing. | Unique to this type | single-end or paired-end | True | | | | | | +| library_adapter_sequence | Adapter sequence to be used for adapter trimming. | Unique to this type | | True | | | | | | +| puck_id | Slide-seq captures RNA sequence data on spatially barcoded arrays of beads. Beads are fixed to a slide in a region shaped like a round puck. Each puck has a unique puck_id. | Unique to this type | | True | | | | | | +| is_technical_replicate | Is the sequencing reaction run in repliucate, TRUE or FALSE. | Unique to this type | | True | | | boolean | | | +| bead_barcode_read | Which read file contains the bead barcode. | Unique to this type | | True | | | | | | +| bead_barcode_offset | Position(s) in the read at which the bead barcode starts. | Unique to this type | | True | | | | | | +| bead_barcode_size | Length of the bead barcode in base pairs. | Unique to this type | | True | | | | | | +| library_pcr_cycles | Number of PCR cycles to amplify cDNA. | Unique to this type | | True | | | integer | | | +| library_pcr_cycles_for_sample_index | Number of PCR cycles performed for library indexing. | Unique to this type | | True | | | integer | | | +| library_final_yield_value | Total number of ng of library after final pcr amplification step. This is the concentration (ng/ul) * volume (ul) | Unique to this type | | True | | | number | | | +| library_final_yield_unit | Units of final library yield. Leave blank if not applicable. | Unique to this type | ng | False | | library_final_yield_value present | | | | +| library_average_fragment_size | Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. | Unique to this type | | True | | | integer | | | +| sequencing_reagent_kit | Reagent kit used for sequencing. | Unique to this type | | True | | | | | | +| sequencing_read_format | Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56. | Unique to this type | | True | | | | \d+(/\d+)+ | | +| sequencing_read_percent_q30 | Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …) | Unique to this type | | True | | | number | | | +| sequencing_phix_percent | Percent PhiX loaded to the run. | Unique to this type | | True | | | number | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/stained.md b/docs/search-indices/assay-type-schemas/stained.md new file mode 100644 index 0000000..fc888e5 --- /dev/null +++ b/docs/search-indices/assay-type-schemas/stained.md @@ -0,0 +1,43 @@ +--- +layout: page +--- +# PAS microscopy + +## Overview: +This schema is for microscopy of tissue treated with periodic acid–Schiff stain (stained). For an example of a PAS (Periodic acid-Schiff) dataset & directory, see this example PAS stained dataset and click the Globus link. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | PAS microscopy | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. Leave blank if not applicable. | Shared by all types | | False | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| resolution_x_value | The width of a pixel. | Unique to this type | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Unique to this type | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Unique to this type | nm or um | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices ie. the microscope stage is moved up or down in increments to capture images of several focal planes. The best one will be used & the rest discarded. The thickness of the sample itself is sample metadata. Leave blank if not applicable. | Unique to this type | | True | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices. Leave blank if not applicable. | Unique to this type | mm, um, or nm | False | | resolution_z_value present | | | | +| stain | Chemical stains (dyes) applied to histology samples to highlight important features of the tissue as well as to enhance the tissue contrast. | Unique to this type | | True | | | | | | +| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| overall_protocols_io_doi | DOI for protocols.io for the overall process. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/ultrasound.md b/docs/search-indices/assay-type-schemas/ultrasound.md new file mode 100644 index 0000000..6d3373d --- /dev/null +++ b/docs/search-indices/assay-type-schemas/ultrasound.md @@ -0,0 +1,56 @@ +--- +layout: page +--- +# Ultrasound + +## Overview: +This schema is for clinical imaging using ultrasound. + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | clinical_imaging | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | Ultrasound | True | | | | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| single_file_export_format | The format in which each single imaging file will be exported. (Example: DICOM, tiff, avi, etc.) | Shared by all clinical imaging assays | | True | | | | | | +| max_x_width_value | Image width value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_x_width_unit | Units of image width of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_x_width_value present | | | | +| max_y_height_value | Image height value of the ROI acquisition. | Shared by all clinical imaging assays | | True | | | number | | | +| max_y_height_unit | Units of image height of the ROI acquisition. Leave blank if not applicable. | Shared by all clinical imaging assays | um or mm | False | | max_y_height_value present | | | | +| roi_description | A description of the region of interest (ROI) captured in the image. | Shared by all clinical imaging assays | | True | | | | | | +| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | integer | | | +| resolution_x_value | The width of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_x_unit | The unit of measurement of the width of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_x_value present | | | | +| resolution_y_value | The height of a pixel. | Shared by all clinical imaging assays | | True | | | number | | | +| resolution_y_unit | The unit of measurement of the height of a pixel. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_y_value present | | | | +| resolution_z_value | Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes. Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| resolution_z_unit | The unit of incremental distance between image slices.(um) Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | resolution_z_value present | | | | +| pixel_size_z_value | Depth value of the pixel or voxel measurement (distinct from the image resolution_z_value). Leave blank if not applicable. | Shared by all clinical imaging assays | | False | | | number | | | +| pixel_size_z_unit | Depth unit of the pixel or voxel measurement. Leave blank if not applicable. | Shared by all clinical imaging assays | nm, um, or mm | False | | pixel_size_z_value present | | | | +| number_of_images | The total number of images in the dataset. | Shared by all clinical imaging assays | | True | | | integer | | | +| quality_view | The quality of the acquired ultrasound images. Leave blank if not applicable. | Unique to this type | high confidence/optimal, low confidence/sub-optimal, or no confidence | False | | | | | | +| probe | The specific ultrasound device used to produce sound waves (String -free text). Examples: C1-5-D, C4-8-D, AB2-7-D, RIC5-9-D, RAB6-D, RAB4-8-D, 4C-D, RM6C. Leave blank if not applicable. | Unique to this type | | False | | | | | | +| dynamic_contrast | Level of echo intensity on an ultrasound. Examples: none (blank) or 1-10. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| speckle_reduction_imaging | Level used to reduce speckle noise in ultrasound images. Examples: numbers ranging from 0-5. Leave blank if not applicable. | Unique to this type | 0, 1, 2, 3, 4, or 5 | False | | | integer | | | +| compound_imaging | Level used to increase image resolution in ultrasounds by using multiple lines of site to eliminate artifacts, shadows, and increase edge detail (aka crossbeam). Examples: Either none or 0-5. Leave blank if not applicable. | Unique to this type | | False | | | integer | | | +| harmonics | Multiples of the fundamental or transmitted frequency used to help optimize an ultrasound image. Examples: None, Low, Medium or High. Leave blank if not applicable. | Unique to this type | None, Low, Medium, or High | False | | | | | | +| frequency_value | Frequency at which the imaging device is operating. Leave blank if not applicable. | Unique to this type | | False | | | number | | | +| frequency_unit | Unit of frequency at which the imaging device is operating. Example: Hz, kHz, MHz. Leave blank if not applicable. | Unique to this type | Hz, kHz, or MHz | False | | frequency_value present | | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/assay-type-schemas/wgs.md b/docs/search-indices/assay-type-schemas/wgs.md new file mode 100644 index 0000000..b9034ea --- /dev/null +++ b/docs/search-indices/assay-type-schemas/wgs.md @@ -0,0 +1,48 @@ +--- +layout: page +--- +# WGS + +## Overview: +Directory schemas + +### Last Updated: 2023-04-25 + +### Version 1 (current) + +## Metadata Schema + +| Attribute | Description | shared/unique | enum | required | format | required if | type | pattern (regular expression) | url | +|-----------|-------------|---------------|------|----------|--------|-------------|------|------------------------------|-----| +| version | Version of the schema to use when validating this metadata. | Shared by all types | 1 | True | | | | | | +| description | Free-text description of this assay. | Shared by all types | | True | | | | | | +| donor_id | HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123. | Shared by all types | | True | | | | [A-Z]+[0-9]+ | | +| tissue_id | HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456. | Shared by all types | | True | | | | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* | | +| execution_datetime | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. | Shared by all types | | True | %Y-%m-%d %H:%M | | datetime | | | +| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | Shared by all types | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| operator | Name of the person responsible for executing the assay. | Shared by all types | | True | | | | | | +| operator_email | Email address for the operator. | Shared by all types | | True | email | | | | | +| pi | Name of the principal investigator responsible for the data. | Shared by all types | | True | | | | | | +| pi_email | Email address for the principal investigator. | Shared by all types | | True | email | | | | | +| assay_category | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | Shared by all types | sequence | True | | | | | | +| assay_type | The specific type of assay being executed. | Shared by all types | WGS | True | | | | | | +| analyte_class | Analytes are the target molecules being measured with the assay. | Shared by all types | DNA | True | | | | | | +| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | Shared by all types | | True | | | boolean | | | +| acquisition_instrument_vendor | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | Shared by all types | | True | | | | | | +| acquisition_instrument_model | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | Shared by all types | | True | | | | | | +| gdna_fragmentation_quality_assurance | Is the gDNA integrity good enough for WGS? This is usually checked through running a gel. | Unique to this type | Pass or Fail | True | | | | | | +| dna_assay_input_value | Amount of DNA input into library preparation. | Unique to this type | | True | | | number | | | +| dna_assay_input_unit | Units of DNA input into library preparation. Leave blank if not applicable. | Unique to this type | ug | False | | dna_assay_input_value present | | | | +| library_construction_method | Describes DNA library preparation kit. Modality of isolating gDNA, Fragmentation and generating sequencing libraries. | Unique to this type | | True | | | | | | +| library_construction_protocols_io_doi | A link to the protocol document containing the library construction method (including version) that was used. | Unique to this type | | True | | | | 10\.17504/.* | prefix: https://dx.doi.org/ | +| library_layout | State whether the library was generated for single-end or paired end sequencing. | Unique to this type | single-end or paired-end | True | | | | | | +| library_adapter_sequence | The adapter sequence to be used for adapter trimming starting with the 5’ end. (eg. 5-ATCCTGAGAA) Example: 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. | Unique to this type | | True | | | | 5-[GATCU]+ | | +| library_final_yield | Total amount of library after final pcr amplification step. | Unique to this type | | True | | | number | | | +| library_final_yield_unit | Total units of library after final pcr amplification step. Leave blank if not applicable. | Unique to this type | ng | False | | library_final_yield present | | | | +| library_average_fragment_size | Average size in basepairs (bp) of sequencing library fragments estimated via gel electrophoresis or bioanalyzer/tapestation. | Unique to this type | | True | | | integer | | | +| sequencing_reagent_kit | Reagent kit used for sequencing. | Unique to this type | | True | | | | | | +| sequencing_read_format | Slash-delimited list of the number of sequencing cycles for, for example, Read1, i7 index, i5 index, and Read2. Example: 12/34/56. | Unique to this type | | True | | | | \d+(/\d+)+ | | +| sequencing_read_percent_q30 | Q30 is the weighted average of all the reads (e.g. # bases UMI * q30 UMI + # bases R2 * q30 R2 + …) | Unique to this type | | True | | | number | | | +| sequencing_phix_percent | Percent PhiX loaded to the run. | Unique to this type | | True | | | number | | | +| contributors_path | Relative path to file with ORCID IDs for contributors for this dataset. | Unique to this type | | True | | | | | | +| data_path | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | Unique to this type | | True | | | | | | diff --git a/docs/search-indices/files.md b/docs/search-indices/files.md index f7ed655..461aa35 100644 --- a/docs/search-indices/files.md +++ b/docs/search-indices/files.md @@ -3,7 +3,7 @@ layout: page --- # HuBMAP File Indices -### Last Updated: 2022-12-20 +### Last Updated: 2023-04-25 ## Overview: This page describes File Info documents stored in the HuBMAP indices for Files associated with Datasets. These indices are accessible via the [HuBMAP Search API](https://smart-api.info/ui/7aaf02b838022d564da776b03f357158) using the index name `files`. For example with the search endpoint like: @@ -12,7 +12,7 @@ This page describes File Info documents stored in the HuBMAP indices for Files a ``` ## Description: -Per the standard [Search API](https://smart-api.info/ui/7aaf02b838022d564da776b03f357158) functionality the indices are stored as a pair of [Elasticsearch](https://www.elastic.co/guide/en/elasticsearch/reference/7.17/index.html) indicies consisting of a private/consortium only index and a public/open to all index. The Search API will automatically direct to the index based on the user authroization. +Per the standard [Search API](https://smart-api.info/ui/7aaf02b838022d564da776b03f357158) functionality the indices are stored as a pair of [OpenSearch](https://opensearch.org/docs/latest/) indicies consisting of a private/consortium only index and a public/open to all index. The Search API will automatically direct to the index based on the user authorization. Each document in the files index contains information about one File entity in a Dataset. The structure of these documents is described below. @@ -26,7 +26,7 @@ processed, and may not reflect subsequent changes until a re-index is complete. | Document Element | Description | |------------------|----------------------------------------------------------------------------------------------------------------------------| | file_uuid | The uuid of the file | -| checksum | The hexidecimal representation of the MD5 checksum of the file | +| checksum | The hexadecimal representation of the MD5 checksum of the file | | size | Integer size of the file in bytes | | rel_path | The local file system path of the file relative to its Dataset directory, including the file name | | file_extension | The part of rel_path after the final period in the file name, which is after the final directory separator | @@ -61,111 +61,1616 @@ processed, and may not reflect subsequent changes until a re-index is complete. | units | The unit of measure for the age concept of the Donor entity metadata | | race | A UMLS preferred term from the Donor entity metadata for the [UMLS race group CUI C0034510](https://uts.nlm.nih.gov/uts/umls/concept/C0034510) | -### Organ Type Codes -Examples are enumerated below, but the current, authoritative list is in the [organ_types.yaml](https://raw.githubusercontent.com/hubmapconsortium/search-api/master/src/search-schema/data/definitions/enums/organ_types.yaml) file of the search-api repository. -- AO -- BL -- BD -- BM -- BR -- LF -- RF -- HT -- LB -- LE -- LI -- LK -- LL -- LN -- LV -- LY -- LO -- RO -- OT -- PA -- PL -- RB -- RE -- RK -- RL -- RN -- SI -- SK -- SP -- ST -- TH -- TR -- UR -- UT - -### Assay Type Codes -Examples are enumerated as follows, but the current, authoritative list is in the [assay_types.yaml](https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/assay_types.yaml) file of the search-api repository. -- AF -- AF_pyramid -- ATACseq-bulk -- CODEX -- CODEX2 -- DART-FISH -- IMC2D -- IMC2D_pyramid -- IMC3D -- IMC3D_pyramid -- LC-MS -- LC-MS-untargeted -- LC-MS_bottom_up -- LC-MS_top_down -- Lightsheet -- MALDI-IMS -- MALDI-IMS_pyramid -- MIBI -- MS -- MS_bottom_up -- MS_top_down -- MxIF -- MxIF_pyramid -- NanoDESI -- NanoDESI_pyramid -- NanoPOTS -- NanoPOTS_pyramid -- PAS -- PAS_pyramid -- SNARE-ATACseq2 -- SNARE-RNAseq2 -- Slide-seq -- TMT-LC-MS -- Targeted-Shotgun-LC-MS -- WGS -- bulk-RNA -- bulk_atacseq -- cell-dive -- celldive_deepcell -- codex_cytokit -- codex_cytokit_v1 -- image_pyramid -- lc-ms-ms_label-free -- lc-ms-ms_labeled -- lc-ms_label-free -- lc-ms_labeled -- mibi_deepcell -- salmon_rnaseq_10x -- salmon_rnaseq_bulk -- salmon_rnaseq_sciseq -- salmon_rnaseq_slideseq -- salmon_rnaseq_snareseq -- salmon_sn_rnaseq_10x -- scRNAseq-10xGenomics-v2 -- scRNAseq-10xGenomics-v3 -- sc_atac_seq_sci -- sc_atac_seq_snare -- sc_atac_seq_snare_lab -- sc_rna_seq_snare_lab -- sciATACseq -- sciRNAseq -- seqFish -- seqFish_lab_processed -- seqFish_pyramid -- snATACseq -- snRNAseq-10xGenomics-v2 -- snRNAseq-10xGenomics-v3 -- sn_atac_seq +``` +https://github.com/hubmapconsortium/software-docs/issues/79 +``` +Create full documentation on the software.docs site for the new parameterized search feature which: + +Explains how to use the new /param-search/ endpoint +Fully documents the schemata for the entities types supported as a way of documenting the available, searchable attributes. This should explain the construction of multilevel attributes, for example if searching in Sample space the attribute donor.protocol_url is constructed from the top level Sample attribute donor (which points to the Donor schema), then protocol_url attribute from Donor. + + +### OpenSearch document keyword attributes +Examples are enumerated as follows, but the current, authoritative list is returned from a call +to the search-api endpoint [/attribute-values?attribute_name_list](/attribute-values?attribute_name_list). +- visit +- uuid +- title +- tissue_type +- submission_id +- status +- specimen_type_other +- specimen_type +- sample_category +- rui_location +- registered_doi +- publication_venue +- publication_url +- publication_doi +- publication_date +- provider_info +- protocol_url +- previous_revision_uuid +- pages_or_article_num +- organ +- next_revision_uuid +- label +- lab_tissue_sample_id +- lab_donor_id +- lab_dataset_id +- index_version +- hubmap_id +- group_uuid +- group_name +- error_message +- entity_type +- doi_url +- display_subtype +- description +- descendant_ids +- dbgap_study_url +- dbgap_sra_experiment_url +- dataset_info +- data_types +- data_access_level +- created_by_user_email +- created_by_user_displayname +- ancestor_ids +- all_text +- thumbnail_file.filename +- thumbnail_file.file_uuid + +#### source_samples keyword attributes + +Examples are enumerated as follows, but the current, authoritative list is returned from a call +to the search-api endpoint [/attribute-values?attribute_name_list](/attribute-values?attribute_name_list). + +- source_samples.visit +- source_samples.uuid +- source_samples.tissue_type +- source_samples.submission_id +- source_samples.specimen_type_other +- source_samples.specimen_type +- source_samples.sample_category +- source_samples.rui_location +- source_samples.protocol_url +- source_samples.organ +- source_samples.lab_tissue_sample_id +- source_samples.hubmap_id +- source_samples.group_uuid +- source_samples.entity_type +- source_samples.description +- source_samples.data_access_level +- source_samples.created_by_user_email +- source_samples.created_by_user_displayname +- source_sample.visit +- source_sample.uuid +- source_sample.tissue_type +- source_sample.submission_id +- source_sample.specimen_type_other +- source_sample.specimen_type +- source_sample.sample_category +- source_sample.rui_location +- source_sample.protocol_url +- source_sample.organ +- source_sample.lab_tissue_sample_id +- source_sample.hubmap_id +- source_sample.group_uuid +- source_sample.entity_type +- source_sample.description +- source_sample.data_access_level +- source_sample.created_by_user_email +- source_sample.created_by_user_displayname +- portal_metadata_upload_files.filepath +- portal_metadata_upload_files.description +- origin_samples.visit +- origin_samples.uuid +- origin_samples.tissue_type +- origin_samples.submission_id +- origin_samples.specimen_type +- origin_samples.sample_category +- origin_samples.protocol_url +- origin_samples.organ +- origin_samples.lab_tissue_sample_id +- origin_samples.hubmap_id +- origin_samples.group_uuid +- origin_samples.entity_type +- origin_samples.description +- origin_samples.data_access_level +- origin_samples.created_by_user_email +- origin_samples.created_by_user_displayname +- origin_sample.visit +- origin_sample.uuid +- origin_sample.tissue_type +- origin_sample.submission_id +- origin_sample.specimen_type +- origin_sample.sample_category +- origin_sample.protocol_url +- origin_sample.organ +- origin_sample.lab_tissue_sample_id +- origin_sample.hubmap_id +- origin_sample.group_uuid +- origin_sample.entity_type +- origin_sample.description +- origin_sample.data_access_level +- origin_sample.created_by_user_email +- origin_sample.created_by_user_displayname +- metadata.warm_ischemia_time_value +- metadata.warm_ischemia_time_unit +- metadata.vital_state +- metadata.thumbnail_file_abs_path +- metadata.specimen_tumor_distance_value +- metadata.specimen_tumor_distance_unit +- metadata.specimen_quality_criteria +- metadata.specimen_preservation_temperature +- metadata.sample_id +- metadata.procedure_date +- metadata.perfusion_solution +- metadata.pathologist_report +- metadata.organ_condition +- metadata.health_status +- metadata.files_info_alt_path +- metadata.cold_ischemia_time_value +- metadata.cold_ischemia_time_unit +- metadata.Preservation_media +- metadata.Preservation_condition +- metadata.PPID +- immediate_descendants.visit +- immediate_descendants.uuid +- immediate_descendants.title +- immediate_descendants.tissue_type +- immediate_descendants.submission_id +- immediate_descendants.status +- immediate_descendants.specimen_type_other +- immediate_descendants.specimen_type +- immediate_descendants.sample_category +- immediate_descendants.rui_location +- immediate_descendants.registered_doi +- immediate_descendants.publication_venue +- immediate_descendants.publication_url +- immediate_descendants.publication_doi +- immediate_descendants.publication_date +- immediate_descendants.provider_info +- immediate_descendants.protocol_url +- immediate_descendants.previous_revision_uuid +- immediate_descendants.pages_or_article_num +- immediate_descendants.organ +- immediate_descendants.next_revision_uuid +- immediate_descendants.lab_tissue_sample_id +- immediate_descendants.lab_dataset_id +- immediate_descendants.hubmap_id +- immediate_descendants.group_uuid +- immediate_descendants.error_message +- immediate_descendants.entity_type +- immediate_descendants.doi_url +- immediate_descendants.description +- immediate_descendants.dbgap_study_url +- immediate_descendants.dbgap_sra_experiment_url +- immediate_descendants.dataset_info +- immediate_descendants.data_types +- immediate_descendants.data_access_level +- immediate_descendants.created_by_user_email +- immediate_descendants.created_by_user_displayname +- immediate_ancestors.visit +- immediate_ancestors.uuid +- immediate_ancestors.title +- immediate_ancestors.tissue_type +- immediate_ancestors.submission_id +- immediate_ancestors.status +- immediate_ancestors.specimen_type_other +- immediate_ancestors.specimen_type +- immediate_ancestors.sample_category +- immediate_ancestors.rui_location +- immediate_ancestors.registered_doi +- immediate_ancestors.provider_info +- immediate_ancestors.protocol_url +- immediate_ancestors.organ +- immediate_ancestors.next_revision_uuid +- immediate_ancestors.label +- immediate_ancestors.lab_tissue_sample_id +- immediate_ancestors.lab_donor_id +- immediate_ancestors.lab_dataset_id +- immediate_ancestors.hubmap_id +- immediate_ancestors.group_uuid +- immediate_ancestors.entity_type +- immediate_ancestors.doi_url +- immediate_ancestors.description +- immediate_ancestors.dataset_info +- immediate_ancestors.data_types +- immediate_ancestors.data_access_level +- immediate_ancestors.created_by_user_email +- immediate_ancestors.created_by_user_displayname +- image_file_metadata.filepath +- image_file_metadata.description +- files.type +- files.rel_path +- files.edam_term +- files.description +- donor.uuid +- donor.submission_id +- donor.protocol_url +- donor.label +- donor.lab_donor_id +- donor.hubmap_id +- donor.group_uuid +- donor.entity_type +- donor.description +- donor.data_access_level +- donor.created_by_user_email +- donor.created_by_user_displayname +- descendants.visit +- descendants.uuid +- descendants.title +- descendants.tissue_type +- descendants.submission_id +- descendants.status +- descendants.specimen_type_other +- descendants.specimen_type +- descendants.sample_category +- descendants.rui_location +- descendants.registered_doi +- descendants.publication_venue +- descendants.publication_url +- descendants.publication_doi +- descendants.publication_date +- descendants.provider_info +- descendants.protocol_url +- descendants.previous_revision_uuid +- descendants.pages_or_article_num +- descendants.organ +- descendants.next_revision_uuid +- descendants.lab_tissue_sample_id +- descendants.lab_dataset_id +- descendants.hubmap_id +- descendants.group_uuid +- descendants.error_message +- descendants.entity_type +- descendants.doi_url +- descendants.description +- descendants.dbgap_study_url +- descendants.dbgap_sra_experiment_url +- descendants.dataset_info +- descendants.data_types +- descendants.data_access_level +- descendants.created_by_user_email +- descendants.created_by_user_displayname +- datasets.uuid +- datasets.title +- datasets.status +- datasets.registered_doi +- datasets.provider_info +- datasets.lab_dataset_id +- datasets.index_version +- datasets.hubmap_id +- datasets.group_uuid +- datasets.group_name +- datasets.entity_type +- datasets.doi_url +- datasets.display_subtype +- datasets.description +- datasets.dataset_info +- datasets.data_types +- datasets.data_access_level +- datasets.created_by_user_email +- datasets.created_by_user_displayname +- creators.orcid_id +- creators.name +- creators.middle_name_or_initial +- creators.last_name +- creators.first_name +- creators.affiliation +- contributors.version +- contributors.orcid_id +- contributors.orchid_id +- contributors.orc_id +- contributors.name +- contributors.middle_name_or_initial +- contributors.last_name +- contributors.is_contact +- contributors.first_name +- contributors.affiliation +- contacts.version +- contacts.orcid_id +- contacts.orc_id +- contacts.name +- contacts.middle_name_or_initial +- contacts.middle_name_or_initia +- contacts.last_name +- contacts.is_contact +- contacts.first_name +- contacts.affiliation +- ancestors.visit +- ancestors.uuid +- ancestors.title +- ancestors.tissue_type +- ancestors.submission_id +- ancestors.status +- ancestors.specimen_type_other +- ancestors.specimen_type +- ancestors.sample_category +- ancestors.rui_location +- ancestors.registered_doi +- ancestors.provider_info +- ancestors.protocol_url +- ancestors.organ +- ancestors.next_revision_uuid +- ancestors.label +- ancestors.lab_tissue_sample_id +- ancestors.lab_donor_id +- ancestors.lab_dataset_id +- ancestors.hubmap_id +- ancestors.group_uuid +- ancestors.entity_type +- ancestors.doi_url +- ancestors.description +- ancestors.dataset_info +- ancestors.data_types +- ancestors.data_access_level +- ancestors.created_by_user_email +- ancestors.created_by_user_displayname +- source_samples.thumbnail_file.filename +- source_samples.thumbnail_file.file_uuid +- source_samples.portal_metadata_upload_files.filepath +- source_samples.portal_metadata_upload_files.description +- source_samples.metadata.warm_ischemia_time_value +- source_samples.metadata.warm_ischemia_time_unit +- source_samples.metadata.vital_state +- source_samples.metadata.specimen_tumor_distance_value +- source_samples.metadata.specimen_tumor_distance_unit +- source_samples.metadata.specimen_quality_criteria +- source_samples.metadata.specimen_preservation_temperature +- source_samples.metadata.sample_id +- source_samples.metadata.procedure_date +- source_samples.metadata.perfusion_solution +- source_samples.metadata.pathologist_report +- source_samples.metadata.organ_condition +- source_samples.metadata.health_status +- source_samples.metadata.cold_ischemia_time_value +- source_samples.metadata.cold_ischemia_time_unit +- source_sample.thumbnail_file.filename +- source_sample.thumbnail_file.file_uuid +- source_sample.portal_metadata_upload_files.filepath +- source_sample.portal_metadata_upload_files.description +- source_sample.metadata.warm_ischemia_time_value +- source_sample.metadata.warm_ischemia_time_unit +- source_sample.metadata.vital_state +- source_sample.metadata.specimen_tumor_distance_value +- source_sample.metadata.specimen_tumor_distance_unit +- source_sample.metadata.specimen_quality_criteria +- source_sample.metadata.specimen_preservation_temperature +- source_sample.metadata.sample_id +- source_sample.metadata.procedure_date +- source_sample.metadata.perfusion_solution +- source_sample.metadata.pathologist_report +- source_sample.metadata.organ_condition +- source_sample.metadata.health_status +- source_sample.metadata.cold_ischemia_time_value +- source_sample.metadata.cold_ischemia_time_unit +- origin_samples.portal_metadata_upload_files.filepath +- origin_samples.portal_metadata_upload_files.description +- origin_samples.metadata.warm_ischemia_time_value +- origin_samples.metadata.warm_ischemia_time_unit +- origin_samples.metadata.vital_state +- origin_samples.metadata.specimen_tumor_distance_value +- origin_samples.metadata.specimen_tumor_distance_unit +- origin_samples.metadata.specimen_quality_criteria +- origin_samples.metadata.specimen_preservation_temperature +- origin_samples.metadata.sample_id +- origin_samples.metadata.procedure_date +- origin_samples.metadata.perfusion_solution +- origin_samples.metadata.pathologist_report +- origin_samples.metadata.organ_condition +- origin_samples.metadata.health_status +- origin_samples.metadata.cold_ischemia_time_value +- origin_samples.metadata.cold_ischemia_time_unit +- origin_samples.image_file_metadata.filepath +- origin_samples.image_file_metadata.description +- origin_sample.portal_metadata_upload_files.filepath +- origin_sample.portal_metadata_upload_files.description +- origin_sample.metadata.warm_ischemia_time_value +- origin_sample.metadata.warm_ischemia_time_unit +- origin_sample.metadata.vital_state +- origin_sample.metadata.specimen_tumor_distance_value +- origin_sample.metadata.specimen_tumor_distance_unit +- origin_sample.metadata.specimen_quality_criteria +- origin_sample.metadata.specimen_preservation_temperature +- origin_sample.metadata.sample_id +- origin_sample.metadata.procedure_date +- origin_sample.metadata.perfusion_solution +- origin_sample.metadata.pathologist_report +- origin_sample.metadata.organ_condition +- origin_sample.metadata.health_status +- origin_sample.metadata.cold_ischemia_time_value +- origin_sample.metadata.cold_ischemia_time_unit +- origin_sample.image_file_metadata.filepath +- origin_sample.image_file_metadata.description +- metadata.organ_donor_data.units +- metadata.organ_donor_data.start_datetime +- metadata.organ_donor_data.sab +- metadata.organ_donor_data.preferred_term +- metadata.organ_donor_data.numeric_operator +- metadata.organ_donor_data.grouping_sab +- metadata.organ_donor_data.grouping_concept_preferred_term +- metadata.organ_donor_data.grouping_concept +- metadata.organ_donor_data.grouping_code +- metadata.organ_donor_data.graph_version +- metadata.organ_donor_data.end_datetime +- metadata.organ_donor_data.data_value +- metadata.organ_donor_data.data_type +- metadata.organ_donor_data.concept_id +- metadata.organ_donor_data.code +- metadata.metadata.version +- metadata.metadata.umi_size +- metadata.metadata.umi_read +- metadata.metadata.umi_offset +- metadata.metadata.transposition_transposase_source +- metadata.metadata.transposition_method +- metadata.metadata.transposition_kit_number +- metadata.metadata.transposition_input +- metadata.metadata.tissue_id +- metadata.metadata.step_z_value +- metadata.metadata.start_datetime +- metadata.metadata.stain +- metadata.metadata.source_project +- metadata.metadata.signal_type +- metadata.metadata.sequencing_reagent_kit +- metadata.metadata.sequencing_read_percent_q30 +- metadata.metadata.sequencing_read_format +- metadata.metadata.sequencing_phix_percent +- metadata.metadata.segment_data_format +- metadata.metadata.section_prep_protocols_io_doi +- metadata.metadata.sc_isolation_tissue_dissociation +- metadata.metadata.sc_isolation_quality_metric +- metadata.metadata.sc_isolation_protocols_io_doi +- metadata.metadata.sc_isolation_entity +- metadata.metadata.sc_isolation_enrichment +- metadata.metadata.sc_isolation_cell_number +- metadata.metadata.sample_quality_metric +- metadata.metadata.roi_id +- metadata.metadata.roi_description +- metadata.metadata.rnaseq_assay_method +- metadata.metadata.rnaseq_assay_input_value +- metadata.metadata.rnaseq_assay_input_unit +- metadata.metadata.rnaseq_assay_input +- metadata.metadata.resolution_z_value +- metadata.metadata.resolution_z_unit +- metadata.metadata.resolution_y_value +- metadata.metadata.resolution_y_unit +- metadata.metadata.resolution_x_value +- metadata.metadata.resolution_x_unit +- metadata.metadata.reagent_prep_protocols_io_doi +- metadata.metadata.range_z_value +- metadata.metadata.range_z_unit +- metadata.metadata.puck_id +- metadata.metadata.protocols_io_doi +- metadata.metadata.processing_search +- metadata.metadata.processing_protocols_io_doi +- metadata.metadata.preparation_type +- metadata.metadata.preparation_maldi_matrix +- metadata.metadata.preparation_instrument_vendor +- metadata.metadata.preparation_instrument_model +- metadata.metadata.polarity +- metadata.metadata.pi_email +- metadata.metadata.pi +- metadata.metadata.overall_protocols_io_doi +- metadata.metadata.operator_email +- metadata.metadata.operator +- metadata.metadata.number_of_sections +- metadata.metadata.number_of_readout_probes_per_channel +- metadata.metadata.number_of_pseudocolors_per_channel +- metadata.metadata.number_of_imaging_rounds +- metadata.metadata.number_of_cycles +- metadata.metadata.number_of_channels +- metadata.metadata.number_of_barcode_regions_per_barcode_probe +- metadata.metadata.number_of_barcode_probes +- metadata.metadata.number_of_antibodies +- metadata.metadata.mz_resolving_power +- metadata.metadata.mz_range_low_value +- metadata.metadata.mz_range_high_value +- metadata.metadata.ms_source +- metadata.metadata.ms_scan_mode +- metadata.metadata.metadata_path +- metadata.metadata.max_y_height_value +- metadata.metadata.max_y_height_unit +- metadata.metadata.max_x_width_value +- metadata.metadata.max_x_width_unit +- metadata.metadata.mass_resolving_power +- metadata.metadata.library_preparation_kit +- metadata.metadata.library_pcr_cycles_for_sample_index +- metadata.metadata.library_pcr_cycles +- metadata.metadata.library_layout +- metadata.metadata.library_id +- metadata.metadata.library_final_yield_value +- metadata.metadata.library_final_yield_unit +- metadata.metadata.library_final_yield +- metadata.metadata.library_creation_date +- metadata.metadata.library_construction_protocols_io_doi +- metadata.metadata.library_construction_method +- metadata.metadata.library_concentration_value +- metadata.metadata.library_concentration_unit +- metadata.metadata.library_average_fragment_size +- metadata.metadata.library_adapter_sequence +- metadata.metadata.lc_temp_value +- metadata.metadata.lc_temp_unit +- metadata.metadata.lc_resin +- metadata.metadata.lc_mobile_phase_b +- metadata.metadata.lc_mobile_phase_a +- metadata.metadata.lc_length_value +- metadata.metadata.lc_length_unit +- metadata.metadata.lc_instrument_vendor +- metadata.metadata.lc_instrument_model +- metadata.metadata.lc_id_value +- metadata.metadata.lc_id_unit +- metadata.metadata.lc_gradient +- metadata.metadata.lc_flow_rate_value +- metadata.metadata.lc_flow_rate_unit +- metadata.metadata.lc_column_vendor +- metadata.metadata.lc_column_model +- metadata.metadata.labeling +- metadata.metadata.is_technical_replicate +- metadata.metadata.is_targeted +- metadata.metadata.increment_z_value +- metadata.metadata.increment_z_unit +- metadata.metadata.gdna_fragmentation_quality_assurance +- metadata.metadata.expected_cell_count +- metadata.metadata.execution_datetime +- metadata.metadata.end_datetime +- metadata.metadata.dual_count_start +- metadata.metadata.donor_id +- metadata.metadata.dna_assay_input_value +- metadata.metadata.dna_assay_input_unit +- metadata.metadata.dms +- metadata.metadata.description +- metadata.metadata.data_precision_bytes +- metadata.metadata.data_path +- metadata.metadata.data_collection_mode +- metadata.metadata.contributors_path +- metadata.metadata.collectiontype +- metadata.metadata.cell_barcode_size +- metadata.metadata.cell_barcode_read +- metadata.metadata.cell_barcode_offset +- metadata.metadata.bulk_transposition_input_number_nuclei +- metadata.metadata.bulk_rna_yield_value +- metadata.metadata.bulk_rna_yield_units_per_tissue_unit +- metadata.metadata.bulk_rna_isolation_quality_metric_value +- metadata.metadata.bulk_rna_isolation_protocols_io_doi +- metadata.metadata.bulk_atac_cell_isolation_protocols_io_doi +- metadata.metadata.bead_barcode_size +- metadata.metadata.bead_barcode_read +- metadata.metadata.bead_barcode_offset +- metadata.metadata.assay_type +- metadata.metadata.assay_category +- metadata.metadata.antibodies_path +- metadata.metadata.analyte_class +- metadata.metadata.acquisition_instrument_vendor +- metadata.metadata.acquisition_instrument_model +- metadata.metadata.acquisition_id +- metadata.metadata.ablation_frequency_value +- metadata.metadata.ablation_frequency_unit +- metadata.metadata.ablation_distance_between_shots_y_value +- metadata.metadata.ablation_distance_between_shots_y_units +- metadata.metadata.ablation_distance_between_shots_x_value +- metadata.metadata.ablation_distance_between_shots_x_units +- metadata.living_donor_data.units +- metadata.living_donor_data.start_datetime +- metadata.living_donor_data.sab +- metadata.living_donor_data.preferred_term +- metadata.living_donor_data.numeric_operator +- metadata.living_donor_data.grouping_sab +- metadata.living_donor_data.grouping_concept_preferred_term +- metadata.living_donor_data.grouping_concept +- metadata.living_donor_data.grouping_code +- metadata.living_donor_data.graph_version +- metadata.living_donor_data.end_datetime +- metadata.living_donor_data.data_value +- metadata.living_donor_data.data_type +- metadata.living_donor_data.concept_id +- metadata.living_donor_data.code +- metadata.files.type +- metadata.files.rel_path +- metadata.files.edam_term +- metadata.files.description +- metadata.extra_metadata.collectiontype +- metadata.dag_provenance_list.origin +- metadata.dag_provenance_list.name +- metadata.dag_provenance_list.hash +- immediate_descendants.thumbnail_file.filename +- immediate_descendants.thumbnail_file.file_uuid +- immediate_descendants.portal_metadata_upload_files.filepath +- immediate_descendants.portal_metadata_upload_files.description +- immediate_descendants.metadata.warm_ischemia_time_value +- immediate_descendants.metadata.warm_ischemia_time_unit +- immediate_descendants.metadata.vital_state +- immediate_descendants.metadata.thumbnail_file_abs_path +- immediate_descendants.metadata.specimen_tumor_distance_value +- immediate_descendants.metadata.specimen_tumor_distance_unit +- immediate_descendants.metadata.specimen_quality_criteria +- immediate_descendants.metadata.specimen_preservation_temperature +- immediate_descendants.metadata.sample_id +- immediate_descendants.metadata.procedure_date +- immediate_descendants.metadata.perfusion_solution +- immediate_descendants.metadata.pathologist_report +- immediate_descendants.metadata.organ_condition +- immediate_descendants.metadata.health_status +- immediate_descendants.metadata.files_info_alt_path +- immediate_descendants.metadata.cold_ischemia_time_value +- immediate_descendants.metadata.cold_ischemia_time_unit +- immediate_descendants.metadata.Preservation_media +- immediate_descendants.metadata.Preservation_condition +- immediate_descendants.metadata.PPID +- immediate_descendants.image_file_metadata.filepath +- immediate_descendants.image_file_metadata.description +- immediate_descendants.files.type +- immediate_descendants.files.rel_path +- immediate_descendants.files.edam_term +- immediate_descendants.files.description +- immediate_descendants.contributors.version +- immediate_descendants.contributors.orcid_id +- immediate_descendants.contributors.orchid_id +- immediate_descendants.contributors.orc_id +- immediate_descendants.contributors.name +- immediate_descendants.contributors.middle_name_or_initial +- immediate_descendants.contributors.last_name +- immediate_descendants.contributors.is_contact +- immediate_descendants.contributors.first_name +- immediate_descendants.contributors.affiliation +- immediate_descendants.contacts.version +- immediate_descendants.contacts.orcid_id +- immediate_descendants.contacts.orc_id +- immediate_descendants.contacts.name +- immediate_descendants.contacts.middle_name_or_initial +- immediate_descendants.contacts.middle_name_or_initia +- immediate_descendants.contacts.last_name +- immediate_descendants.contacts.is_contact +- immediate_descendants.contacts.first_name +- immediate_descendants.contacts.affiliation +- immediate_ancestors.thumbnail_file.filename +- immediate_ancestors.thumbnail_file.file_uuid +- immediate_ancestors.portal_metadata_upload_files.filepath +- immediate_ancestors.portal_metadata_upload_files.description +- immediate_ancestors.metadata.warm_ischemia_time_value +- immediate_ancestors.metadata.warm_ischemia_time_unit +- immediate_ancestors.metadata.vital_state +- immediate_ancestors.metadata.thumbnail_file_abs_path +- immediate_ancestors.metadata.specimen_tumor_distance_value +- immediate_ancestors.metadata.specimen_tumor_distance_unit +- immediate_ancestors.metadata.specimen_quality_criteria +- immediate_ancestors.metadata.specimen_preservation_temperature +- immediate_ancestors.metadata.sample_id +- immediate_ancestors.metadata.procedure_date +- immediate_ancestors.metadata.perfusion_solution +- immediate_ancestors.metadata.pathologist_report +- immediate_ancestors.metadata.organ_condition +- immediate_ancestors.metadata.health_status +- immediate_ancestors.metadata.files_info_alt_path +- immediate_ancestors.metadata.cold_ischemia_time_value +- immediate_ancestors.metadata.cold_ischemia_time_unit +- immediate_ancestors.metadata.Preservation_media +- immediate_ancestors.metadata.Preservation_condition +- immediate_ancestors.metadata.PPID +- immediate_ancestors.image_file_metadata.filepath +- immediate_ancestors.image_file_metadata.description +- immediate_ancestors.files.type +- immediate_ancestors.files.rel_path +- immediate_ancestors.files.edam_term +- immediate_ancestors.files.description +- immediate_ancestors.contributors.version +- immediate_ancestors.contributors.orcid_id +- immediate_ancestors.contributors.name +- immediate_ancestors.contributors.middle_name_or_initial +- immediate_ancestors.contributors.last_name +- immediate_ancestors.contributors.is_contact +- immediate_ancestors.contributors.first_name +- immediate_ancestors.contributors.affiliation +- immediate_ancestors.contacts.version +- immediate_ancestors.contacts.orcid_id +- immediate_ancestors.contacts.name +- immediate_ancestors.contacts.middle_name_or_initial +- immediate_ancestors.contacts.middle_name_or_initia +- immediate_ancestors.contacts.last_name +- immediate_ancestors.contacts.is_contact +- immediate_ancestors.contacts.first_name +- immediate_ancestors.contacts.affiliation +- donor.portal_metadata_upload_files.filepath +- donor.portal_metadata_upload_files.description +- descendants.thumbnail_file.filename +- descendants.thumbnail_file.file_uuid +- descendants.portal_metadata_upload_files.filepath +- descendants.portal_metadata_upload_files.description +- descendants.metadata.warm_ischemia_time_value +- descendants.metadata.warm_ischemia_time_unit +- descendants.metadata.vital_state +- descendants.metadata.thumbnail_file_abs_path +- descendants.metadata.specimen_tumor_distance_value +- descendants.metadata.specimen_tumor_distance_unit +- descendants.metadata.specimen_quality_criteria +- descendants.metadata.specimen_preservation_temperature +- descendants.metadata.sample_id +- descendants.metadata.procedure_date +- descendants.metadata.perfusion_solution +- descendants.metadata.pathologist_report +- descendants.metadata.organ_condition +- descendants.metadata.health_status +- descendants.metadata.files_info_alt_path +- descendants.metadata.cold_ischemia_time_value +- descendants.metadata.cold_ischemia_time_unit +- descendants.metadata.Preservation_media +- descendants.metadata.Preservation_condition +- descendants.metadata.PPID +- descendants.image_file_metadata.filepath +- descendants.image_file_metadata.description +- descendants.files.type +- descendants.files.rel_path +- descendants.files.edam_term +- descendants.files.description +- descendants.contributors.version +- descendants.contributors.orcid_id +- descendants.contributors.orchid_id +- descendants.contributors.orc_id +- descendants.contributors.name +- descendants.contributors.middle_name_or_initial +- descendants.contributors.last_name +- descendants.contributors.is_contact +- descendants.contributors.first_name +- descendants.contributors.affiliation +- descendants.contacts.version +- descendants.contacts.orcid_id +- descendants.contacts.orc_id +- descendants.contacts.name +- descendants.contacts.middle_name_or_initial +- descendants.contacts.middle_name_or_initia +- descendants.contacts.last_name +- descendants.contacts.is_contact +- descendants.contacts.first_name +- descendants.contacts.affiliation +- datasets.contributors.version +- datasets.contributors.orcid_id +- datasets.contributors.orc_id +- datasets.contributors.name +- datasets.contributors.middle_name_or_initial +- datasets.contributors.last_name +- datasets.contributors.is_contact +- datasets.contributors.first_name +- datasets.contributors.affiliation +- datasets.contacts.version +- datasets.contacts.orcid_id +- datasets.contacts.orc_id +- datasets.contacts.name +- datasets.contacts.middle_name_or_initial +- datasets.contacts.last_name +- datasets.contacts.is_contact +- datasets.contacts.first_name +- datasets.contacts.affiliation +- ancestors.thumbnail_file.filename +- ancestors.thumbnail_file.file_uuid +- ancestors.portal_metadata_upload_files.filepath +- ancestors.portal_metadata_upload_files.description +- ancestors.metadata.warm_ischemia_time_value +- ancestors.metadata.warm_ischemia_time_unit +- ancestors.metadata.vital_state +- ancestors.metadata.thumbnail_file_abs_path +- ancestors.metadata.specimen_tumor_distance_value +- ancestors.metadata.specimen_tumor_distance_unit +- ancestors.metadata.specimen_quality_criteria +- ancestors.metadata.specimen_preservation_temperature +- ancestors.metadata.sample_id +- ancestors.metadata.procedure_date +- ancestors.metadata.perfusion_solution +- ancestors.metadata.pathologist_report +- ancestors.metadata.organ_condition +- ancestors.metadata.health_status +- ancestors.metadata.files_info_alt_path +- ancestors.metadata.cold_ischemia_time_value +- ancestors.metadata.cold_ischemia_time_unit +- ancestors.metadata.Preservation_media +- ancestors.metadata.Preservation_condition +- ancestors.metadata.PPID +- ancestors.image_file_metadata.filepath +- ancestors.image_file_metadata.description +- ancestors.files.type +- ancestors.files.rel_path +- ancestors.files.edam_term +- ancestors.files.description +- ancestors.contributors.version +- ancestors.contributors.orcid_id +- ancestors.contributors.name +- ancestors.contributors.middle_name_or_initial +- ancestors.contributors.last_name +- ancestors.contributors.is_contact +- ancestors.contributors.first_name +- ancestors.contributors.affiliation +- ancestors.contacts.version +- ancestors.contacts.orcid_id +- ancestors.contacts.name +- ancestors.contacts.middle_name_or_initial +- ancestors.contacts.middle_name_or_initia +- ancestors.contacts.last_name +- ancestors.contacts.is_contact +- ancestors.contacts.first_name +- ancestors.contacts.affiliation +- immediate_descendants.metadata.metadata.version +- immediate_descendants.metadata.metadata.umi_size +- immediate_descendants.metadata.metadata.umi_read +- immediate_descendants.metadata.metadata.umi_offset +- immediate_descendants.metadata.metadata.transposition_transposase_source +- immediate_descendants.metadata.metadata.transposition_method +- immediate_descendants.metadata.metadata.transposition_kit_number +- immediate_descendants.metadata.metadata.transposition_input +- immediate_descendants.metadata.metadata.tissue_id +- immediate_descendants.metadata.metadata.step_z_value +- immediate_descendants.metadata.metadata.start_datetime +- immediate_descendants.metadata.metadata.stain +- immediate_descendants.metadata.metadata.source_project +- immediate_descendants.metadata.metadata.signal_type +- immediate_descendants.metadata.metadata.sequencing_reagent_kit +- immediate_descendants.metadata.metadata.sequencing_read_percent_q30 +- immediate_descendants.metadata.metadata.sequencing_read_format +- immediate_descendants.metadata.metadata.sequencing_phix_percent +- immediate_descendants.metadata.metadata.segment_data_format +- immediate_descendants.metadata.metadata.section_prep_protocols_io_doi +- immediate_descendants.metadata.metadata.sc_isolation_tissue_dissociation +- immediate_descendants.metadata.metadata.sc_isolation_quality_metric +- immediate_descendants.metadata.metadata.sc_isolation_protocols_io_doi +- immediate_descendants.metadata.metadata.sc_isolation_entity +- immediate_descendants.metadata.metadata.sc_isolation_enrichment +- immediate_descendants.metadata.metadata.sc_isolation_cell_number +- immediate_descendants.metadata.metadata.sample_quality_metric +- immediate_descendants.metadata.metadata.roi_id +- immediate_descendants.metadata.metadata.roi_description +- immediate_descendants.metadata.metadata.rnaseq_assay_method +- immediate_descendants.metadata.metadata.rnaseq_assay_input_value +- immediate_descendants.metadata.metadata.rnaseq_assay_input_unit +- immediate_descendants.metadata.metadata.rnaseq_assay_input +- immediate_descendants.metadata.metadata.resolution_z_value +- immediate_descendants.metadata.metadata.resolution_z_unit +- immediate_descendants.metadata.metadata.resolution_y_value +- immediate_descendants.metadata.metadata.resolution_y_unit +- immediate_descendants.metadata.metadata.resolution_x_value +- immediate_descendants.metadata.metadata.resolution_x_unit +- immediate_descendants.metadata.metadata.reagent_prep_protocols_io_doi +- immediate_descendants.metadata.metadata.range_z_value +- immediate_descendants.metadata.metadata.range_z_unit +- immediate_descendants.metadata.metadata.puck_id +- immediate_descendants.metadata.metadata.protocols_io_doi +- immediate_descendants.metadata.metadata.processing_search +- immediate_descendants.metadata.metadata.processing_protocols_io_doi +- immediate_descendants.metadata.metadata.preparation_type +- immediate_descendants.metadata.metadata.preparation_maldi_matrix +- immediate_descendants.metadata.metadata.preparation_instrument_vendor +- immediate_descendants.metadata.metadata.preparation_instrument_model +- immediate_descendants.metadata.metadata.polarity +- immediate_descendants.metadata.metadata.pi_email +- immediate_descendants.metadata.metadata.pi +- immediate_descendants.metadata.metadata.overall_protocols_io_doi +- immediate_descendants.metadata.metadata.operator_email +- immediate_descendants.metadata.metadata.operator +- immediate_descendants.metadata.metadata.number_of_sections +- immediate_descendants.metadata.metadata.number_of_readout_probes_per_channel +- immediate_descendants.metadata.metadata.number_of_pseudocolors_per_channel +- immediate_descendants.metadata.metadata.number_of_imaging_rounds +- immediate_descendants.metadata.metadata.number_of_cycles +- immediate_descendants.metadata.metadata.number_of_channels +- immediate_descendants.metadata.metadata.number_of_barcode_regions_per_barcode_probe +- immediate_descendants.metadata.metadata.number_of_barcode_probes +- immediate_descendants.metadata.metadata.number_of_antibodies +- immediate_descendants.metadata.metadata.mz_resolving_power +- immediate_descendants.metadata.metadata.mz_range_low_value +- immediate_descendants.metadata.metadata.mz_range_high_value +- immediate_descendants.metadata.metadata.ms_source +- immediate_descendants.metadata.metadata.ms_scan_mode +- immediate_descendants.metadata.metadata.metadata_path +- immediate_descendants.metadata.metadata.max_y_height_value +- immediate_descendants.metadata.metadata.max_y_height_unit +- immediate_descendants.metadata.metadata.max_x_width_value +- immediate_descendants.metadata.metadata.max_x_width_unit +- immediate_descendants.metadata.metadata.mass_resolving_power +- immediate_descendants.metadata.metadata.library_preparation_kit +- immediate_descendants.metadata.metadata.library_pcr_cycles_for_sample_index +- immediate_descendants.metadata.metadata.library_pcr_cycles +- immediate_descendants.metadata.metadata.library_layout +- immediate_descendants.metadata.metadata.library_id +- immediate_descendants.metadata.metadata.library_final_yield_value +- immediate_descendants.metadata.metadata.library_final_yield_unit +- immediate_descendants.metadata.metadata.library_final_yield +- immediate_descendants.metadata.metadata.library_creation_date +- immediate_descendants.metadata.metadata.library_construction_protocols_io_doi +- immediate_descendants.metadata.metadata.library_construction_method +- immediate_descendants.metadata.metadata.library_concentration_value +- immediate_descendants.metadata.metadata.library_concentration_unit +- immediate_descendants.metadata.metadata.library_average_fragment_size +- immediate_descendants.metadata.metadata.library_adapter_sequence +- immediate_descendants.metadata.metadata.lc_temp_value +- immediate_descendants.metadata.metadata.lc_temp_unit +- immediate_descendants.metadata.metadata.lc_resin +- immediate_descendants.metadata.metadata.lc_mobile_phase_b +- immediate_descendants.metadata.metadata.lc_mobile_phase_a +- immediate_descendants.metadata.metadata.lc_length_value +- immediate_descendants.metadata.metadata.lc_length_unit +- immediate_descendants.metadata.metadata.lc_instrument_vendor +- immediate_descendants.metadata.metadata.lc_instrument_model +- immediate_descendants.metadata.metadata.lc_id_value +- immediate_descendants.metadata.metadata.lc_id_unit +- immediate_descendants.metadata.metadata.lc_gradient +- immediate_descendants.metadata.metadata.lc_flow_rate_value +- immediate_descendants.metadata.metadata.lc_flow_rate_unit +- immediate_descendants.metadata.metadata.lc_column_vendor +- immediate_descendants.metadata.metadata.lc_column_model +- immediate_descendants.metadata.metadata.labeling +- immediate_descendants.metadata.metadata.is_technical_replicate +- immediate_descendants.metadata.metadata.is_targeted +- immediate_descendants.metadata.metadata.increment_z_value +- immediate_descendants.metadata.metadata.increment_z_unit +- immediate_descendants.metadata.metadata.gdna_fragmentation_quality_assurance +- immediate_descendants.metadata.metadata.expected_cell_count +- immediate_descendants.metadata.metadata.execution_datetime +- immediate_descendants.metadata.metadata.end_datetime +- immediate_descendants.metadata.metadata.dual_count_start +- immediate_descendants.metadata.metadata.donor_id +- immediate_descendants.metadata.metadata.dna_assay_input_value +- immediate_descendants.metadata.metadata.dna_assay_input_unit +- immediate_descendants.metadata.metadata.dms +- immediate_descendants.metadata.metadata.description +- immediate_descendants.metadata.metadata.data_precision_bytes +- immediate_descendants.metadata.metadata.data_path +- immediate_descendants.metadata.metadata.data_collection_mode +- immediate_descendants.metadata.metadata.contributors_path +- immediate_descendants.metadata.metadata.collectiontype +- immediate_descendants.metadata.metadata.cell_barcode_size +- immediate_descendants.metadata.metadata.cell_barcode_read +- immediate_descendants.metadata.metadata.cell_barcode_offset +- immediate_descendants.metadata.metadata.bulk_transposition_input_number_nuclei +- immediate_descendants.metadata.metadata.bulk_rna_yield_value +- immediate_descendants.metadata.metadata.bulk_rna_yield_units_per_tissue_unit +- immediate_descendants.metadata.metadata.bulk_rna_isolation_quality_metric_value +- immediate_descendants.metadata.metadata.bulk_rna_isolation_protocols_io_doi +- immediate_descendants.metadata.metadata.bulk_atac_cell_isolation_protocols_io_doi +- immediate_descendants.metadata.metadata.bead_barcode_size +- immediate_descendants.metadata.metadata.bead_barcode_read +- immediate_descendants.metadata.metadata.bead_barcode_offset +- immediate_descendants.metadata.metadata.assay_type +- immediate_descendants.metadata.metadata.assay_category +- immediate_descendants.metadata.metadata.antibodies_path +- immediate_descendants.metadata.metadata.analyte_class +- immediate_descendants.metadata.metadata.acquisition_instrument_vendor +- immediate_descendants.metadata.metadata.acquisition_instrument_model +- immediate_descendants.metadata.metadata.acquisition_id +- immediate_descendants.metadata.metadata.ablation_frequency_value +- immediate_descendants.metadata.metadata.ablation_frequency_unit +- immediate_descendants.metadata.metadata.ablation_distance_between_shots_y_value +- immediate_descendants.metadata.metadata.ablation_distance_between_shots_y_units +- immediate_descendants.metadata.metadata.ablation_distance_between_shots_x_value +- immediate_descendants.metadata.metadata.ablation_distance_between_shots_x_units +- immediate_descendants.metadata.files.type +- immediate_descendants.metadata.files.rel_path +- immediate_descendants.metadata.files.edam_term +- immediate_descendants.metadata.files.description +- immediate_descendants.metadata.extra_metadata.collectiontype +- immediate_descendants.metadata.dag_provenance_list.origin +- immediate_descendants.metadata.dag_provenance_list.name +- immediate_descendants.metadata.dag_provenance_list.hash +- immediate_ancestors.metadata.organ_donor_data.units +- immediate_ancestors.metadata.organ_donor_data.start_datetime +- immediate_ancestors.metadata.organ_donor_data.sab +- immediate_ancestors.metadata.organ_donor_data.preferred_term +- immediate_ancestors.metadata.organ_donor_data.numeric_operator +- immediate_ancestors.metadata.organ_donor_data.grouping_sab +- immediate_ancestors.metadata.organ_donor_data.grouping_concept_preferred_term +- immediate_ancestors.metadata.organ_donor_data.grouping_concept +- immediate_ancestors.metadata.organ_donor_data.grouping_code +- immediate_ancestors.metadata.organ_donor_data.graph_version +- immediate_ancestors.metadata.organ_donor_data.end_datetime +- immediate_ancestors.metadata.organ_donor_data.data_value +- immediate_ancestors.metadata.organ_donor_data.data_type +- immediate_ancestors.metadata.organ_donor_data.concept_id +- 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datasets.metadata.extra_metadata.collectiontype +- datasets.metadata.dag_provenance_list.origin +- datasets.metadata.dag_provenance_list.hash +- ancestors.metadata.organ_donor_data.units +- ancestors.metadata.organ_donor_data.start_datetime +- ancestors.metadata.organ_donor_data.sab +- ancestors.metadata.organ_donor_data.preferred_term +- ancestors.metadata.organ_donor_data.numeric_operator +- ancestors.metadata.organ_donor_data.grouping_sab +- ancestors.metadata.organ_donor_data.grouping_concept_preferred_term +- ancestors.metadata.organ_donor_data.grouping_concept +- ancestors.metadata.organ_donor_data.grouping_code +- ancestors.metadata.organ_donor_data.graph_version +- ancestors.metadata.organ_donor_data.end_datetime +- ancestors.metadata.organ_donor_data.data_value +- ancestors.metadata.organ_donor_data.data_type +- ancestors.metadata.organ_donor_data.concept_id +- ancestors.metadata.organ_donor_data.code +- ancestors.metadata.metadata.version +- ancestors.metadata.metadata.umi_size +- ancestors.metadata.metadata.umi_read +- ancestors.metadata.metadata.umi_offset +- ancestors.metadata.metadata.transposition_transposase_source +- ancestors.metadata.metadata.transposition_method +- ancestors.metadata.metadata.transposition_kit_number +- ancestors.metadata.metadata.transposition_input +- ancestors.metadata.metadata.tissue_id +- ancestors.metadata.metadata.step_z_value +- ancestors.metadata.metadata.start_datetime +- ancestors.metadata.metadata.stain +- ancestors.metadata.metadata.source_project +- ancestors.metadata.metadata.signal_type +- ancestors.metadata.metadata.sequencing_reagent_kit +- ancestors.metadata.metadata.sequencing_read_percent_q30 +- ancestors.metadata.metadata.sequencing_read_format +- ancestors.metadata.metadata.sequencing_phix_percent +- ancestors.metadata.metadata.segment_data_format +- ancestors.metadata.metadata.section_prep_protocols_io_doi +- ancestors.metadata.metadata.sc_isolation_tissue_dissociation +- ancestors.metadata.metadata.sc_isolation_quality_metric +- ancestors.metadata.metadata.sc_isolation_protocols_io_doi +- ancestors.metadata.metadata.sc_isolation_entity +- ancestors.metadata.metadata.sc_isolation_enrichment +- ancestors.metadata.metadata.sc_isolation_cell_number +- ancestors.metadata.metadata.sample_quality_metric +- ancestors.metadata.metadata.roi_id +- ancestors.metadata.metadata.roi_description +- ancestors.metadata.metadata.rnaseq_assay_method +- ancestors.metadata.metadata.rnaseq_assay_input_value +- ancestors.metadata.metadata.rnaseq_assay_input_unit +- ancestors.metadata.metadata.rnaseq_assay_input +- ancestors.metadata.metadata.resolution_z_value +- ancestors.metadata.metadata.resolution_z_unit +- ancestors.metadata.metadata.resolution_y_value +- ancestors.metadata.metadata.resolution_y_unit +- ancestors.metadata.metadata.resolution_x_value +- ancestors.metadata.metadata.resolution_x_unit +- ancestors.metadata.metadata.reagent_prep_protocols_io_doi +- ancestors.metadata.metadata.range_z_value +- ancestors.metadata.metadata.range_z_unit +- ancestors.metadata.metadata.puck_id +- ancestors.metadata.metadata.protocols_io_doi +- ancestors.metadata.metadata.preparation_type +- ancestors.metadata.metadata.preparation_maldi_matrix +- ancestors.metadata.metadata.preparation_instrument_vendor +- ancestors.metadata.metadata.preparation_instrument_model +- ancestors.metadata.metadata.polarity +- ancestors.metadata.metadata.pi_email +- ancestors.metadata.metadata.pi +- ancestors.metadata.metadata.overall_protocols_io_doi +- ancestors.metadata.metadata.operator_email +- ancestors.metadata.metadata.operator +- ancestors.metadata.metadata.number_of_sections +- ancestors.metadata.metadata.number_of_readout_probes_per_channel +- ancestors.metadata.metadata.number_of_pseudocolors_per_channel +- ancestors.metadata.metadata.number_of_imaging_rounds +- ancestors.metadata.metadata.number_of_cycles +- ancestors.metadata.metadata.number_of_channels +- ancestors.metadata.metadata.number_of_barcode_regions_per_barcode_probe +- ancestors.metadata.metadata.number_of_barcode_probes +- ancestors.metadata.metadata.number_of_antibodies +- ancestors.metadata.metadata.mz_range_low_value +- ancestors.metadata.metadata.mz_range_high_value +- ancestors.metadata.metadata.ms_source +- ancestors.metadata.metadata.metadata_path +- ancestors.metadata.metadata.max_y_height_value +- ancestors.metadata.metadata.max_y_height_unit +- ancestors.metadata.metadata.max_x_width_value +- ancestors.metadata.metadata.max_x_width_unit +- ancestors.metadata.metadata.library_preparation_kit +- ancestors.metadata.metadata.library_pcr_cycles_for_sample_index +- ancestors.metadata.metadata.library_pcr_cycles +- ancestors.metadata.metadata.library_layout +- ancestors.metadata.metadata.library_id +- ancestors.metadata.metadata.library_final_yield_value +- ancestors.metadata.metadata.library_final_yield_unit +- ancestors.metadata.metadata.library_final_yield +- ancestors.metadata.metadata.library_creation_date +- ancestors.metadata.metadata.library_construction_protocols_io_doi +- ancestors.metadata.metadata.library_concentration_value +- ancestors.metadata.metadata.library_concentration_unit +- ancestors.metadata.metadata.library_average_fragment_size +- ancestors.metadata.metadata.library_adapter_sequence +- ancestors.metadata.metadata.is_technical_replicate +- ancestors.metadata.metadata.is_targeted +- ancestors.metadata.metadata.increment_z_value +- ancestors.metadata.metadata.increment_z_unit +- ancestors.metadata.metadata.expected_cell_count +- ancestors.metadata.metadata.execution_datetime +- ancestors.metadata.metadata.end_datetime +- ancestors.metadata.metadata.dual_count_start +- ancestors.metadata.metadata.donor_id +- ancestors.metadata.metadata.description +- ancestors.metadata.metadata.data_precision_bytes +- ancestors.metadata.metadata.data_path +- ancestors.metadata.metadata.contributors_path +- ancestors.metadata.metadata.collectiontype +- ancestors.metadata.metadata.cell_barcode_size +- ancestors.metadata.metadata.cell_barcode_read +- ancestors.metadata.metadata.cell_barcode_offset +- ancestors.metadata.metadata.bulk_transposition_input_number_nuclei +- ancestors.metadata.metadata.bulk_rna_yield_value +- ancestors.metadata.metadata.bulk_rna_yield_units_per_tissue_unit +- ancestors.metadata.metadata.bulk_rna_isolation_quality_metric_value +- ancestors.metadata.metadata.bulk_rna_isolation_protocols_io_doi +- ancestors.metadata.metadata.bulk_atac_cell_isolation_protocols_io_doi +- ancestors.metadata.metadata.bead_barcode_size +- ancestors.metadata.metadata.bead_barcode_read +- ancestors.metadata.metadata.bead_barcode_offset +- ancestors.metadata.metadata.assay_type +- ancestors.metadata.metadata.assay_category +- ancestors.metadata.metadata.antibodies_path +- ancestors.metadata.metadata.analyte_class +- ancestors.metadata.metadata.acquisition_instrument_vendor +- ancestors.metadata.metadata.acquisition_instrument_model +- ancestors.metadata.metadata.acquisition_id +- ancestors.metadata.metadata.ablation_frequency_value +- ancestors.metadata.metadata.ablation_frequency_unit +- ancestors.metadata.metadata.ablation_distance_between_shots_y_value +- ancestors.metadata.metadata.ablation_distance_between_shots_y_units +- ancestors.metadata.metadata.ablation_distance_between_shots_x_value +- ancestors.metadata.metadata.ablation_distance_between_shots_x_units +- ancestors.metadata.living_donor_data.units +- ancestors.metadata.living_donor_data.start_datetime +- ancestors.metadata.living_donor_data.sab +- ancestors.metadata.living_donor_data.preferred_term +- ancestors.metadata.living_donor_data.numeric_operator +- ancestors.metadata.living_donor_data.grouping_sab +- ancestors.metadata.living_donor_data.grouping_concept_preferred_term +- ancestors.metadata.living_donor_data.grouping_concept +- ancestors.metadata.living_donor_data.grouping_code +- ancestors.metadata.living_donor_data.graph_version +- ancestors.metadata.living_donor_data.end_datetime +- ancestors.metadata.living_donor_data.data_value +- ancestors.metadata.living_donor_data.data_type +- ancestors.metadata.living_donor_data.concept_id +- ancestors.metadata.living_donor_data.code +- ancestors.metadata.files.type +- ancestors.metadata.files.rel_path +- ancestors.metadata.files.edam_term +- ancestors.metadata.files.description +- ancestors.metadata.extra_metadata.collectiontype +- ancestors.metadata.dag_provenance_list.origin +- ancestors.metadata.dag_provenance_list.name +- ancestors.metadata.dag_provenance_list.hash diff --git a/docs/search-indices/parameterized-search.md b/docs/search-indices/parameterized-search.md new file mode 100644 index 0000000..b6cb4dd --- /dev/null +++ b/docs/search-indices/parameterized-search.md @@ -0,0 +1,1707 @@ +--- +layout: page +--- +# HuBMAP Parameterized Search + +### Last Updated: 2023-04-25 + +## Overview: +This page describes ReSTful, parameterized search of OpenSearch indices as part of the [HuBMAP Search API](https://smart-api.info/ui/7aaf02b838022d564da776b03f357158). + +## Description: +The [Search API](https://smart-api.info/ui/7aaf02b838022d564da776b03f357158) allows access to a pair of [OpenSearch](https://opensearch.org/docs/latest/) indices consisting of a private/consortium-only index and a public/open to all index. The Search API will automatically direct to the index based on the user authorization. + +Each document in the `entities` indices contains information about one entity in a Dataset. The structure of these documents is described below. + +## Examples: +For the `param-search/samples` endpoint with the argument `organ=HT`: +``` + POST https://search.api.hubmapconsortium.org/param-search/samples?organ=HT +``` +A search for Sample entities from heart is performed. An array of OpenSearch documents is returned, with elements as shown in the following elided Javascript +``` +[ + { + "ancestor_ids": [ + "8124e9475115786c1fae3683a6714c32", ... + ], + "ancestors": [ + { + "created_by_user_displayname": "daniel Cotter", + ... + "uuid": "8124e9475115786c1fae3683a6714c32" + }, + { + "created_by_user_displayname": "amir Bahmani", + ... + "uuid": "8cdf44a106338aada6da04c71eeb767e" + }, + ... + ], + "created_by_user_displayname": "Derek Furst", + "created_by_user_email": "DRF57@pitt.edu", + "created_timestamp": 1676920682769, + "data_access_level": "consortium", + "descendant_ids": [], + "descendants": [], + "description": "updated test sample", + "display_subtype": "Section", + "donor": { + "created_by_user_displayname": "Yiing Lin", + ... + }, + "entity_type": "Sample", + "group_name": "IEC Testing Group", + "group_uuid": "5bd084c8-edc2-11e8-802f-0e368f3075e8", + "hubmap_id": "HBM369.VTXF.528", + "immediate_ancestors": [ + { + "created_by_user_displayname": "daniel Cotter", + ... + "uuid": "8124e9475115786c1fae3683a6714c32" + } + ], + "immediate_descendants": [], + "index_version": "3.1.2", + "last_modified_timestamp": 1676920722518, + "origin_sample": { + "created_by_user_displayname": "Yiing Lin", + ... + "uuid": "068aef7b9a77c6c61b85ad69cc8cf0d5" + }, + "origin_samples": [ + { + "created_by_user_displayname": "Yiing Lin", + ... + "uuid": "068aef7b9a77c6c61b85ad69cc8cf0d5" + } + ], + "protocol_url": "11.1111/protocols.io/test", + "sample_category": "section", + "submission_id": "STAN0003-LI-2-6-1", + "uuid": "7d35602e0803164985296fef43dcd508" + }, + ... +] +``` + +## Limitations: +- The current index only includes documents for Files in primary Datasets which are published and do not contain genetic information. +- The document from the OpenSearch index contains accurate information from the time the Dataset was processed, and may not reflect subsequent changes until a re-index is complete. + +## Common document elements: + +Stored documents are enhanced with the following attributes for convenient use within the JSON response. + +| Document Element | Description | +|-----------------------|-------------------------------------------------------------------------------------------------------| +| ancestor_ids | A Javascript array with identifiers for all ancestors of the entity | +| ancestors | A Javascript array with a JSON object for each ancestor of the entity | +| descendant_ids | A Javascript array with identifiers for all descendants of the entity | +| descendants | A Javascript array with a JSON object for each descendant of the entity | +| display_subtype | A string with the name of the entity's type | +| donor | A JSON object with information for the Donor associated with the entity | +| immediate_ancestors | A Javascript array with a JSON object for the subset of ancestors which are "a parent to" the entity | +| immediate_descendants | A Javascript array with a JSON object for the subset of descendants which are "a child of" the entity | +| index_version | A string indicating the version of the indexing software used to create the document in the index | +| origin_sample | A JSON object with information for the ancestor Sample associated with the entity | +| origin_samples | A Javascript array with a JSON object for the ancestor Sample associated with the entity | + +### OpenSearch document keyword attributes +Elements of the list below may be used to compose "terms" of a query for value matching. +Examples are enumerated as follows, but the current, authoritative list is returned from a call +to the search-api endpoint [/attribute-values?attribute_name_list](/attribute-values?attribute_name_list). +- visit +- uuid +- title +- tissue_type +- submission_id +- status +- specimen_type_other +- specimen_type +- sample_category +- rui_location +- registered_doi +- publication_venue +- publication_url +- publication_doi +- publication_date +- provider_info +- protocol_url +- previous_revision_uuid +- pages_or_article_num +- organ +- next_revision_uuid +- label +- lab_tissue_sample_id +- lab_donor_id +- lab_dataset_id +- index_version +- hubmap_id +- group_uuid +- group_name +- error_message +- entity_type +- doi_url +- display_subtype +- description +- descendant_ids +- dbgap_study_url +- dbgap_sra_experiment_url +- dataset_info +- data_types +- data_access_level +- created_by_user_email +- created_by_user_displayname +- ancestor_ids +- all_text +- thumbnail_file.filename +- thumbnail_file.file_uuid +- source_samples.visit +- source_samples.uuid +- source_samples.tissue_type +- source_samples.submission_id +- source_samples.specimen_type_other +- source_samples.specimen_type +- source_samples.sample_category +- source_samples.rui_location +- source_samples.protocol_url +- source_samples.organ +- source_samples.lab_tissue_sample_id +- source_samples.hubmap_id +- source_samples.group_uuid +- source_samples.entity_type +- source_samples.description +- source_samples.data_access_level +- source_samples.created_by_user_email +- source_samples.created_by_user_displayname +- source_sample.visit +- source_sample.uuid +- source_sample.tissue_type +- source_sample.submission_id +- source_sample.specimen_type_other +- source_sample.specimen_type +- source_sample.sample_category +- source_sample.rui_location +- source_sample.protocol_url +- source_sample.organ +- source_sample.lab_tissue_sample_id +- source_sample.hubmap_id +- source_sample.group_uuid +- source_sample.entity_type +- source_sample.description +- source_sample.data_access_level +- source_sample.created_by_user_email +- source_sample.created_by_user_displayname +- portal_metadata_upload_files.filepath +- portal_metadata_upload_files.description +- origin_samples.visit +- origin_samples.uuid +- origin_samples.tissue_type +- origin_samples.submission_id +- origin_samples.specimen_type +- origin_samples.sample_category +- origin_samples.protocol_url +- origin_samples.organ +- origin_samples.lab_tissue_sample_id +- origin_samples.hubmap_id +- origin_samples.group_uuid +- origin_samples.entity_type +- origin_samples.description +- origin_samples.data_access_level +- origin_samples.created_by_user_email +- origin_samples.created_by_user_displayname +- origin_sample.visit +- origin_sample.uuid +- origin_sample.tissue_type +- origin_sample.submission_id +- origin_sample.specimen_type +- origin_sample.sample_category +- origin_sample.protocol_url +- origin_sample.organ +- origin_sample.lab_tissue_sample_id +- origin_sample.hubmap_id +- origin_sample.group_uuid +- origin_sample.entity_type +- origin_sample.description +- origin_sample.data_access_level +- origin_sample.created_by_user_email +- origin_sample.created_by_user_displayname +- metadata.warm_ischemia_time_value +- metadata.warm_ischemia_time_unit +- metadata.vital_state +- metadata.thumbnail_file_abs_path +- metadata.specimen_tumor_distance_value +- metadata.specimen_tumor_distance_unit +- metadata.specimen_quality_criteria +- metadata.specimen_preservation_temperature +- metadata.sample_id +- metadata.procedure_date +- metadata.perfusion_solution +- metadata.pathologist_report +- metadata.organ_condition +- metadata.health_status +- metadata.files_info_alt_path +- metadata.cold_ischemia_time_value +- metadata.cold_ischemia_time_unit +- metadata.Preservation_media +- metadata.Preservation_condition +- metadata.PPID +- immediate_descendants.visit +- immediate_descendants.uuid +- immediate_descendants.title +- immediate_descendants.tissue_type +- immediate_descendants.submission_id +- immediate_descendants.status +- immediate_descendants.specimen_type_other +- immediate_descendants.specimen_type +- immediate_descendants.sample_category +- immediate_descendants.rui_location +- immediate_descendants.registered_doi +- immediate_descendants.publication_venue +- immediate_descendants.publication_url +- immediate_descendants.publication_doi +- immediate_descendants.publication_date +- immediate_descendants.provider_info +- immediate_descendants.protocol_url +- immediate_descendants.previous_revision_uuid +- immediate_descendants.pages_or_article_num +- immediate_descendants.organ +- immediate_descendants.next_revision_uuid +- immediate_descendants.lab_tissue_sample_id +- immediate_descendants.lab_dataset_id +- immediate_descendants.hubmap_id +- immediate_descendants.group_uuid +- immediate_descendants.error_message +- immediate_descendants.entity_type +- immediate_descendants.doi_url +- immediate_descendants.description +- immediate_descendants.dbgap_study_url +- immediate_descendants.dbgap_sra_experiment_url +- immediate_descendants.dataset_info +- immediate_descendants.data_types +- immediate_descendants.data_access_level +- immediate_descendants.created_by_user_email +- immediate_descendants.created_by_user_displayname +- immediate_ancestors.visit +- immediate_ancestors.uuid +- immediate_ancestors.title +- immediate_ancestors.tissue_type +- immediate_ancestors.submission_id +- immediate_ancestors.status +- immediate_ancestors.specimen_type_other +- immediate_ancestors.specimen_type +- immediate_ancestors.sample_category +- immediate_ancestors.rui_location +- immediate_ancestors.registered_doi +- immediate_ancestors.provider_info +- immediate_ancestors.protocol_url +- immediate_ancestors.organ +- immediate_ancestors.next_revision_uuid +- immediate_ancestors.label +- immediate_ancestors.lab_tissue_sample_id +- immediate_ancestors.lab_donor_id +- immediate_ancestors.lab_dataset_id +- immediate_ancestors.hubmap_id +- immediate_ancestors.group_uuid +- immediate_ancestors.entity_type +- immediate_ancestors.doi_url +- immediate_ancestors.description +- immediate_ancestors.dataset_info +- immediate_ancestors.data_types +- immediate_ancestors.data_access_level +- immediate_ancestors.created_by_user_email +- immediate_ancestors.created_by_user_displayname +- image_file_metadata.filepath +- image_file_metadata.description +- files.type +- files.rel_path +- files.edam_term +- files.description +- donor.uuid +- donor.submission_id +- donor.protocol_url +- donor.label +- donor.lab_donor_id +- donor.hubmap_id +- donor.group_uuid +- donor.entity_type +- donor.description +- donor.data_access_level +- donor.created_by_user_email +- donor.created_by_user_displayname +- descendants.visit +- descendants.uuid +- descendants.title +- descendants.tissue_type +- descendants.submission_id +- descendants.status +- descendants.specimen_type_other +- descendants.specimen_type +- descendants.sample_category +- descendants.rui_location +- descendants.registered_doi +- descendants.publication_venue +- descendants.publication_url +- descendants.publication_doi +- descendants.publication_date +- descendants.provider_info +- descendants.protocol_url +- descendants.previous_revision_uuid +- descendants.pages_or_article_num +- descendants.organ +- descendants.next_revision_uuid +- descendants.lab_tissue_sample_id +- descendants.lab_dataset_id +- descendants.hubmap_id +- descendants.group_uuid +- descendants.error_message +- descendants.entity_type +- descendants.doi_url +- descendants.description +- descendants.dbgap_study_url +- descendants.dbgap_sra_experiment_url +- descendants.dataset_info +- descendants.data_types +- descendants.data_access_level +- descendants.created_by_user_email +- descendants.created_by_user_displayname +- datasets.uuid +- datasets.title +- datasets.status +- datasets.registered_doi +- datasets.provider_info +- datasets.lab_dataset_id +- datasets.index_version +- datasets.hubmap_id +- datasets.group_uuid +- datasets.group_name +- datasets.entity_type +- datasets.doi_url +- datasets.display_subtype +- datasets.description +- datasets.dataset_info +- datasets.data_types +- datasets.data_access_level +- datasets.created_by_user_email +- datasets.created_by_user_displayname +- creators.orcid_id +- creators.name +- creators.middle_name_or_initial +- creators.last_name +- creators.first_name +- creators.affiliation +- contributors.version +- contributors.orcid_id +- contributors.orchid_id +- contributors.orc_id +- contributors.name +- contributors.middle_name_or_initial +- contributors.last_name +- contributors.is_contact +- contributors.first_name +- contributors.affiliation +- contacts.version +- contacts.orcid_id +- contacts.orc_id +- contacts.name +- contacts.middle_name_or_initial +- contacts.middle_name_or_initia +- contacts.last_name +- contacts.is_contact +- contacts.first_name +- contacts.affiliation +- ancestors.visit +- ancestors.uuid +- ancestors.title +- ancestors.tissue_type +- ancestors.submission_id +- ancestors.status +- ancestors.specimen_type_other +- ancestors.specimen_type +- ancestors.sample_category +- ancestors.rui_location +- ancestors.registered_doi +- ancestors.provider_info +- ancestors.protocol_url +- ancestors.organ +- ancestors.next_revision_uuid +- ancestors.label +- ancestors.lab_tissue_sample_id +- ancestors.lab_donor_id +- ancestors.lab_dataset_id +- ancestors.hubmap_id +- ancestors.group_uuid +- ancestors.entity_type +- ancestors.doi_url +- ancestors.description +- ancestors.dataset_info +- ancestors.data_types +- ancestors.data_access_level +- ancestors.created_by_user_email +- ancestors.created_by_user_displayname +- source_samples.thumbnail_file.filename +- source_samples.thumbnail_file.file_uuid +- source_samples.portal_metadata_upload_files.filepath +- source_samples.portal_metadata_upload_files.description +- source_samples.metadata.warm_ischemia_time_value +- source_samples.metadata.warm_ischemia_time_unit +- source_samples.metadata.vital_state +- source_samples.metadata.specimen_tumor_distance_value +- source_samples.metadata.specimen_tumor_distance_unit +- source_samples.metadata.specimen_quality_criteria +- source_samples.metadata.specimen_preservation_temperature +- source_samples.metadata.sample_id +- source_samples.metadata.procedure_date +- source_samples.metadata.perfusion_solution +- source_samples.metadata.pathologist_report +- source_samples.metadata.organ_condition +- source_samples.metadata.health_status +- source_samples.metadata.cold_ischemia_time_value +- source_samples.metadata.cold_ischemia_time_unit +- source_sample.thumbnail_file.filename +- source_sample.thumbnail_file.file_uuid +- source_sample.portal_metadata_upload_files.filepath +- source_sample.portal_metadata_upload_files.description +- source_sample.metadata.warm_ischemia_time_value +- source_sample.metadata.warm_ischemia_time_unit +- source_sample.metadata.vital_state +- source_sample.metadata.specimen_tumor_distance_value +- source_sample.metadata.specimen_tumor_distance_unit +- source_sample.metadata.specimen_quality_criteria +- source_sample.metadata.specimen_preservation_temperature +- source_sample.metadata.sample_id +- source_sample.metadata.procedure_date +- source_sample.metadata.perfusion_solution +- source_sample.metadata.pathologist_report +- source_sample.metadata.organ_condition +- source_sample.metadata.health_status +- source_sample.metadata.cold_ischemia_time_value +- source_sample.metadata.cold_ischemia_time_unit +- origin_samples.portal_metadata_upload_files.filepath +- origin_samples.portal_metadata_upload_files.description +- origin_samples.metadata.warm_ischemia_time_value +- origin_samples.metadata.warm_ischemia_time_unit +- origin_samples.metadata.vital_state +- origin_samples.metadata.specimen_tumor_distance_value +- origin_samples.metadata.specimen_tumor_distance_unit +- origin_samples.metadata.specimen_quality_criteria +- origin_samples.metadata.specimen_preservation_temperature +- origin_samples.metadata.sample_id +- origin_samples.metadata.procedure_date +- origin_samples.metadata.perfusion_solution +- origin_samples.metadata.pathologist_report +- origin_samples.metadata.organ_condition +- origin_samples.metadata.health_status +- origin_samples.metadata.cold_ischemia_time_value +- origin_samples.metadata.cold_ischemia_time_unit +- origin_samples.image_file_metadata.filepath +- origin_samples.image_file_metadata.description +- origin_sample.portal_metadata_upload_files.filepath +- origin_sample.portal_metadata_upload_files.description +- origin_sample.metadata.warm_ischemia_time_value +- origin_sample.metadata.warm_ischemia_time_unit +- origin_sample.metadata.vital_state +- origin_sample.metadata.specimen_tumor_distance_value +- origin_sample.metadata.specimen_tumor_distance_unit +- origin_sample.metadata.specimen_quality_criteria +- origin_sample.metadata.specimen_preservation_temperature +- origin_sample.metadata.sample_id +- origin_sample.metadata.procedure_date +- origin_sample.metadata.perfusion_solution +- origin_sample.metadata.pathologist_report +- origin_sample.metadata.organ_condition +- origin_sample.metadata.health_status +- origin_sample.metadata.cold_ischemia_time_value +- origin_sample.metadata.cold_ischemia_time_unit +- origin_sample.image_file_metadata.filepath +- origin_sample.image_file_metadata.description +- metadata.organ_donor_data.units +- metadata.organ_donor_data.start_datetime +- metadata.organ_donor_data.sab +- metadata.organ_donor_data.preferred_term +- metadata.organ_donor_data.numeric_operator +- metadata.organ_donor_data.grouping_sab +- metadata.organ_donor_data.grouping_concept_preferred_term +- metadata.organ_donor_data.grouping_concept +- metadata.organ_donor_data.grouping_code +- metadata.organ_donor_data.graph_version +- metadata.organ_donor_data.end_datetime +- metadata.organ_donor_data.data_value +- metadata.organ_donor_data.data_type +- metadata.organ_donor_data.concept_id +- metadata.organ_donor_data.code +- metadata.metadata.version +- metadata.metadata.umi_size +- metadata.metadata.umi_read +- metadata.metadata.umi_offset +- metadata.metadata.transposition_transposase_source +- metadata.metadata.transposition_method +- metadata.metadata.transposition_kit_number +- metadata.metadata.transposition_input +- metadata.metadata.tissue_id +- metadata.metadata.step_z_value +- metadata.metadata.start_datetime +- metadata.metadata.stain +- metadata.metadata.source_project +- metadata.metadata.signal_type +- metadata.metadata.sequencing_reagent_kit +- metadata.metadata.sequencing_read_percent_q30 +- metadata.metadata.sequencing_read_format +- metadata.metadata.sequencing_phix_percent +- metadata.metadata.segment_data_format +- metadata.metadata.section_prep_protocols_io_doi +- metadata.metadata.sc_isolation_tissue_dissociation +- metadata.metadata.sc_isolation_quality_metric +- metadata.metadata.sc_isolation_protocols_io_doi +- metadata.metadata.sc_isolation_entity +- metadata.metadata.sc_isolation_enrichment +- metadata.metadata.sc_isolation_cell_number +- metadata.metadata.sample_quality_metric +- metadata.metadata.roi_id +- metadata.metadata.roi_description +- metadata.metadata.rnaseq_assay_method +- metadata.metadata.rnaseq_assay_input_value +- metadata.metadata.rnaseq_assay_input_unit +- metadata.metadata.rnaseq_assay_input +- metadata.metadata.resolution_z_value +- metadata.metadata.resolution_z_unit +- metadata.metadata.resolution_y_value +- metadata.metadata.resolution_y_unit +- metadata.metadata.resolution_x_value +- metadata.metadata.resolution_x_unit +- metadata.metadata.reagent_prep_protocols_io_doi +- metadata.metadata.range_z_value +- metadata.metadata.range_z_unit +- metadata.metadata.puck_id +- metadata.metadata.protocols_io_doi +- metadata.metadata.processing_search +- metadata.metadata.processing_protocols_io_doi +- metadata.metadata.preparation_type +- metadata.metadata.preparation_maldi_matrix +- metadata.metadata.preparation_instrument_vendor +- metadata.metadata.preparation_instrument_model +- metadata.metadata.polarity +- metadata.metadata.pi_email +- metadata.metadata.pi +- metadata.metadata.overall_protocols_io_doi +- metadata.metadata.operator_email +- metadata.metadata.operator +- metadata.metadata.number_of_sections +- metadata.metadata.number_of_readout_probes_per_channel +- metadata.metadata.number_of_pseudocolors_per_channel +- metadata.metadata.number_of_imaging_rounds +- metadata.metadata.number_of_cycles +- metadata.metadata.number_of_channels +- metadata.metadata.number_of_barcode_regions_per_barcode_probe +- metadata.metadata.number_of_barcode_probes +- metadata.metadata.number_of_antibodies +- metadata.metadata.mz_resolving_power +- metadata.metadata.mz_range_low_value +- metadata.metadata.mz_range_high_value +- metadata.metadata.ms_source +- metadata.metadata.ms_scan_mode +- metadata.metadata.metadata_path +- metadata.metadata.max_y_height_value +- metadata.metadata.max_y_height_unit +- metadata.metadata.max_x_width_value +- metadata.metadata.max_x_width_unit +- metadata.metadata.mass_resolving_power +- metadata.metadata.library_preparation_kit +- metadata.metadata.library_pcr_cycles_for_sample_index +- metadata.metadata.library_pcr_cycles +- metadata.metadata.library_layout +- metadata.metadata.library_id +- metadata.metadata.library_final_yield_value +- metadata.metadata.library_final_yield_unit +- metadata.metadata.library_final_yield +- metadata.metadata.library_creation_date +- metadata.metadata.library_construction_protocols_io_doi +- metadata.metadata.library_construction_method +- metadata.metadata.library_concentration_value +- metadata.metadata.library_concentration_unit +- metadata.metadata.library_average_fragment_size +- metadata.metadata.library_adapter_sequence +- metadata.metadata.lc_temp_value +- metadata.metadata.lc_temp_unit +- metadata.metadata.lc_resin +- metadata.metadata.lc_mobile_phase_b +- metadata.metadata.lc_mobile_phase_a +- metadata.metadata.lc_length_value +- metadata.metadata.lc_length_unit +- metadata.metadata.lc_instrument_vendor +- metadata.metadata.lc_instrument_model +- metadata.metadata.lc_id_value +- metadata.metadata.lc_id_unit +- metadata.metadata.lc_gradient +- metadata.metadata.lc_flow_rate_value +- metadata.metadata.lc_flow_rate_unit +- metadata.metadata.lc_column_vendor +- metadata.metadata.lc_column_model +- metadata.metadata.labeling +- metadata.metadata.is_technical_replicate +- metadata.metadata.is_targeted +- metadata.metadata.increment_z_value +- metadata.metadata.increment_z_unit +- metadata.metadata.gdna_fragmentation_quality_assurance +- metadata.metadata.expected_cell_count +- metadata.metadata.execution_datetime +- metadata.metadata.end_datetime +- metadata.metadata.dual_count_start +- metadata.metadata.donor_id +- metadata.metadata.dna_assay_input_value +- metadata.metadata.dna_assay_input_unit +- metadata.metadata.dms +- metadata.metadata.description +- metadata.metadata.data_precision_bytes +- metadata.metadata.data_path +- metadata.metadata.data_collection_mode +- metadata.metadata.contributors_path +- metadata.metadata.collectiontype +- metadata.metadata.cell_barcode_size +- metadata.metadata.cell_barcode_read +- metadata.metadata.cell_barcode_offset +- metadata.metadata.bulk_transposition_input_number_nuclei +- metadata.metadata.bulk_rna_yield_value +- metadata.metadata.bulk_rna_yield_units_per_tissue_unit +- metadata.metadata.bulk_rna_isolation_quality_metric_value +- metadata.metadata.bulk_rna_isolation_protocols_io_doi +- metadata.metadata.bulk_atac_cell_isolation_protocols_io_doi +- metadata.metadata.bead_barcode_size +- metadata.metadata.bead_barcode_read +- metadata.metadata.bead_barcode_offset +- metadata.metadata.assay_type +- metadata.metadata.assay_category +- metadata.metadata.antibodies_path +- metadata.metadata.analyte_class +- metadata.metadata.acquisition_instrument_vendor +- metadata.metadata.acquisition_instrument_model +- metadata.metadata.acquisition_id +- metadata.metadata.ablation_frequency_value +- metadata.metadata.ablation_frequency_unit +- metadata.metadata.ablation_distance_between_shots_y_value +- metadata.metadata.ablation_distance_between_shots_y_units +- metadata.metadata.ablation_distance_between_shots_x_value +- metadata.metadata.ablation_distance_between_shots_x_units +- metadata.living_donor_data.units +- metadata.living_donor_data.start_datetime +- metadata.living_donor_data.sab +- metadata.living_donor_data.preferred_term +- metadata.living_donor_data.numeric_operator +- metadata.living_donor_data.grouping_sab +- metadata.living_donor_data.grouping_concept_preferred_term +- metadata.living_donor_data.grouping_concept +- metadata.living_donor_data.grouping_code +- metadata.living_donor_data.graph_version +- metadata.living_donor_data.end_datetime +- metadata.living_donor_data.data_value +- metadata.living_donor_data.data_type +- metadata.living_donor_data.concept_id +- metadata.living_donor_data.code +- metadata.files.type +- metadata.files.rel_path +- metadata.files.edam_term +- metadata.files.description +- metadata.extra_metadata.collectiontype +- metadata.dag_provenance_list.origin +- metadata.dag_provenance_list.name +- metadata.dag_provenance_list.hash +- immediate_descendants.thumbnail_file.filename +- immediate_descendants.thumbnail_file.file_uuid +- immediate_descendants.portal_metadata_upload_files.filepath +- immediate_descendants.portal_metadata_upload_files.description +- immediate_descendants.metadata.warm_ischemia_time_value +- immediate_descendants.metadata.warm_ischemia_time_unit +- immediate_descendants.metadata.vital_state +- immediate_descendants.metadata.thumbnail_file_abs_path +- immediate_descendants.metadata.specimen_tumor_distance_value +- immediate_descendants.metadata.specimen_tumor_distance_unit +- immediate_descendants.metadata.specimen_quality_criteria +- immediate_descendants.metadata.specimen_preservation_temperature +- immediate_descendants.metadata.sample_id +- immediate_descendants.metadata.procedure_date +- immediate_descendants.metadata.perfusion_solution +- immediate_descendants.metadata.pathologist_report +- immediate_descendants.metadata.organ_condition +- immediate_descendants.metadata.health_status +- immediate_descendants.metadata.files_info_alt_path +- immediate_descendants.metadata.cold_ischemia_time_value +- immediate_descendants.metadata.cold_ischemia_time_unit +- immediate_descendants.metadata.Preservation_media +- immediate_descendants.metadata.Preservation_condition +- immediate_descendants.metadata.PPID +- immediate_descendants.image_file_metadata.filepath +- immediate_descendants.image_file_metadata.description +- immediate_descendants.files.type +- immediate_descendants.files.rel_path +- immediate_descendants.files.edam_term +- immediate_descendants.files.description +- immediate_descendants.contributors.version +- immediate_descendants.contributors.orcid_id +- immediate_descendants.contributors.orchid_id +- immediate_descendants.contributors.orc_id +- immediate_descendants.contributors.name +- immediate_descendants.contributors.middle_name_or_initial +- immediate_descendants.contributors.last_name +- immediate_descendants.contributors.is_contact +- immediate_descendants.contributors.first_name +- immediate_descendants.contributors.affiliation +- immediate_descendants.contacts.version +- immediate_descendants.contacts.orcid_id +- immediate_descendants.contacts.orc_id +- immediate_descendants.contacts.name +- immediate_descendants.contacts.middle_name_or_initial +- immediate_descendants.contacts.middle_name_or_initia +- immediate_descendants.contacts.last_name +- immediate_descendants.contacts.is_contact +- immediate_descendants.contacts.first_name +- immediate_descendants.contacts.affiliation +- immediate_ancestors.thumbnail_file.filename +- immediate_ancestors.thumbnail_file.file_uuid +- immediate_ancestors.portal_metadata_upload_files.filepath +- immediate_ancestors.portal_metadata_upload_files.description +- immediate_ancestors.metadata.warm_ischemia_time_value +- immediate_ancestors.metadata.warm_ischemia_time_unit +- immediate_ancestors.metadata.vital_state +- immediate_ancestors.metadata.thumbnail_file_abs_path +- immediate_ancestors.metadata.specimen_tumor_distance_value +- immediate_ancestors.metadata.specimen_tumor_distance_unit +- immediate_ancestors.metadata.specimen_quality_criteria +- immediate_ancestors.metadata.specimen_preservation_temperature +- immediate_ancestors.metadata.sample_id +- immediate_ancestors.metadata.procedure_date +- immediate_ancestors.metadata.perfusion_solution +- immediate_ancestors.metadata.pathologist_report +- immediate_ancestors.metadata.organ_condition +- immediate_ancestors.metadata.health_status +- immediate_ancestors.metadata.files_info_alt_path +- immediate_ancestors.metadata.cold_ischemia_time_value +- immediate_ancestors.metadata.cold_ischemia_time_unit +- immediate_ancestors.metadata.Preservation_media +- immediate_ancestors.metadata.Preservation_condition +- immediate_ancestors.metadata.PPID +- immediate_ancestors.image_file_metadata.filepath +- immediate_ancestors.image_file_metadata.description +- immediate_ancestors.files.type +- immediate_ancestors.files.rel_path +- immediate_ancestors.files.edam_term +- immediate_ancestors.files.description +- immediate_ancestors.contributors.version +- immediate_ancestors.contributors.orcid_id +- immediate_ancestors.contributors.name +- immediate_ancestors.contributors.middle_name_or_initial +- immediate_ancestors.contributors.last_name +- immediate_ancestors.contributors.is_contact +- immediate_ancestors.contributors.first_name +- immediate_ancestors.contributors.affiliation +- immediate_ancestors.contacts.version +- immediate_ancestors.contacts.orcid_id +- immediate_ancestors.contacts.name +- immediate_ancestors.contacts.middle_name_or_initial +- immediate_ancestors.contacts.middle_name_or_initia +- immediate_ancestors.contacts.last_name +- immediate_ancestors.contacts.is_contact +- immediate_ancestors.contacts.first_name +- immediate_ancestors.contacts.affiliation +- donor.portal_metadata_upload_files.filepath +- donor.portal_metadata_upload_files.description +- descendants.thumbnail_file.filename +- descendants.thumbnail_file.file_uuid +- descendants.portal_metadata_upload_files.filepath +- descendants.portal_metadata_upload_files.description +- descendants.metadata.warm_ischemia_time_value +- descendants.metadata.warm_ischemia_time_unit +- descendants.metadata.vital_state +- descendants.metadata.thumbnail_file_abs_path +- descendants.metadata.specimen_tumor_distance_value +- descendants.metadata.specimen_tumor_distance_unit +- descendants.metadata.specimen_quality_criteria +- descendants.metadata.specimen_preservation_temperature +- descendants.metadata.sample_id +- descendants.metadata.procedure_date +- descendants.metadata.perfusion_solution +- descendants.metadata.pathologist_report +- descendants.metadata.organ_condition +- descendants.metadata.health_status +- descendants.metadata.files_info_alt_path +- descendants.metadata.cold_ischemia_time_value +- descendants.metadata.cold_ischemia_time_unit +- descendants.metadata.Preservation_media +- descendants.metadata.Preservation_condition +- descendants.metadata.PPID +- descendants.image_file_metadata.filepath +- descendants.image_file_metadata.description +- descendants.files.type +- descendants.files.rel_path +- descendants.files.edam_term +- descendants.files.description +- descendants.contributors.version +- descendants.contributors.orcid_id +- descendants.contributors.orchid_id +- descendants.contributors.orc_id +- descendants.contributors.name +- descendants.contributors.middle_name_or_initial +- descendants.contributors.last_name +- descendants.contributors.is_contact +- descendants.contributors.first_name +- descendants.contributors.affiliation +- descendants.contacts.version +- descendants.contacts.orcid_id +- descendants.contacts.orc_id +- descendants.contacts.name +- descendants.contacts.middle_name_or_initial +- descendants.contacts.middle_name_or_initia +- descendants.contacts.last_name +- descendants.contacts.is_contact +- descendants.contacts.first_name +- descendants.contacts.affiliation +- datasets.contributors.version +- datasets.contributors.orcid_id +- datasets.contributors.orc_id +- datasets.contributors.name +- datasets.contributors.middle_name_or_initial +- datasets.contributors.last_name +- datasets.contributors.is_contact +- datasets.contributors.first_name +- datasets.contributors.affiliation +- datasets.contacts.version +- datasets.contacts.orcid_id +- datasets.contacts.orc_id +- datasets.contacts.name +- datasets.contacts.middle_name_or_initial +- datasets.contacts.last_name +- datasets.contacts.is_contact +- datasets.contacts.first_name +- datasets.contacts.affiliation +- ancestors.thumbnail_file.filename +- ancestors.thumbnail_file.file_uuid +- ancestors.portal_metadata_upload_files.filepath +- ancestors.portal_metadata_upload_files.description +- ancestors.metadata.warm_ischemia_time_value +- ancestors.metadata.warm_ischemia_time_unit +- ancestors.metadata.vital_state +- ancestors.metadata.thumbnail_file_abs_path +- ancestors.metadata.specimen_tumor_distance_value +- ancestors.metadata.specimen_tumor_distance_unit +- ancestors.metadata.specimen_quality_criteria +- ancestors.metadata.specimen_preservation_temperature +- ancestors.metadata.sample_id +- ancestors.metadata.procedure_date +- ancestors.metadata.perfusion_solution +- ancestors.metadata.pathologist_report +- ancestors.metadata.organ_condition +- ancestors.metadata.health_status +- ancestors.metadata.files_info_alt_path +- ancestors.metadata.cold_ischemia_time_value +- ancestors.metadata.cold_ischemia_time_unit +- ancestors.metadata.Preservation_media +- ancestors.metadata.Preservation_condition +- ancestors.metadata.PPID +- ancestors.image_file_metadata.filepath +- ancestors.image_file_metadata.description +- ancestors.files.type +- ancestors.files.rel_path +- ancestors.files.edam_term +- ancestors.files.description +- ancestors.contributors.version +- ancestors.contributors.orcid_id +- ancestors.contributors.name +- ancestors.contributors.middle_name_or_initial +- ancestors.contributors.last_name +- ancestors.contributors.is_contact +- ancestors.contributors.first_name +- ancestors.contributors.affiliation +- ancestors.contacts.version +- ancestors.contacts.orcid_id +- ancestors.contacts.name +- ancestors.contacts.middle_name_or_initial +- ancestors.contacts.middle_name_or_initia +- ancestors.contacts.last_name +- ancestors.contacts.is_contact +- ancestors.contacts.first_name +- ancestors.contacts.affiliation +- immediate_descendants.metadata.metadata.version +- immediate_descendants.metadata.metadata.umi_size +- immediate_descendants.metadata.metadata.umi_read +- immediate_descendants.metadata.metadata.umi_offset +- immediate_descendants.metadata.metadata.transposition_transposase_source +- immediate_descendants.metadata.metadata.transposition_method +- immediate_descendants.metadata.metadata.transposition_kit_number +- immediate_descendants.metadata.metadata.transposition_input +- immediate_descendants.metadata.metadata.tissue_id +- immediate_descendants.metadata.metadata.step_z_value +- immediate_descendants.metadata.metadata.start_datetime +- immediate_descendants.metadata.metadata.stain +- immediate_descendants.metadata.metadata.source_project +- immediate_descendants.metadata.metadata.signal_type +- immediate_descendants.metadata.metadata.sequencing_reagent_kit +- immediate_descendants.metadata.metadata.sequencing_read_percent_q30 +- immediate_descendants.metadata.metadata.sequencing_read_format +- immediate_descendants.metadata.metadata.sequencing_phix_percent +- immediate_descendants.metadata.metadata.segment_data_format +- immediate_descendants.metadata.metadata.section_prep_protocols_io_doi +- immediate_descendants.metadata.metadata.sc_isolation_tissue_dissociation +- immediate_descendants.metadata.metadata.sc_isolation_quality_metric +- immediate_descendants.metadata.metadata.sc_isolation_protocols_io_doi +- immediate_descendants.metadata.metadata.sc_isolation_entity +- immediate_descendants.metadata.metadata.sc_isolation_enrichment +- immediate_descendants.metadata.metadata.sc_isolation_cell_number +- immediate_descendants.metadata.metadata.sample_quality_metric +- immediate_descendants.metadata.metadata.roi_id +- immediate_descendants.metadata.metadata.roi_description +- immediate_descendants.metadata.metadata.rnaseq_assay_method +- immediate_descendants.metadata.metadata.rnaseq_assay_input_value +- immediate_descendants.metadata.metadata.rnaseq_assay_input_unit +- immediate_descendants.metadata.metadata.rnaseq_assay_input +- immediate_descendants.metadata.metadata.resolution_z_value +- immediate_descendants.metadata.metadata.resolution_z_unit +- immediate_descendants.metadata.metadata.resolution_y_value +- immediate_descendants.metadata.metadata.resolution_y_unit +- immediate_descendants.metadata.metadata.resolution_x_value +- immediate_descendants.metadata.metadata.resolution_x_unit +- immediate_descendants.metadata.metadata.reagent_prep_protocols_io_doi +- immediate_descendants.metadata.metadata.range_z_value +- immediate_descendants.metadata.metadata.range_z_unit +- immediate_descendants.metadata.metadata.puck_id +- immediate_descendants.metadata.metadata.protocols_io_doi +- immediate_descendants.metadata.metadata.processing_search +- immediate_descendants.metadata.metadata.processing_protocols_io_doi +- immediate_descendants.metadata.metadata.preparation_type +- immediate_descendants.metadata.metadata.preparation_maldi_matrix +- immediate_descendants.metadata.metadata.preparation_instrument_vendor +- immediate_descendants.metadata.metadata.preparation_instrument_model +- immediate_descendants.metadata.metadata.polarity +- immediate_descendants.metadata.metadata.pi_email +- immediate_descendants.metadata.metadata.pi +- immediate_descendants.metadata.metadata.overall_protocols_io_doi +- immediate_descendants.metadata.metadata.operator_email +- immediate_descendants.metadata.metadata.operator +- immediate_descendants.metadata.metadata.number_of_sections +- immediate_descendants.metadata.metadata.number_of_readout_probes_per_channel +- immediate_descendants.metadata.metadata.number_of_pseudocolors_per_channel +- immediate_descendants.metadata.metadata.number_of_imaging_rounds +- immediate_descendants.metadata.metadata.number_of_cycles +- immediate_descendants.metadata.metadata.number_of_channels +- immediate_descendants.metadata.metadata.number_of_barcode_regions_per_barcode_probe +- immediate_descendants.metadata.metadata.number_of_barcode_probes +- immediate_descendants.metadata.metadata.number_of_antibodies +- immediate_descendants.metadata.metadata.mz_resolving_power +- immediate_descendants.metadata.metadata.mz_range_low_value +- immediate_descendants.metadata.metadata.mz_range_high_value +- immediate_descendants.metadata.metadata.ms_source +- immediate_descendants.metadata.metadata.ms_scan_mode +- immediate_descendants.metadata.metadata.metadata_path +- immediate_descendants.metadata.metadata.max_y_height_value +- immediate_descendants.metadata.metadata.max_y_height_unit +- immediate_descendants.metadata.metadata.max_x_width_value +- immediate_descendants.metadata.metadata.max_x_width_unit +- immediate_descendants.metadata.metadata.mass_resolving_power +- immediate_descendants.metadata.metadata.library_preparation_kit +- immediate_descendants.metadata.metadata.library_pcr_cycles_for_sample_index +- immediate_descendants.metadata.metadata.library_pcr_cycles +- immediate_descendants.metadata.metadata.library_layout +- immediate_descendants.metadata.metadata.library_id +- immediate_descendants.metadata.metadata.library_final_yield_value +- immediate_descendants.metadata.metadata.library_final_yield_unit +- immediate_descendants.metadata.metadata.library_final_yield +- immediate_descendants.metadata.metadata.library_creation_date +- immediate_descendants.metadata.metadata.library_construction_protocols_io_doi +- immediate_descendants.metadata.metadata.library_construction_method +- immediate_descendants.metadata.metadata.library_concentration_value +- immediate_descendants.metadata.metadata.library_concentration_unit +- immediate_descendants.metadata.metadata.library_average_fragment_size +- immediate_descendants.metadata.metadata.library_adapter_sequence +- immediate_descendants.metadata.metadata.lc_temp_value +- immediate_descendants.metadata.metadata.lc_temp_unit +- immediate_descendants.metadata.metadata.lc_resin +- immediate_descendants.metadata.metadata.lc_mobile_phase_b +- immediate_descendants.metadata.metadata.lc_mobile_phase_a +- immediate_descendants.metadata.metadata.lc_length_value +- immediate_descendants.metadata.metadata.lc_length_unit +- immediate_descendants.metadata.metadata.lc_instrument_vendor +- immediate_descendants.metadata.metadata.lc_instrument_model +- immediate_descendants.metadata.metadata.lc_id_value +- immediate_descendants.metadata.metadata.lc_id_unit +- immediate_descendants.metadata.metadata.lc_gradient +- immediate_descendants.metadata.metadata.lc_flow_rate_value +- immediate_descendants.metadata.metadata.lc_flow_rate_unit +- immediate_descendants.metadata.metadata.lc_column_vendor +- immediate_descendants.metadata.metadata.lc_column_model +- immediate_descendants.metadata.metadata.labeling +- immediate_descendants.metadata.metadata.is_technical_replicate +- immediate_descendants.metadata.metadata.is_targeted +- immediate_descendants.metadata.metadata.increment_z_value +- immediate_descendants.metadata.metadata.increment_z_unit +- immediate_descendants.metadata.metadata.gdna_fragmentation_quality_assurance +- immediate_descendants.metadata.metadata.expected_cell_count +- immediate_descendants.metadata.metadata.execution_datetime +- immediate_descendants.metadata.metadata.end_datetime +- immediate_descendants.metadata.metadata.dual_count_start +- immediate_descendants.metadata.metadata.donor_id +- immediate_descendants.metadata.metadata.dna_assay_input_value +- immediate_descendants.metadata.metadata.dna_assay_input_unit +- immediate_descendants.metadata.metadata.dms +- immediate_descendants.metadata.metadata.description +- immediate_descendants.metadata.metadata.data_precision_bytes +- immediate_descendants.metadata.metadata.data_path +- immediate_descendants.metadata.metadata.data_collection_mode +- immediate_descendants.metadata.metadata.contributors_path +- immediate_descendants.metadata.metadata.collectiontype +- immediate_descendants.metadata.metadata.cell_barcode_size +- immediate_descendants.metadata.metadata.cell_barcode_read +- immediate_descendants.metadata.metadata.cell_barcode_offset +- immediate_descendants.metadata.metadata.bulk_transposition_input_number_nuclei +- immediate_descendants.metadata.metadata.bulk_rna_yield_value +- immediate_descendants.metadata.metadata.bulk_rna_yield_units_per_tissue_unit +- immediate_descendants.metadata.metadata.bulk_rna_isolation_quality_metric_value +- immediate_descendants.metadata.metadata.bulk_rna_isolation_protocols_io_doi +- immediate_descendants.metadata.metadata.bulk_atac_cell_isolation_protocols_io_doi +- immediate_descendants.metadata.metadata.bead_barcode_size +- immediate_descendants.metadata.metadata.bead_barcode_read +- immediate_descendants.metadata.metadata.bead_barcode_offset +- immediate_descendants.metadata.metadata.assay_type +- immediate_descendants.metadata.metadata.assay_category +- immediate_descendants.metadata.metadata.antibodies_path +- immediate_descendants.metadata.metadata.analyte_class +- immediate_descendants.metadata.metadata.acquisition_instrument_vendor +- immediate_descendants.metadata.metadata.acquisition_instrument_model +- immediate_descendants.metadata.metadata.acquisition_id +- immediate_descendants.metadata.metadata.ablation_frequency_value +- immediate_descendants.metadata.metadata.ablation_frequency_unit +- immediate_descendants.metadata.metadata.ablation_distance_between_shots_y_value +- immediate_descendants.metadata.metadata.ablation_distance_between_shots_y_units +- immediate_descendants.metadata.metadata.ablation_distance_between_shots_x_value +- immediate_descendants.metadata.metadata.ablation_distance_between_shots_x_units +- immediate_descendants.metadata.files.type +- immediate_descendants.metadata.files.rel_path +- immediate_descendants.metadata.files.edam_term +- immediate_descendants.metadata.files.description +- immediate_descendants.metadata.extra_metadata.collectiontype +- immediate_descendants.metadata.dag_provenance_list.origin +- 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immediate_ancestors.metadata.metadata.preparation_instrument_model +- immediate_ancestors.metadata.metadata.polarity +- immediate_ancestors.metadata.metadata.pi_email +- immediate_ancestors.metadata.metadata.pi +- immediate_ancestors.metadata.metadata.overall_protocols_io_doi +- immediate_ancestors.metadata.metadata.operator_email +- immediate_ancestors.metadata.metadata.operator +- immediate_ancestors.metadata.metadata.number_of_sections +- immediate_ancestors.metadata.metadata.number_of_readout_probes_per_channel +- immediate_ancestors.metadata.metadata.number_of_pseudocolors_per_channel +- immediate_ancestors.metadata.metadata.number_of_imaging_rounds +- immediate_ancestors.metadata.metadata.number_of_cycles +- immediate_ancestors.metadata.metadata.number_of_channels +- immediate_ancestors.metadata.metadata.number_of_barcode_regions_per_barcode_probe +- immediate_ancestors.metadata.metadata.number_of_barcode_probes +- immediate_ancestors.metadata.metadata.number_of_antibodies +- 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datasets.metadata.metadata.donor_id +- datasets.metadata.metadata.dna_assay_input_value +- datasets.metadata.metadata.dna_assay_input_unit +- datasets.metadata.metadata.description +- datasets.metadata.metadata.data_path +- datasets.metadata.metadata.data_collection_mode +- datasets.metadata.metadata.contributors_path +- datasets.metadata.metadata.collectiontype +- datasets.metadata.metadata.cell_barcode_size +- datasets.metadata.metadata.cell_barcode_read +- datasets.metadata.metadata.cell_barcode_offset +- datasets.metadata.metadata.bead_barcode_size +- datasets.metadata.metadata.bead_barcode_read +- datasets.metadata.metadata.bead_barcode_offset +- datasets.metadata.metadata.assay_type +- datasets.metadata.metadata.assay_category +- datasets.metadata.metadata.antibodies_path +- datasets.metadata.metadata.analyte_class +- datasets.metadata.metadata.acquisition_instrument_vendor +- datasets.metadata.metadata.acquisition_instrument_model +- datasets.metadata.extra_metadata.collectiontype +- datasets.metadata.dag_provenance_list.origin +- datasets.metadata.dag_provenance_list.hash +- ancestors.metadata.organ_donor_data.units +- ancestors.metadata.organ_donor_data.start_datetime +- ancestors.metadata.organ_donor_data.sab +- ancestors.metadata.organ_donor_data.preferred_term +- ancestors.metadata.organ_donor_data.numeric_operator +- ancestors.metadata.organ_donor_data.grouping_sab +- ancestors.metadata.organ_donor_data.grouping_concept_preferred_term +- ancestors.metadata.organ_donor_data.grouping_concept +- ancestors.metadata.organ_donor_data.grouping_code +- ancestors.metadata.organ_donor_data.graph_version +- ancestors.metadata.organ_donor_data.end_datetime +- ancestors.metadata.organ_donor_data.data_value +- ancestors.metadata.organ_donor_data.data_type +- ancestors.metadata.organ_donor_data.concept_id +- ancestors.metadata.organ_donor_data.code +- ancestors.metadata.metadata.version +- ancestors.metadata.metadata.umi_size +- ancestors.metadata.metadata.umi_read +- ancestors.metadata.metadata.umi_offset +- ancestors.metadata.metadata.transposition_transposase_source +- ancestors.metadata.metadata.transposition_method +- ancestors.metadata.metadata.transposition_kit_number +- ancestors.metadata.metadata.transposition_input +- ancestors.metadata.metadata.tissue_id +- ancestors.metadata.metadata.step_z_value +- ancestors.metadata.metadata.start_datetime +- ancestors.metadata.metadata.stain +- ancestors.metadata.metadata.source_project +- ancestors.metadata.metadata.signal_type +- ancestors.metadata.metadata.sequencing_reagent_kit +- ancestors.metadata.metadata.sequencing_read_percent_q30 +- ancestors.metadata.metadata.sequencing_read_format +- ancestors.metadata.metadata.sequencing_phix_percent +- ancestors.metadata.metadata.segment_data_format +- ancestors.metadata.metadata.section_prep_protocols_io_doi +- ancestors.metadata.metadata.sc_isolation_tissue_dissociation +- ancestors.metadata.metadata.sc_isolation_quality_metric +- ancestors.metadata.metadata.sc_isolation_protocols_io_doi +- ancestors.metadata.metadata.sc_isolation_entity +- ancestors.metadata.metadata.sc_isolation_enrichment +- ancestors.metadata.metadata.sc_isolation_cell_number +- ancestors.metadata.metadata.sample_quality_metric +- ancestors.metadata.metadata.roi_id +- ancestors.metadata.metadata.roi_description +- ancestors.metadata.metadata.rnaseq_assay_method +- ancestors.metadata.metadata.rnaseq_assay_input_value +- ancestors.metadata.metadata.rnaseq_assay_input_unit +- ancestors.metadata.metadata.rnaseq_assay_input +- ancestors.metadata.metadata.resolution_z_value +- ancestors.metadata.metadata.resolution_z_unit +- ancestors.metadata.metadata.resolution_y_value +- ancestors.metadata.metadata.resolution_y_unit +- ancestors.metadata.metadata.resolution_x_value +- ancestors.metadata.metadata.resolution_x_unit +- ancestors.metadata.metadata.reagent_prep_protocols_io_doi +- ancestors.metadata.metadata.range_z_value +- ancestors.metadata.metadata.range_z_unit +- ancestors.metadata.metadata.puck_id +- ancestors.metadata.metadata.protocols_io_doi +- ancestors.metadata.metadata.preparation_type +- ancestors.metadata.metadata.preparation_maldi_matrix +- ancestors.metadata.metadata.preparation_instrument_vendor +- ancestors.metadata.metadata.preparation_instrument_model +- ancestors.metadata.metadata.polarity +- ancestors.metadata.metadata.pi_email +- ancestors.metadata.metadata.pi +- ancestors.metadata.metadata.overall_protocols_io_doi +- ancestors.metadata.metadata.operator_email +- ancestors.metadata.metadata.operator +- ancestors.metadata.metadata.number_of_sections +- ancestors.metadata.metadata.number_of_readout_probes_per_channel +- ancestors.metadata.metadata.number_of_pseudocolors_per_channel +- ancestors.metadata.metadata.number_of_imaging_rounds +- ancestors.metadata.metadata.number_of_cycles +- ancestors.metadata.metadata.number_of_channels +- ancestors.metadata.metadata.number_of_barcode_regions_per_barcode_probe +- ancestors.metadata.metadata.number_of_barcode_probes +- ancestors.metadata.metadata.number_of_antibodies +- ancestors.metadata.metadata.mz_range_low_value +- ancestors.metadata.metadata.mz_range_high_value +- ancestors.metadata.metadata.ms_source +- ancestors.metadata.metadata.metadata_path +- ancestors.metadata.metadata.max_y_height_value +- ancestors.metadata.metadata.max_y_height_unit +- ancestors.metadata.metadata.max_x_width_value +- ancestors.metadata.metadata.max_x_width_unit +- ancestors.metadata.metadata.library_preparation_kit +- ancestors.metadata.metadata.library_pcr_cycles_for_sample_index +- ancestors.metadata.metadata.library_pcr_cycles +- ancestors.metadata.metadata.library_layout +- ancestors.metadata.metadata.library_id +- ancestors.metadata.metadata.library_final_yield_value +- ancestors.metadata.metadata.library_final_yield_unit +- ancestors.metadata.metadata.library_final_yield +- ancestors.metadata.metadata.library_creation_date +- ancestors.metadata.metadata.library_construction_protocols_io_doi +- ancestors.metadata.metadata.library_concentration_value +- ancestors.metadata.metadata.library_concentration_unit +- ancestors.metadata.metadata.library_average_fragment_size +- ancestors.metadata.metadata.library_adapter_sequence +- ancestors.metadata.metadata.is_technical_replicate +- ancestors.metadata.metadata.is_targeted +- ancestors.metadata.metadata.increment_z_value +- ancestors.metadata.metadata.increment_z_unit +- ancestors.metadata.metadata.expected_cell_count +- ancestors.metadata.metadata.execution_datetime +- ancestors.metadata.metadata.end_datetime +- ancestors.metadata.metadata.dual_count_start +- ancestors.metadata.metadata.donor_id +- ancestors.metadata.metadata.description +- ancestors.metadata.metadata.data_precision_bytes +- ancestors.metadata.metadata.data_path +- ancestors.metadata.metadata.contributors_path +- ancestors.metadata.metadata.collectiontype +- ancestors.metadata.metadata.cell_barcode_size +- ancestors.metadata.metadata.cell_barcode_read +- ancestors.metadata.metadata.cell_barcode_offset +- ancestors.metadata.metadata.bulk_transposition_input_number_nuclei +- ancestors.metadata.metadata.bulk_rna_yield_value +- ancestors.metadata.metadata.bulk_rna_yield_units_per_tissue_unit +- ancestors.metadata.metadata.bulk_rna_isolation_quality_metric_value +- ancestors.metadata.metadata.bulk_rna_isolation_protocols_io_doi +- ancestors.metadata.metadata.bulk_atac_cell_isolation_protocols_io_doi +- ancestors.metadata.metadata.bead_barcode_size +- ancestors.metadata.metadata.bead_barcode_read +- ancestors.metadata.metadata.bead_barcode_offset +- ancestors.metadata.metadata.assay_type +- ancestors.metadata.metadata.assay_category +- ancestors.metadata.metadata.antibodies_path +- ancestors.metadata.metadata.analyte_class +- ancestors.metadata.metadata.acquisition_instrument_vendor +- ancestors.metadata.metadata.acquisition_instrument_model +- ancestors.metadata.metadata.acquisition_id +- ancestors.metadata.metadata.ablation_frequency_value +- ancestors.metadata.metadata.ablation_frequency_unit +- ancestors.metadata.metadata.ablation_distance_between_shots_y_value +- ancestors.metadata.metadata.ablation_distance_between_shots_y_units +- ancestors.metadata.metadata.ablation_distance_between_shots_x_value +- ancestors.metadata.metadata.ablation_distance_between_shots_x_units +- ancestors.metadata.living_donor_data.units +- ancestors.metadata.living_donor_data.start_datetime +- ancestors.metadata.living_donor_data.sab +- ancestors.metadata.living_donor_data.preferred_term +- ancestors.metadata.living_donor_data.numeric_operator +- ancestors.metadata.living_donor_data.grouping_sab +- ancestors.metadata.living_donor_data.grouping_concept_preferred_term +- ancestors.metadata.living_donor_data.grouping_concept +- ancestors.metadata.living_donor_data.grouping_code +- ancestors.metadata.living_donor_data.graph_version +- ancestors.metadata.living_donor_data.end_datetime +- ancestors.metadata.living_donor_data.data_value +- ancestors.metadata.living_donor_data.data_type +- ancestors.metadata.living_donor_data.concept_id +- ancestors.metadata.living_donor_data.code +- ancestors.metadata.files.type +- ancestors.metadata.files.rel_path +- ancestors.metadata.files.edam_term +- ancestors.metadata.files.description +- ancestors.metadata.extra_metadata.collectiontype +- ancestors.metadata.dag_provenance_list.origin +- ancestors.metadata.dag_provenance_list.name +- ancestors.metadata.dag_provenance_list.hash diff --git a/docs/search-indices/schema-antibody.md b/docs/search-indices/schema-antibody.md new file mode 100644 index 0000000..46c083f --- /dev/null +++ b/docs/search-indices/schema-antibody.md @@ -0,0 +1,25 @@ +--- +layout: page +--- + +# HuBMAP Antibody schema + +### Last Updated: 2023-04-17 + +## Overview: +This page describes the Antibody schema for HuBMAP data. Antibody data occurs in the Dataset schema. +The antibody-api is used to search the antibody index, rather than search-api. + +## Antibody Schema +attributes as listed at [entity-api Dataset schema drop-down, antibodies drop-down, Antibody schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Constraint | Description | +|--------------------------|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------| +| antibody_name | string | The name of the antibody. | +| channel_id | string | The assay specific identifier for the channel corresponding to the antibody. | +| conjugated_cat_number | string | An antibody may be conjugated to a fluorescent tag or a metal tag for detection. Conjugated antibodies may be purchased from commercial providers. Blank if not applicable. | +| conjugated_tag | string | An antibody may be conjugated to a fluorescent tag or a metal tag for detection. Conjugated antibodies may be purchased from commercial providers. Blank if not applicable. | +| dilution | string | The dilition ratio, e.g. 1/200 for the antibody. Blank if not applicable. | +| lot_number | string | The antibody lot number from the vendor. | +| rr_id | string | The unique antibody identifier from the Antibody Registry (https://antibodyregistry.org). | +| uniprot_accession_number | string | The unique identifier for the target protein in the UniProt database (https://www.uniprot.org). | diff --git a/docs/search-indices/schema-collections.md b/docs/search-indices/schema-collections.md new file mode 100644 index 0000000..1074c7c --- /dev/null +++ b/docs/search-indices/schema-collections.md @@ -0,0 +1,41 @@ +--- +layout: page +--- + +# HuBMAP Collections schema + +### Last Updated: 2023-04-17 + +## Overview: +This page describes the Collections schema for HuBMAP data. Collections data occurs in the Dataset schema. +``` +GET https://search.api.hubmapconsortium.org/param-search/samples?group_name=Stanford TMC&organ=LI +``` + +And the following search for Datasets matched to a particular Sample, which is contained in the Dataset's `ancestors`: +``` +GET https://search.api.hubmapconsortium.org/param-search/datasets?ancestors.lab_tissue_sample_id=B001-A-406 +``` + +## Collections Schema +attributes as listed at [entity-api Dataset schema drop-down, collections drop-down, Collection schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Constraint | Description | +|--------------------------------|----------------------------------------------------|------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| created_timestamp | integer | read-only | The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970 | +| created_by_user_displayname | string | read-only | The name of the person or process authenticated when creating the object | +| created_by_user_email | string | read-only | The email address of the person or process authenticated when creating the object. | +| created_by_user_sub | string | read-only | The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object. | +| uuid | string | read-only | The HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17 | +| hubmap_id | string | read-only | A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.ABCD.### for every entity. | +| last_modified_timestamp | integer | read-only | The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970 | +| last_modified_user_sub | string | read-only | The subject id of the user who last modified the entity as provided by the authorization mechanism for the person or process authenticated when the object was modified. | +| last_modified_user_email | string | read-only | The email address of the person or process which authenticated when the object was last modified. | +| last_modified_user_displayname | string | read-only | The name of the person or process which authenticated when the object was last modified. | +| entity_type | string | read-only | One of the normalized entity types: Dataset, Collection, Sample, Donor | +| registered_doi | string | | The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets. | +| doi_url | string | read-only | The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487 | +| title | string | | The title of the Collection | +| creators | array of [`Person Schema`](./schema-person.html) | | A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication. | +| contacts | array of [`Person Schema`](./schema-person.html) | | A list of the people who are the main contacts to get information about the entity. | +| datasets | array of [`Dataset Schema`](./schema-dataset.html) | read-only | The datasets that are contained in the Collection. | diff --git a/docs/search-indices/schema-dataset.md b/docs/search-indices/schema-dataset.md new file mode 100644 index 0000000..ff13966 --- /dev/null +++ b/docs/search-indices/schema-dataset.md @@ -0,0 +1,210 @@ +--- +layout: page +--- + +# HuBMAP Dataset schema + +### Last Updated: 2023-04-17 + +## Overview: +This page describes the Dataset schema for HuBMAP data. Dataset data may be returned itself or a part of another entity. For example, this endpoint searches Datasets for a specified group and data type: +``` +GET https://search.api.hubmapconsortium.org/param-search/datasets?data_types=LC-MS_top_down&contacts.affiliation=Northwestern University +``` + +And the following search for the Sample of which is the Dataset is a descendant: +``` +GET https://search.api.hubmapconsortium.org/param-search/samples?group_name=Stanford TMC&descendants.uuid=277152f17b5a2f308820ab4d85c5a426 +``` + +## Description: +A query string is built by combining schema elements documented below with matching values. Each "term" of the query is combined using the & character, and the entire query is attached to the base URL after a ? character, per web standards. + +Query terms may be composited from attributes deeper in the schema type of an attribute. For example, the Dataset Schema attribute ```contacts``` is has a type of Person Schema, and Person Schema has an attribute ```affiliation```. Querying Datasets supports a term to search for contact's affiliation such as ```contacts.affiliation=Northwestern University```. + +Multiple schema types may be listed for an attribute, but the same principle to build a query term applies. For example, the Dataset Schema attribute ```metadata``` may contain many kinds of assay types, each with its own schema. Looking at the [LC-MS Schema](https://hubmapconsortium.github.io/ingest-validation-tools/lcms), we see it contains a Metadata Schema, and we can search using the attributes it contains by prefixing the term with ```metadata.metadata```. Searching for an assay catagory of mass spectrometry would lead to the term ```metadata.metadata.assay_category=mass_spectrometry```, and a query like: +``` +GET https://search.api.hubmapconsortium.org/param-search/datasets?metadata.metadata.assay_category=mass_spectrometry +``` + +## Limitations: +- This document lists resources pulled from configuration files. The content of those files, at the provided links, may be newer. + +## Dataset Schema +attributes as listed at [entity-api Dataset schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Constraint | Description | +|----------------------------------|-----------------------------------------------------------------------------------------|-----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| description | string | | Free text description of the dataset | +| created_timestamp | integer | read-only | The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970 | +| created_by_user_displayname | string | read-only | The name of the person or process authenticated when creating the object | +| created_by_user_email | string | read-only | The email address of the person or process authenticated when creating the object. | +| created_by_user_sub | string | read-only | The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object. | +| uuid | string | read-only | The HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17 | +| hubmap_id | string | read-only | A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.ABCD.### for every entity. | +| error_message | string | readOnly: false | An open text field that holds the last error message that arose from pipeline validation or analysis. | +| last_modified_timestamp | integer | read-only | The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970 | +| creators | array of [`Person Schema`](./schema-person.html) | | A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication. | +| contacts | array of [`Person Schema`](./schema-person.html) | | A list of the people who are the main contacts to get information about the entity. | +| entity_type | string | read-only | One of the normalized entity types: Dataset, Collection, Sample, Donor | +| registered_doi | string | | The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets. | +| doi_url | string | read-only | The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487 | +| contains_human_genetic_sequences | boolean | | True if the data contains any human genetic sequence information. Can only be set at CREATE/POST time | +| title | string | | The dataset title. | +| published_timestamp | integer | read-only | The timestamp of when the dataset was published. The format is an integer representing milliseconds since midnight, Jan 1, 1970. | +| published_user_displayname | string | read-only | The name of the authenticated user or process that published the data. | +| published_user_sub | string | read-only | The subject id for the user who published the data as provided by the authorization mechanism for the person or process authenticated when the dataset was publised. | +| published_user_email | string | read-only | The email address of the user who published the provided by the authorization mechanism for the person or process authenticated when published. | +| local_directory_rel_path | string | read-only | The path on the local HIVE file system, relative to the base data directory, where the data is stored. | +| group_uuid | string | | The uuid of globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Donor is a member of more than one write group. This property cannot be set via PUT (only on Create/POST). | +| group_name | string | read-only | The displayname of globus group which the user who created this entity is a member of | +| previous_revision_uuid | string | | The uuid of previous revision dataset. Can only be set at Create/POST time. | +| next_revision_uuid | string | read-only | The uuid of next revision dataset | +| sub_status | string | | A sub-status provided to further define the status. The only current allowable value is "Retracted" | +| retraction_reason | string | | Information recorded about why a the dataset was retracted. | +| dbgap_sra_experiment_url | string | | A URL linking the dataset to the associated uploaded data at dbGaP. | +| dbgap_study_url | string | | A URL linking the dataset to the particular study on dbGap it belongs to | +| data_access_level | string from [`data_access_level` attribute values](#data_access_level-attribute-values) | read-only | One of the values: public, consortium. | +| status | string string from [`status` attribute values](#status-attribute-values) | | One of: NewProcessing, QA Published Error Hold Invalid | +| contributors | array of [`Person Schema`](./schema-person.html) | read-only | A list of people who contributed to the creation of this dataset. Returned as an array of contributors, with each element a Person schema instance. | +| data_types | string from [`data_types` attribute values](#data_types-attribute-values) | | The data or assay types contained in this dataset as a json array of strings. Each is an assay code from [assay types](https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/assay_types.yaml) | +| antibodies | array of [`Antibody Schema`](./schema-antibody.html) | | A list of antibodies used in the assay that created the dataset | +| metadata | JSON-encoded string for a supported [assay type schema](#assay-type-schemas) | | The metadata returned from the ingest pipeline processing at data submission time. Provided as json. | +| thumbnail_file | string | | The dataset thumbnail file detail. Stored in db as a stringfied json, e.g., {"filename": "thumbnail.jpg", "file_uuid": "c35002f9c3d49f8b77e1e2cd4a01803d"} | +| lab_dataset_id | string | | A name or identifier used by the lab who is uploading the data to cross reference the data locally | +| files | array of [`File Schema`](./schema-file.html) | | An array of information about the files contained in the dataset. | + + +### `data_access_level` attribute values +The data_access_level of the `Dataset Schema` is one of the values following enumerated values: +- `public` +- `consortium` + +### `status` attribute values +The status attribute of the `Dataset Schema` is one of the values following enumerated values: +- `New` +- `Processing` +- `QA` +- `Published` +- `Error` +- `Hold` +- `Invalid` + +### `data_types` attribute values +The data_types attribute of the `Dataset Schema` is a value from the current, authoritative list of [assay types](https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/assay_types.yaml). Examples include: +- `AF`: Autofluorescence Microscopy +- `AF_pyramid`: Autofluorescence Microscopy [Image Pyramid] +- `ATACseq-bulk`: Bulk ATAC-seq +- `bulk_atacseq`: Bulk ATAC-seq [BWA + MACS2] +- `cell-dive`: Cell DIVE +- `celldive_deepcell`: CellDIVE [DeepCell + SPRM] +- `CODEX`: CODEX +- `CODEX2`: CODEX (CODEX2 assay type) +- `codex_cytokit_v1`: CODEX [Cytokit + SPRM] +- `codex_cytokit`: CODEX [Cytokit + SPRM] +- `DART-FISH`: DART-FISH +- `DESI`: DESI +- `DESI_pyramid`: DESI [Image Pyramid] +- `image_pyramid`: Image Pyramid +- `IMC2D`: Imaging Mass Cytometry (2D) +- `IMC3D`: Imaging Mass Cytometry (3D) +- `IMC2D_pyramid`: Imaging Mass Cytometry (2D) [Image Pyramid] +- `IMC3D_pyramid`: Imaging Mass Cytometry (3D) [Image Pyramid] +- `lc-ms_label-free`: Label-free LC-MS +- `lc-ms_labeled`: Labeled LC-MS +- `lc-ms-ms_label-free`: Label-free LC-MS/MS +- `lc-ms-ms_labeled`: Labeled LC-MS/MS +- `LC-MS-untargeted`: Untargeted LC-MS +- `Lightsheet`: Lightsheet Microscopy +- `MALDI-IMS`: MALDI IMS +- `MALDI-IMS_pyramid`: MALDI IMS [Image Pyramid] +- `MIBI`: Multiplex Ion Beam Imaging +- `mibi_deepcell`: Multiplex Ion Beam Imaging [DeepCell + SPRM] +- `NanoDESI`: NanoDESI +- `NanoDESI_pyramid`: NanoDESI [Image Pyramid] +- `NanoPOTS`: NanoPOTS +- `NanoPOTS_pyramid`: NanoPOTS [Image Pyramid] +- `MxIF`: Multiplexed IF Microscopy +- `MxIF_pyramid`: Multiplexed IF Microscopy [Image Pyramid] +- `PAS`: PAS Stained Microscopy +- `PAS_pyramid`: PAS Stained Microscopy [Image Pyramid] +- `publication`: Publication Data +- `bulk-RNA`: Bulk RNA-seq +- `salmon_rnaseq_bulk`: Bulk RNA-seq [Salmon] +- `SNARE-ATACseq2`: snATACseq (SNARE-seq2) +- `SNARE-RNAseq2`: snRNAseq (SNARE-seq2) +- `sc_atac_seq_snare_lab`: snATAC-seq (SNARE-seq2) [Lab Processed] +- `sc_rna_seq_snare_lab`: snRNA-seq (SNARE-seq2) [Lab Processed] +- `salmon_rnaseq_snareseq`: snRNA-seq (SNARE-seq2) [Salmon] +- `sc_atac_seq_snare`: snATAC-seq (SNARE-seq2) [SnapATAC] +- `scRNAseq-10xGenomics-v2`: scRNA-seq (10x Genomics v2) +- `scRNAseq-10xGenomics-v3`: scRNA-seq (10x Genomics v3) +- `salmon_rnaseq_10x`: scRNA-seq (10x Genomics) [Salmon] +- `sciATACseq`: sciATAC-seq +- `sc_atac_seq_sci`: sciATAC-seq [SnapATAC] +- `sciRNAseq`: sciRNA-seq +- `salmon_rnaseq_sciseq`: sciRNA-seq [Salmon] +- `seqFish`: seqFISH +- `seqFish_pyramid`: seqFISH [Image Pyramid] +- `seqFish_lab_processed`: seqFISH [Lab Processed] +- `SIMS-IMS`: SIMS-IMS +- `snATACseq`: snATAC-seq +- `sn_atac_seq`: snATAC-seq [SnapATAC] +- `snRNAseq-10xGenomics-v2`: snRNA-seq (10x Genomics v2) +- `snRNAseq-10xGenomics-v3`: snRNA-seq (10x Genomics v3) +- `salmon_sn_rnaseq_10x`: snRNA-seq [Salmon] +- `Slide-seq`: Slide-seq +- `salmon_rnaseq_slideseq`: Slide-seq [Salmon] +- `Targeted-Shotgun-LC-MS`: Targeted Shotgun / Flow-injection LC-MS +- `TMT-LC-MS`: TMT LC-MS +- `WGS`: Whole Genome Sequencing +- `LC-MS`: LC-MS +- `MS`: MS +- `LC-MS_bottom_up`: LC-MS Bottom Up +- `MS_bottom_up`: MS Bottom Up +- `LC-MS_top_down`: LC-MS Top Down +- `MS_top_down`: MS Top Down + +# Assay type schemas +### Imaging mass spectrometry +- [3D Imaging Mass Cytometry](https://hubmapconsortium.github.io/ingest-validation-tools/imc3d) +- [Imaging Mass Cytometry](https://hubmapconsortium.github.io/ingest-validation-tools/imc) +- [MALDI-IMS / SIMS-IMS / NanoDESI / DESI](https://hubmapconsortium.github.io/ingest-validation-tools/ims) +- [MIBI](https://hubmapconsortium.github.io/ingest-validation-tools/mibi) + +### Other TSVs +- [antibodies](https://hubmapconsortium.github.io/ingest-validation-tools/antibodies) +- [contributors](https://hubmapconsortium.github.io/ingest-validation-tools/contributors) +- [sample](https://hubmapconsortium.github.io/ingest-validation-tools/sample) +- [sample-block](https://hubmapconsortium.github.io/ingest-validation-tools/sample-block) +- [sample-section](https://hubmapconsortium.github.io/ingest-validation-tools/sample-section) +- [sample-suspension](https://hubmapconsortium.github.io/ingest-validation-tools/sample-suspension) + +### Sequence assays +- [SNARE-seq2 / sciATACseq / snATACseq](https://hubmapconsortium.github.io/ingest-validation-tools/scatacseq) +- [Slide-seq](https://hubmapconsortium.github.io/ingest-validation-tools/slideseq) +- [WGS](https://hubmapconsortium.github.io/ingest-validation-tools/wgs) +- [bulk RNA](https://hubmapconsortium.github.io/ingest-validation-tools/bulkrnaseq) +- [bulkATACseq](https://hubmapconsortium.github.io/ingest-validation-tools/bulkatacseq) +- [scRNAseq-10xGenomics-v2 / scRNAseq-10xGenomics-v3 / snRNAseq-10xGenomics-v2 / snRNAseq-10xGenomics-v3 / scRNAseq / sciRNAseq / snRNAseq / SNARE2-RNAseq](https://hubmapconsortium.github.io/ingest-validation-tools/scrnaseq) + +### Mass spectrometry +- [CE-MS](https://hubmapconsortium.github.io/ingest-validation-tools/cems) +- [GC-MS](https://hubmapconsortium.github.io/ingest-validation-tools/gcms) +- [LC-MS / MS / LC-MS Bottom-Up / MS Bottom-Up / LC-MS Top-Down / MS Top-Down](https://hubmapconsortium.github.io/ingest-validation-tools/lcms) + +### Clinical imaging modalities +- [Body CT](https://hubmapconsortium.github.io/ingest-validation-tools/bodyct) +- [MRI](https://hubmapconsortium.github.io/ingest-validation-tools/mri) +- [Micro CT](https://hubmapconsortium.github.io/ingest-validation-tools/microct) +- [OCT](https://hubmapconsortium.github.io/ingest-validation-tools/oct) +- [Ultrasound](https://hubmapconsortium.github.io/ingest-validation-tools/ultrasound) + +### Imaging assays +- [AF](https://hubmapconsortium.github.io/ingest-validation-tools/af) +- [CODEX / CODEX2](https://hubmapconsortium.github.io/ingest-validation-tools/codex) +- [Cell DIVE / cell-dive](https://hubmapconsortium.github.io/ingest-validation-tools/celldive) +- [Light Sheet](https://hubmapconsortium.github.io/ingest-validation-tools/lightsheet) +- [MxIF](https://hubmapconsortium.github.io/ingest-validation-tools/mxif) +- [PAS microscopy](https://hubmapconsortium.github.io/ingest-validation-tools/stained) +- [seqFISH](https://hubmapconsortium.github.io/ingest-validation-tools/seqfish) diff --git a/docs/search-indices/schema-donor.md b/docs/search-indices/schema-donor.md new file mode 100644 index 0000000..8ec8bc4 --- /dev/null +++ b/docs/search-indices/schema-donor.md @@ -0,0 +1,100 @@ +--- +layout: page +--- + +# HuBMAP Donor schema + +### Last Updated: 2023-04-17 + +## Overview: +This page describes the Donor schema for HuBMAP data. Donor data may be returned itself or a part of another entity. For example, this endpoint searches Donors for a specified group and organ type: +``` +GET https://search.api.hubmapconsortium.org/param-search/donors?group_name=Stanford TMC&descendants.organ=LI +``` + +And the following search for Samples matched to a particular Donor, which is contained in the Sample's `ancestors`: +``` +GET https://search.api.hubmapconsortium.org/param-search/samples?ancestors.lab_donor_id=W83/B001 +``` + +## Description: +A query string is built by combining schema elements documented below with matching values. Each "term" of the query is combined using the & character, and the entire query is attached to the base URL after a ? character, per web standards. + +Query terms may be composited from attributes deeper in the schema type of an attribute. For example, the Donor Schema attribute ```metadata.living_donor_data``` is has a type of Donor Metadata Schema, and Donor Metadata Schema has an attribute ```preferred_term``` supporting UMLS concepts. Querying Donors supports a term to search for living donors with information about coronary artery disease, such as ```metadata.living_donor_data.preferred_term=Coronary artery disease```, and a query like: +``` +GET https://search.api.hubmapconsortium.org/param-search/donors?metadata.living_donor_data.preferred_term=Coronary artery disease +``` + +## Limitations: +- This document lists resources pulled from configuration files. The content of those files, at the provided links, may be newer. + +## Donor Schema +attributes as listed at [entity-api Donor schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Constraint | Description | +|--------------------------------|---------------------------------------------------------------------------------------|------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| description | string | | Free text description of the donor | +| created_timestamp | integer | read-only | The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970 | +| created_by_user_displayname | string | read-only | The name of the person or process authenticated when creating the object | +| created_by_user_email | string | read-only | The email address of the person or process authenticated when creating the object. | +| uuid | string | read-only | The HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17 | +| hubmap_id | string | read-only | A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.ABCD.### for every entity. | +| last_modified_timestamp | integer | read-only | The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970 | +| entity_type | string | read-only | One of the normalized entity types: Dataset, Collection, Sample, Donor, Upload | +| data_access_level | string from [`data_access_level` attribute values](#dataaccesslevel-attribute-values) | read-only | One of the values: public, consortium | +| protocol_url | string | | The protocols.io doi url pointing the protocol describing the donor selection, inclusion/exclusion criteria | +| lab_donor_id | string | | A lab specific identifier for the donor. | +| submission_id | string | read-only | The hubmap internal id with embedded semantic information e.g.: VAN0003. This id is generated at creation time which tracks the lab, donor, organ and sample hierarchy per the following: https://docs.google.com/document/d/1DjHgmqWF1VA5-3mfzLFNfabbzmc8KLSG9xWx1DDLlzo/edit?usp=sharing | +| group_uuid | string | | The uuid of globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Donor is a member of more than one write group. This property cannot be set via PUT (only on Create/POST). | +| group_name | string | read-only | The displayname of globus group which the user who created this entity is a member of | +| label | string | | Lab provided, de-identified name for the donor | +| metadata.living_donor_data | array of [`Donor Metadata Schema`](#donor-metadata-schema) | | Information about the donor who's tissue was used. The tissue was obtained during a procedure. Only living_donor_data or organ_donor_data, not both can be defined for a single donor. | +| metadata.organ_donor_data | array of [`Donor Metadata Schema`](#donor-metadata-schema) | | @Information about the donor who's organ(s) was/were used. The organ was obtained via an organ donation program from a deceaced donor. Only living_donor_data or organ_donor_data, not both can be defined for a single donor. | +| created_by_user_sub | string | read-only | The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object. | +| last_modified_user_sub | string | read-only | The subject id of the user who last modified the entity as provided by the authorization mechanism for the person or process authenticated when the object was modified. | +| last_modified_user_email | string | read-only | The email address of the person or process which authenticated when the object was last modified. | +| last_modified_user_displayname | string | read-only | The name of the person or process which authenticated when the object was last modified. | +| creators | array of [`Person Schema`](./schema-person.html) | | A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogous to the author list on a publication. | +| contacts | array of [`Person Schema`](./schema-person.html) | | A list of the people who are the main contacts to get information about the entity. | +| registered_doi | string | | The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets. | +| doi_url | string | read-only | The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487 | +| image_files | array of [`File Schema`](./schema-file.html) | read-only | List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array. | +| image_files_to_add | string containing JSON array | write-only | List of ***temporary file ids*** with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like ```{"files": [{"temp_file_id":"dzevgd6xjs4d5grmcp4n","description":"This is image file one"},{"temp_file_id":"yrahjadfhadf","description":"This is image file two"}]}``` | +| image_files_to_remove | string containing JSON array | write-only | List of image files ***previously uploaded*** to delete. Provide as a json array of the file_uuids of the file like: ```["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]``` | + +### Donor Metadata Schema +attributes as listed at [entity-api Donor schema drop-down, metadata drop-down, DonorMetadata drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Description | +|---------------------------------|--------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| code | string | This is a Code from a source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS source vocabulary terms. | +| sab | string | This is the source vocabulary in the HuBMAP Knowledge Graph. Currently limited to UMLS source vocabularies. | +| concept_id | string | This is the Concept ID from the HuBMAP Knowledge Graph. Currently limited to UMLS concepts. | +| data_type | string from [`data_type` attribute values](#datatype-attribute-values) | This is the data type of the record. Numeric types will generally have non-null data_value. Nominal types will generally have null data_value. | +| data_value | string | The data value of the record. | +| numeric_operator | string from [`numeric_operator` attribute values](#numericoperator-attribute-values) | This is the numeric operator for the data value .This enables inputing thresholds and ranges for data values by using greater than or less than. | +| units | string | This are the units for the data value. | +| preferred_term | string | This is the preferred display term for the item. It may or may not correspond to a term in UMLS for this concept. | +| grouping_concept | string | This is the Concept ID from the HuBMAP Knowledge Graph, currently limited to UMLS concetps, that is to be used for grouping the record. | +| grouping_concept_preferred_term | string | This is the preferred display term for the facet in which this record should be counted for faceted search in the portal. It may or may not correspond to a term in UMLS for the grouping concept. | +| grouping_code | string | This is a Code from a source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS vocabulary codes. This code corresponds to the grouping_concept. | +| grouping_sab | string | This is a grouping for the source vocabulary in the HuBMAP Knowledge Graph, currently limited to UMLS source vocabularies.. This sab corresponds to the grouping_code. | +| graph_version | string | This is the version of the HuBMAP Knowledge Graph that the Concept appears in, currently the version of UMLS that is used. | +| start_datetime | integer | This is the approximate time difference in seconds between the procurement and the start of this event (this is to construct time series records of clinical data for event-level data not donor-level data). An empty or zero value designates missing data or that this field is not applicable for the concept. | +| end_datetime | integer | This is the approximate time difference in seconds between the procurement and the end of this event (this is to construct time series records of clinical data for event-level data not donor-level data). An epty of zero value designates missing data or that this field is not applicable for the concept | + +### `data_access_level` attribute values +The data_access_level of the `DonorSchema` is one of the values following enumerated values: +- `public` +- `consortium` + +### `data_type` attribute values +The data_type of the `DonorMetadataSchema` is one of the values following enumerated values: +- `Nominal` +- `Numeric` + +### `numeric_operator` attribute values +The numeric_operator of the `DonorMetadataSchema` is one of the values following enumerated values: +- `EQ` +- `GT` +- `LT` diff --git a/docs/search-indices/schema-file.md b/docs/search-indices/schema-file.md new file mode 100644 index 0000000..a951dea --- /dev/null +++ b/docs/search-indices/schema-file.md @@ -0,0 +1,27 @@ +--- +layout: page +--- + +# HuBMAP File schema + +### Last Updated: 2023-04-17 + +## Overview: +This page describes the File schema for HuBMAP data. File data occurs in the Donor and Sample schemas. +``` +GET https://search.api.hubmapconsortium.org/param-search/samples?group_name=Stanford TMC&organ=LI +``` + +And the following search for Datasets matched to a particular Sample, which is contained in the Dataset's `ancestors`: +``` +GET https://search.api.hubmapconsortium.org/param-search/datasets?ancestors.lab_tissue_sample_id=B001-A-406 +``` + +## File Schema +Attributes as listed at [entity-api Donor schema drop-down, image_files drop-down, File schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Description | +|-------------|--------|--------------------------------------------------------------------------------------------| +| filename | string | The name of the file. | +| description | string | A description of the file. The Dataset.thumbnail_file does not have this file description. | +| file_uuid | string | The HuBMAP unique identifier for the file. | diff --git a/docs/search-indices/schema-person.md b/docs/search-indices/schema-person.md new file mode 100644 index 0000000..0dbf2c0 --- /dev/null +++ b/docs/search-indices/schema-person.md @@ -0,0 +1,24 @@ +--- +layout: page +--- + +# HuBMAP Person schema + +### Last Updated: 2023-04-17 + +## Overview: +This page describes the Person schema for HuBMAP data. Person data occurs in the Donor, Sample or Dataset schemas. +``` +GET https://search.api.hubmapconsortium.org/param-search/donors?group_name=Stanford TMC&descendants.organ=LI +``` + +## Person Schema +attributes as listed at [entity-api Donor schema drop-down, creators drop-down, Person schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Description | +|--------------------------|----------|-------------------------------------------------------| +| first_name | string | The full name of the person. | +| last_name | string | The last name of the person. | +| middle_name_or_initial | string | The middle name or initial of the person. | +| orcid_id | string | The ORCID iD of the person. | +| affiliation | string | The institution that the person is affiliated with. | diff --git a/docs/search-indices/schema-sample.md b/docs/search-indices/schema-sample.md new file mode 100644 index 0000000..6dcbd69 --- /dev/null +++ b/docs/search-indices/schema-sample.md @@ -0,0 +1,215 @@ +--- +layout: page +--- + +# HuBMAP Sample schema + +### Last Updated: 2023-04-17 + +## Overview: +This page describes the Sample schema for HuBMAP data. Sample data may be returned itself or a part of another entity. For example, this endpoint searches Samples for a specified group and organ: +``` +GET https://search.api.hubmapconsortium.org/param-search/samples?group_name=Stanford TMC&organ=LI +``` + +And the following search for Datasets matched to a particular Sample, which is contained in the Dataset's `ancestors`: +``` +GET https://search.api.hubmapconsortium.org/param-search/datasets?ancestors.lab_tissue_sample_id=B001-A-406 +``` + +## Description: +A query string is built by combining schema elements documented below with matching values. Each "term" of the query is combined using the & character, and the entire query is attached to the base URL after a ? character, per web standards. + +Query terms may be composited from attributes deeper in the schema type of an attribute. For example, the Sample Schema attribute ```metadata``` is has a type of Sample Metadata Schema, and Sample Metadata Schema has an attribute ```organ_condition```. Querying Samples supports a term to search for samples from healthy organs, such as ```metadata.organ_condition=healthy```, and a query like: +``` +GET https://search.api.hubmapconsortium.org/param-search/samples?metadata.organ_condition=healthy&organ=LI +``` + +## Limitations: +- This document lists resources pulled from configuration files. The content of those files, at the provided links, may be newer. + +## Sample Schema +attributes as listed at [entity-api Sample schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Constraint | Description | +|-----------------------------|-------------------------------------------------------------------------------------------------------|------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| description | string | | Free text description of the sample | +| created_timestamp | integer | read-only | The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970 | +| created_by_user_displayname | string | read-only | The name of the person or process authenticated when creating the object | +| created_by_user_email | string | read-only | The email address of the person or process authenticated when creating the object. | +| created_by_user_sub | string | read-only | The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object. | +| uuid | string | read-only | The HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17 | +| hubmap_id | string | read-only | A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.ABCD.### for every entity. | +| last_modified_timestamp | integer | read-only | The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970 | +| creators | array of [`Person Schema`](./schema-person.html) | | A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogous to the author list on a publication. | +| contacts | array of [`Person Schema`](./schema-person.html) | | A list of the people who are the main contacts to get information about the entity. | +| entity_type | string | read-only | One of the normalized entity types: Dataset, Collection, Sample, Donor | +| registered_doi | string | | The doi of a the registered entity. e.g. 10.35079/hbm289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets. | +| doi_url | string | read-only | The url from the doi registry for this entity. e.g. https://doi.org/10.35079/hbm289.pcbm.487 | +| protocol_url | string | | The protocols.io doi url pointing the protocol under wich the sample was obtained and/or prepared. | +| group_uuid | string | | The uuid of globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Donor is a member of more than one write group. This property cannot be set via PUT (only on Create/POST). | +| group_name | string | read-only | The displayname of globus group which the user who created this entity is a member of | +| submission_id | string | | The hubmap internal id with embedded semantic information e.g.: VAN0003-LK-1-10. This id is generated at creation time which tracks the lab, donor, organ and sample hierarchy per the following: https://docs.google.com/document/d/1DjHgmqWF1VA5-3mfzLFNfabbzmc8KLSG9xWx1DDLlzo/edit?usp=sharing | +| visit | string | | The visit id for the donor/patient when the sample was obtained. | +| data_access_level | string from [`data_access_level` attribute values](#data_access_level-attribute-values) | read-only | One of the values: public, consortium | +| sample_category | string from [`sample_category` attribute values](#sample_category-attribute-values) | | A code representing the category of the specimen. Must be one of organ, block, section , suspension. This is a required field. If set to organ, the organ property must be provided as well. | +| specimen_type | string from [`specimen_type` deprecated attribute values](#specimen_type-deprecated-attribute-values) | | DEPRECATED: No longer a required field. A code representing the type of specimen. Must be one of the codes specified in: [tissue sample types](https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml) | +| organ | string from [`organ` attribute values](#organ-attribute-values) | | Organ code specifier, only set if sample_category == organ. Valid values found in: [organ types](https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/organ_types.yaml) | +| metadata | array of [`Sample Metadata Schema`](#sample-metadata-schema) | | The sample specific metadata derived from the uploaded sample_metadata.tsv file. Returned as a json object. | +| rui_location | string containing JSON dictionary | | The sample location and orientation in the ancestor organ as specified in the RUI tool. Returned as a json object. | + +### Sample Metadata Schema +attributes as listed at [entity-api Sample schema drop-down, metadata drop-down, DonorMetadata drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): +The sample specific metadata derived from the uploaded sample_metadata.tsv file. Returned as a json object. + +| Attribute | Type | Description | +|-----------------------------------|------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| sample_id | string | The HuBMAP Identifier for the sample. | +| procedure_date | string | The date at which the organ from which the tissue sample came from was procurred, in the format YYYY-MM-DD | +| pathologist_report | string | Further details on organ level QC checks. | +| warm_ischemia_time_value | integer | Time interval between cessation of blood flow and cooling to 4C. Blank if not applicable. | +| warm_ischemia_time_unit | string | Time units that the warm_ischemia_time_value is reported in. Blank if not applicable | +| cold_ischemia_time_value | integer | Time interval on ice to the start of preservation protocol. Blank if not applicable. | +| cold_ischemia_time_unit | string | Time units that the cold_ischemia_time_value is reported in. Blank if not applicable. | +| specimen_preservation_temperature | string | The temperature of the medium during the preservation process. Reported as preservation method, temperature and units, e.g. Freezer (-80 Celsius) | +| specimen_quality_criteria | string | RIN score. e.g. RIN: 8.7 | +| specimen_tumor_distance_value | string | If surgical sample from a tumor biopsy, how far from the tumor was the sample obtained from. Typically a number of centimeters. Blank if not applicable or unknown. | +| specimen_tumor_distance_unit | string | | +| vital_state | string from [`vital_state` attribute values](#vitalstate-attribute-values) | The vital state of the donor who the tissue sample came from. | +| health_status | string from [`health_status` attribute values](#healthstatus-attribute-values) | Donor from which the tissue sample came from's baseline physical condition prior to immediate event leading to organ/tissue acquisition. For example, if a relatively healthy patient suffers trauma, and as a result of reparative surgery, a tissue sample is collected, the subject will be deemed 'relatively healthy'. Likewise, a relatively healthy subject may have experienced trauma leading to brain death. As a result of organ donation, a sample is collected. In this scenario, the subject is deemed 'relatively healthy'. | +| organ_condition | string from [`organ_condition` attribute values](#organcondition-attribute-values) | Health status of the organ at the time of tissue sample recovery. | +| perfusion_solution | string from [`perfusion_solution` attribute values](#perfusionsolution-attribute-values) | Health status of the organ at the time of sample recovery. | + +### `data_access_level` attribute values +The data_access_level of the `Sample Schema` is one of the values following enumerated values: +- `public` +- `consortium` + +### `sample_category` attribute values +The sample_category of the `Sample Schema` is one of the values following enumerated values: +- `organ` +- `block` +- `section` + +### `specimen_type` deprecated attribute values +The specimen_type of the `Sample Schema` is deprecated and not required. Its value must be from [tissue sample types](https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml). Examples inlcude: +atacseq +- `biopsy` +- `blood` +- `cell_lysate` +- `clarity_hydrogel` +- `codex` +- `cryosections_curls_from_fresh_frozen_oct` +- `cryosections_curls_rnalater` +- `ffpe_block` +- `ffpe_slide` +- `fixed_frozen_section_slide` +- `fixed_tissue_piece` +- `flash_frozen_liquid_nitrogen` +- `formalin_fixed_oct_block` +- `fresh_frozen_oct_block` +- `fresh_frozen_section_slide` +- `fresh_frozen_tissue` +- `fresh_frozen_tissue_section` +- `fresh_tissue` +- `frozen_cell_pellet_buffy_coat` +- `gdna` +- `module` +- `nuclei` +- `nuclei_rnalater` +- `organ` +- `organ_piece` +- `other` +- `pbmc` +- `pfa_fixed_frozen_oct_block` +- `plasma` +- `protein` +- `ran_poly_a_enriched` +- `rna_total` +- `rnalater_treated_and_stored` +- `rnaseq` +- `scatacseq` +- `scrnaseq` +- `segment` +- `seqfish` +- `sequence_library` +- `serum` +- `single_cell_cryopreserved` +- `snatacseq` +- `snrnaseq` +- `tissue_lysate` +- `wgs` + +### `organ` attribute values +The organ of the `Sample Schema` is a value from the current, authoritative list of [organ types](https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/organ_types.yaml). Examples include: +- `AO`: Aorta +- `BL`: Bladder +- `BD`: Blood +- `BM`: Bone Marrow +- `BR`: Brain +- `LF`: Fallopian Tube (Left) +- `RF`: Fallopian Tube (Right) +- `HT`: Heart +- `LB`: Bronchus (Left) +- `LE`: Eye (Left) +- `LI`: Large Intestine +- `LK`: Kidney (Left) +- `LL`: Lung (Left) +- `LN`: Knee (Left) +- `LV`: Liver +- `LY`: Lymph Node +- `LO`: Ovary (Left) +- `RO`: Ovary (Right) +- `OT`: Other +- `PA`: Pancreas +- `PL`: Placenta +- `RB`: Bronchus (Right) +- `RE`: Eye (Right) +- `RK`: Kidney (Right) +- `RL`: Lung (Right) +- `RN`: Knee (Right) +- `SI`: Small Intestine +- `SK`: Skin +- `SP`: Spleen +- `ST`: Sternum +- `TH`: Thymus +- `TR`: Trachea +- `UR`: Ureter +- `UT`: Uterus + +### `vital_state` attribute values +The vital_state of the `Sample Metadata Schema` is one of the values following enumerated values: +- `living` +- `deceased` + +### `health_status` attribute values +The health_status of the `Sample Metadata Schema` is one of the values following enumerated values: +- `cancer` +- `relatively` +- `healthy` +- `chronic illness` + +### `organ_condition` attribute values +The organ_condition of the `Sample Metadata Schema` is one of the values following enumerated values: +- `healthy` +- `diseased` + +### `perfusion_solution` attribute values +The perfusion_solution of the `Sample Metadata Schema` is one of the values following enumerated values: +- `UWS` +- `HTK` +- `Belzer` +- `MPS/KPS` +- `Formalin` +- `Unknown` +- `None` + +## File Schema +Attributes as listed at [entity-api Donor schema drop-down, image_files drop-down, File schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Description | +|-------------|--------|--------------------------------------------------------------------------------------------| +| filename | string | The name of the file. | +| description | string | A description of the file. The Dataset.thumbnail_file does not have this file description. | +| file_uuid | string | The HuBMAP unique identifier for the file. | + diff --git a/docs/search-indices/schema-upload.md b/docs/search-indices/schema-upload.md new file mode 100644 index 0000000..297d239 --- /dev/null +++ b/docs/search-indices/schema-upload.md @@ -0,0 +1,44 @@ +--- +layout: page +--- + +# HuBMAP Upload schema + +### Last Updated: 2023-04-17 + +## Overview: +This page describes the Upload schema for HuBMAP data. Upload data occurs in the Dataset schema. +``` +GET https://search.api.hubmapconsortium.org/param-search/samples?group_name=Stanford TMC&organ=LI +``` + +And the following search for Datasets matched to a particular Sample, which is contained in the Dataset's `ancestors`: +``` +GET https://search.api.hubmapconsortium.org/param-search/datasets?ancestors.lab_tissue_sample_id=B001-A-406 +``` + +## Upload Schema +attributes as listed at [entity-api Dataset schema drop-down, upload drop-down, Upload schema drop-down](https://smart-api.info/ui/0065e419668f3336a40d1f5ab89c6ba3): + +| Attribute | Type | Constraint | Description | +|--------------------------------|----------------------------------------------------|------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| created_timestamp | integer | read-only | The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970 | +| created_by_user_displayname | string | read-only | The name of the person or process authenticated when creating the object | +| created_by_user_email | string | read-only | The email address of the person or process authenticated when creating the object. | +| created_by_user_sub | string | read-only | The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object. | +| uuid | string | read-only | The HuBMAP unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17 | +| hubmap_id | string | read-only | A HuBMAP Consortium wide unique identifier randomly generated in the format HBM###.ABCD.### for every entity. | +| last_modified_timestamp | integer | read-only | The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970 | +| last_modified_user_sub | string | read-only | The subject id of the user who last modified the entity as provided by the authorization mechanism for the person or process authenticated when the object was modified. | +| last_modified_user_email | string | read-only | The email address of the person or process which authenticated when the object was last modified. | +| last_modified_user_displayname | string | read-only | The name of the person or process which authenticated when the object was last modified. | +| entity_type | string | read-only | One of the normalized entity types: Dataset, Collection, Sample, Donor, Upload | +| description | string | | Free text description of the data being submitted. | +| title | string | | Title of the datasets, a sentence or less | +| status | string | | One of: New, Valid, Invalid, Error, Submitted | +| validation_message | string | | A message from the validation tools describing what is invalid with the upload. | +| group_uuid | string | | The uuid of Globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Donor is a member of more than one write group. This property cannot be set via PUT (only on Create/POST). | +| group_name | string | read-only | The displayname of Globus group which the user who created this entity is a member of | +| dataset_uuids_to_link | string | write-only | List of datasets to add to the Upload. Provide as a json array of the dataset uuids like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"] | +| dataset_uuids_to_unlink | string | write-only | List of datasets to remove from a Upload. Provide as a json array of the dataset uuids like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"] | +| datasets | array of [`Dataset Schema`](./schema-dataset.html) | read-only | The datasets that are contained in this Upload. |