Fields common to all schemas in this document
| Property name | Description | Type | Required? | Example |
|---|---|---|---|---|
| describedBy | The URL reference to the schema. | string | no | |
| schema_version | The version number of the schema in major.minor.patch format. | string | no | 4.6.1 |
Information about a single microscope channel.
Location: module/protocol/channel.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| channel_id | User given ID. If there is an accompanying codebook, this name should correspond to the channel id used in the codebook. | string | yes | Channel ID | 1; A | ||
| excitation_wavelength | Excitation wavelength of the lightsource in nanometers. | number | yes | Excitation wavelength | 640 | ||
| filter_range | Emission filter in nanometers. | string | yes | Filter range | 461/70 | ||
| multiplexed | Whether multiple targets were detected simultaneously in this channel. | string | yes | Multiplexed experiment | yes, no | Should be one of: yes, or no. | |
| target_fluorophore | The name of the fluorophore this channel is designed to assay. | string | no | Target fluorophore | Alexa 647 | ||
| exposure_time | Acquisition time for a single image per channel, in milliseconds. | number | yes | Exposure time | 400 |
Information about probes used to detect targets.
Location: module/protocol/probe.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| probe_label | The label of a probe used to detect target in this experiment. | string | yes | Probe label | ACTA1; cFos | ||
| probe_sequence | Sequence of a probe used to detect target. | string | no | Probe sequence | AGGCTATAGCGGAGCTACG; aggctatagcggagctacg | ||
| target_name | The name of the target molecule. | string | no | Target name | ACTA1_exon1; nuclear cFos | ||
| target_codebook_label | A label used in the codebook for the target. | string | no | Target label in codebook | AKT1; CFOS | ||
| target_label | An identifier for the target molecule. | string | yes | Target label | CHEBI:85345; ENSG00000170345 | ||
| subcellular_structure | Target subcellular structure. | object | no | See module cellular_component_ontology | Target subcellular structure | ||
| probe_reagents | Name of reagents used to construct the probe. | object | no | See module purchased_reagents | Probe construction reagents | ||
| assay_type | Type of assay used to detect target. | object | yes | See module process_type_ontology | Assay type | MERFISH; in situ sequencing | |
| fluorophore | Fluorophore used to detect target. | array | no | Fluorophore | Cy5; Alexa 488 | ||
| channel_label | Channel label used to assay signal. | array | no | Channel | 1; A |
Information relating to generation of matrices
Location: module/protocol/matrix.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| data_normalization_methods | Method(s) used to normalize data in the matrix | array | no | Data normalization method(s) | CPM (counts per million), TPM (transcripts per kilobase million), RPKM (reads per kilobase of exon per million reads mapped), FPKM (fragments per kilobase of exon per million fragments mapped), DESeq2's median of ratios, TMM (EdgeR's trimmed mean of M values), SF (size factor), UQ (Upper quartile), Downsampling, other, unknown | ||
| derivation_process | Type of computational tool used in generating the matrix object. | array | no | Derivation process | alignment, quantification, peak calling, peak annotation, gene filtering, cell filtering, merging, cell calling, ambient RNA correction, doublet removal, batch correction, depth normalization, other |
A term that describes the contents of a file.
Location: module/ontology/file_content_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | General description of the contents of the file. | string | yes | Content description | DNA sequence (raw); Sequence alignment | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Content description ontology ID | EDAM:3494; EDAM:0863 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Content description ontology label | DNA sequence; Sequence alignment |
A term that may be associated with a cell type-related ontology term.
Location: module/ontology/length_unit_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a length unit being used. | string | yes | Length unit | micrometer; meter | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Length unit ontology ID | UO:0000017; UO:0000008 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Length unit ontology label | micrometer; meter |
A term that may be associated with a cell cycle-related ontology term.
Location: module/ontology/cell_cycle_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a cell cycle of the cells in the specimen. | string | yes | Cell cycle | meiotic cell cycle; mitotic G1 phase | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Cell cycle ontology ID | GO:0051321; GO:0000080 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Cell cycle ontology label | meiotic cell cycle; mitotic G1 phase |
A term that may be associated with a process-related ontology term.
Location: module/ontology/library_amplification_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a library amplification approach being used. | string | yes | Library amplification | PCR; in vitro transcription | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Library amplification ontology ID | OBI:0000415; EFO:0009013 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Library amplification ontology label | PCR; in vitro transcription |
A term that describes the role of a contributor in the project.
Location: module/ontology/contributor_role_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The primary role of the contributor in the project. | string | yes | Contributor role | principal investigator; experimental scientist | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Contributor role ontology ID | EFO:0009736; EFO:0009741 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Contributor role ontology label | principal investigator; experimental scientist |
A term that may be associated with a ethnicity-related ontology term.
Location: module/ontology/ethnicity_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The ethnicity of the human donor. | string | yes | Ethnicity | European; Hispanic or Latin American | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Ethnicity ontology ID | HANCESTRO:0005; HANCESTRO:0014 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Ethnicity ontology label | European; Hispanic or Latin American |
A term that may be associated with a process-related ontology term.
Location: module/ontology/target_pathway_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of the treatment target pathway. | string | yes | Target pathway | positive regulation of memory T cell differentiation | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Target pathway ontology ID | GO:0043382 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Target pathway ontology label | positive regulation of memory T cell differentiation |
A term that may be associated with a process-related ontology term.
Location: module/ontology/treatment_method_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a treatment method or approach being used. | string | yes | Treatment method | T cell activation assay | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Treatment ontology ID | EFO:0030037 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Treatment ontology label | T cell activation assay |
A term that may be associated with an intra-cellular structure ontology term.
Location: module/ontology/cellular_component_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a subcellular structure. | string | yes | Subcellular structure | cytoplasm; nucleus | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Subcellular structure ontology ID | GO:0005737; GO:0005634 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Subcellular structure ontology label | cytoplasm; nucleus |
A term that may be associated with a process-related ontology term.
Location: module/ontology/library_construction_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a library construction approach being used. | string | yes | Library construction | 10X v2 sequencing; Smart-seq2 | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Library construction ontology ID | EFO:0009310; EFO:0008931 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Library construction ontology label | 10X v2 sequencing; Smart-seq2 |
A term that may be associated with a process-related ontology term.
Location: module/ontology/process_type_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a process type being used. | string | yes | Process type | enzymatic dissociation; blood draw | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Process type ontology ID | EFO:0009128; EFO:0009121 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Process type ontology label | enzymatic dissociation; blood draw |
A term that may be associated with a gender-related ontology term.
Location: module/ontology/gender_identity_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The gender identity of the human donor at the time of the experiment. | string | yes | Gender identity | Female Gender; Agender; Non-Binary Gender | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Gender identity ontology ID | NCIT:C46110; NCIT:C205469; NCIT:C160941 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Gender identity ontology label | Female Gender; Agender; Non-Binary Gender |
A term that may be associated with a process-related ontology term.
Location: module/ontology/sequencing_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a sequencing approach being used. | string | yes | Sequencing approach | tag based single cell RNA sequencing; full length single cell RNA sequencing | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Sequencing approach ontology ID | EFO:0008440; EFO:0008441 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Sequencing approach ontology label | tag based single cell RNA sequencing; full length single cell RNA sequencing |
A term that may be associated with a species-related ontology term.
Location: module/ontology/species_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of the species to which the organism belongs. | string | yes | Species | Homo sapiens; Mus musculus | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Species ontology ID | NCBITaxon:9606; NCBITaxon:10090 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Species ontology label | Homo sapiens; Mus musculus |
A term that may be associated with a disease-related ontology term.
Location: module/ontology/disease_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The text for the term as the user provides it. | string | yes | Disease | type 2 diabetes mellitus; normal | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Disease ontology ID | MONDO:0005148; PATO:0000461; HP:0001397 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Disease ontology label | type 2 diabetes mellitus; normal |
A term that may be associated with a strain-related ontology term.
Location: module/ontology/strain_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of the strain to which the organism belongs. | string | yes | Strain | C57BL/6; BALB/c | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Strain ontology ID | EFO:0004472; EFO:0000602 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Strain ontology label | C57BL/6; BALB/c |
A term that may be associated with a medication-related ontology term.
Location: module/ontology/medication_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | Medication(s) the individual was taking at time of biomaterial collection. | string | yes | Medication | Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Medication ontology ID | NCIT:C72809; NCIT:C61653; NCIT:C78113 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Medication ontology label | Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride |
A term that may be associated with a file format-related ontology term.
Location: module/ontology/file_format_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of the file format. | string | yes | File format | FASTQ; JSON | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | File format ontology ID | EDAM:1930; EDAM:3464 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | File format ontology label | FASTQ; JSON |
A term that may be associated with a process-related ontology term.
Location: module/ontology/enrichment_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of an enrichment approach being used. | string | yes | Enrichment | fluorescence-activated cell sorting; Ficoll-Hypaque method | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Enrichment ontology ID | EFO:0009108; EFO:0009110 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Enrichment ontology label | fluorescence-activated cell sorting; Ficoll-Hypaque method |
A term that may be associated with an anatomy-related ontology term.
Location: module/ontology/organ_part_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The text for the term as the user provides it. | string | yes | Organ part | bone marrow; islet of Langerhans | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Organ part ontology ID | UBERON:0002371; UBERON:0000006 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Organ part ontology label | bone marrow; islet of Langerhans |
A term that may be associated with a microscopy-related ontology term.
Location: module/ontology/microscopy_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of the type of microscopy used in an imaging experiment. | string | yes | Microscopy | confocal microscopy; fluorescence microscopy | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Microscopy ontology ID | FBbi:00000251; FBbi:00000246 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Microscopy ontology label | confocal microscopy; fluorescence microscopy |
A term that may be associated with a time unit-related ontology term.
Location: module/ontology/time_unit_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a time unit being used. | string | yes | Time unit | second; week | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Time unit ontology ID | UO:0000010; UO:0000034 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Time unit ontology label | second; week |
A term that may be associated with a protocol-related ontology term.
Location: module/ontology/protocol_type_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a protocol type used. | string | yes | Protocol type | dissociation protocol; enrichment protocol | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Protocol type ontology ID | EFO:0009088; EFO:0009089 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Protocol type ontology label | dissociation protocol; enrichment protocol |
A term that may be associated with a development stage-related ontology term.
Location: module/ontology/development_stage_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of the development stage of the organism. | string | yes | Development stage | human adult stage; Theiler stage 28 | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Development stage ontology ID | HsapDv:0000087; EFO:0002588 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Development stage ontology label | human adult stage; Theiler stage 28 |
A term that may be associated with a instrument-related ontology term.
Location: module/ontology/instrument_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The full name of the instrument used. | string | yes | Instrument | Illumina HiSeq 2500; ONT MinION | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Instrument ontology ID | EFO:0008565; EFO:0008632 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Instrument ontology label | Illumina HiSeq 2500; ONT MinION |
A term that may be associated with a cell type-related ontology term.
Location: module/ontology/mass_unit_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a mass unit being used. | string | yes | Mass unit | kilogram; microgram | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Mass unit ontology ID | UO:0000009; UO:0000023 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Mass unit ontology label | kilogram; microgram |
A term that may be associated with a biological macromolecule-related ontology term.
Location: module/ontology/biological_macromolecule_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of the biological macromolecule being used. | string | yes | Biological macromolecule | polyA RNA; mRNA | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Biological macromolecule ontology ID | OBI:0000869; CHEBI:33699 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Biological macromolecule ontology label | polyA RNA; messenger RNA |
A term that may be associated with a cell type-related ontology term.
Location: module/ontology/cell_type_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The name of a cell type supplied by a user. | string | yes | Cell type | bone marrow hematopoietic cell; cardiac muscle cell | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Cell type ontology ID | CL:1001610; CL:0000746 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Cell type ontology label | bone marrow hematopoietic cell; cardiac muscle cell |
A term that may be associated with an anatomy-related ontology term.
Location: module/ontology/organ_ontology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| text | The text for the term as the user provides it. | string | yes | Organ | heart; immune system | ||
| ontology | An ontology term identifier in the form prefix:accession. | string | no | Organ ontology ID | UBERON:0000948; UBERON:0002405 | ||
| ontology_label | The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. | string | no | Organ ontology label | heart; immune system |
Information about the project funding source.
Location: module/project/funder.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| grant_title | The name of the grant funding the project. | string | no | Grant title | Study of single cells in the human body. | ||
| grant_id | The unique grant identifier or reference. | string | yes | Grant ID | BB/P0000001/1 | ||
| organization | The name of the funding organization. | string | yes | Funding organization | Biotechnology and Biological Sciences Research Council (BBSRC); California Institute of Regenerative Medicine (CIRM) |
Information about whether the project is part of a HCA Bionetwork or HCA Atlas.
Location: module/project/hca_bionetwork.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| name | HCA Bionetwork the project is a part of (e.g. Kidney). | string | no | Official HCA Bionetwork | Adipose, Breast, Development, Eye, Genetic Diversity, Gut, Heart, Immune, Kidney, Liver, Lung, Musculoskeletal, Nervous System, Oral and Craniofacial, Organoid, Pancreas, Reproduction, Skin | Kidney; Lung | |
| hca_tissue_atlas | A field describing if the project is part of a HCA Tissue Atlas (e.g. Brain Alzheimer Atlas). | string | no | HCA Tissue Atlas | Adipose, Blood, Brain, Breast, Development, Eye, GDN, Gut, Heart, Immune, Kidney, Liver, Lung, MSK, ORCF, Organoid-Endoderm, Organoid-Neural, Pancreas, Retina, Reproduction, Skin | Retina | |
| hca_tissue_atlas_version | A field describing which version of the HCA Tissue Atlas is associated with the project (e.g. v1.0; v2.0) | string | no | Official HCA Tissue Atlas Version | v1.0; v2.0 | ||
| atlas_project | A field describing if this project is the HCA Tissue Atlas project which integrates data from other datasets. | boolean | no | Project Tissue Atlas Status | Yes; No |
Information about an individual who submitted or contributed to a project.
Location: module/project/contact.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| name | Name of individual who has contributed to the project. | string | yes | Contact name | John,D,Doe; Jane,,Smith | ||
| Email address for the individual. | string | no | Email address | dummy@email.com | |||
| phone | Phone number of the individual or their lab. | string | no | Phone number | (+1) 234-555-6789 | ||
| institution | Name of primary institute where the individual works. | string | yes | Institute | EMBL-EBI; University of Washington | ||
| laboratory | Name of lab or department within the institute where the individual works. | string | no | Laboratory/Department | Division of Vaccine Discovery; Department of Biology | ||
| address | Street address where the individual works. | string | no | Street address | 0000 Main Street, Nowheretown, MA, 12091 | ||
| country | Country where the individual works. | string | no | Country | USA | ||
| corresponding_contributor | Whether the individual is a primary point of contact for the project. | boolean | no | Corresponding contributor | Should be one of: yes, or no. | ||
| project_role | Primary role of the individual in the project. | object | no | See module contributor_role_ontology | Project role | principal investigator; computational scientist | |
| orcid_id | The individual's ORCID ID linked to previous work. | string | no | ORCID ID | 0000-1111-2222-3333 |
Information about a journal article, book, web page, or other external available documentation for a project.
Location: module/project/publication.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| authors | A list of authors associated with the publication. | array | yes | Authors | Doe JD | ||
| title | The title of the publication. | string | yes | Publication title | Study of single cells in the human body. | ||
| doi | The publication digital object identifier (doi) of the publication. | string | no | Publication DOI | 10.1016/j.cell.2016.07.054 | ||
| pmid | The PubMed ID of the publication. | integer | no | Publication PMID | 27565351 | ||
| url | A URL for the publication. | string | no | Publication URL | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5667944/ | ||
| official_hca_publication | Has the publication been accepted as an official HCA publication, according to the process described in https://www.humancellatlas.org/publications/ ? | boolean | yes | Official HCA Publication | yes; no |
Information specific to a donor that is a human (Homo sapiens).
Location: module/biomaterial/human_specific.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| body_mass_index | The body mass index of the donor. | string | no | Body mass index | 36.4; 29-32 | ||
| waist_circumference | Waist circumference of the donor at the time of collection measured in cm. | string | no | Waist circumference | 60; 95; 153 | ||
| waist_hip_ratio | Waist-hip ratio of the donor at the time of collection. | string | no | Waist-hip ratio | 0.85; 0.91; 0.88 | ||
| ethnicity | Ethnicity of the donor. | array | no | See module ethnicity_ontology | Ethnicity | ||
| ethnicity_question | Question and response options posed to donors for collecting metadata on donor self-reported ethnicity and / or tribe and / or dialect group and / or race etc. | string | no | Ethnicity question | What is your ethnicity?; Are you Hispanic/Latino?; Which categories describe you? Select all that apply. Note You may select more than one group. 1. American Indian or Alaska Native (for example, Aztec, Blackfeet Tribe, Mayan, Navajo Nation, Native Village of Barrow (Utqiagvik) Inupiat Traditional Government, Nome Eskimo Community, etc.), 2 - Asian (for example, Asian Indian, Chinese, Filipino, Japanese, Korean, Vietnamese, etc.), 3 - Black, African American, or African (for example, African American, Ethiopian, Haitian, Jamaican, Nigerian, Somali, etc.), 4 - Hispanic, Latino, or Spanish (for example, Columbian, Cuban, Dominican, Mexican or Mexican American, Puerto Rican, Salvadoran, etc.), 5 - Middle Eastern or North African (for example, Algerian, Egyptian, Iranian, Lebanese, Moroccan, Syrian, etc.), 6 - Native Hawaiian or other Pacific Islander (for example, Chamorro, Fijian, Marshallese, Native Hawaiian, Tongan, etc.), 7 - White (for example, English, European, French, German, Irish, Italian, Polish, etc.), 8 - None of these fully describe me (optional free text answer), 9 - Prefer not to answer | ||
| ethnicity_of_parents | Ethnicity(-ies) of the donor's parents. | array | no | See module ethnicity_ontology | Parents ethnicity | ||
| primary_language | Primary language(s), spoken by donor. Can include dialects (for example, Hokkien). | array | no | Donor primary language | Mandarin Chinese; Hokkien; Bahasa Melayu | ||
| language_of_family | Ancestral language(s), spoken by parents (“mother tongue” and / or “father tongue”) and / or grandparents or any other person in the donor family. Can include dialects (for example, Hokkien). | array | no | Language of family | Mandarin Chinese; Hokkien; Bahasa Melayu | ||
| current_residence | Donor's current residence at time of sample collection. | object | no | See module residence | Current residence | ||
| place_of_birth | Donor's place of birth residence. | object | no | See module residence | Place of birth | ||
| lifestyle | Lifestyle and habits of the donor. | object | no | See module lifestyle | Lifestyle |
Information relating to how a biomaterial was grown and/or maintained in a laboratory setting.
Location: module/biomaterial/growth_conditions.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| passage_number | The number of passages that the biomaterial has been through. | integer | no | Passage number | 22 | ||
| growth_medium | The solid, liquid, or semi-solid medium used to support growth. | string | no | Growth medium | human placental cord serum; RPMI 1640 + 2mM Glutamine + 10-20% FBS | ||
| culture_environment | Cell culture environment in which cells are grown. | string | no | Culture environment | Adherent cell culture; Suspension cell culture | ||
| mycoplasma_testing_method | The method by which the biomaterial was tested for mycoplasma contamination. | string | no | Mycoplasma testing method | Direct DNA stain, Indirect DNA stain, Broth and agar culture, PCR, Nested PCR, ELISA, Autoradiography, Immunostaining, Cell-based assay, Microbiological assay | Should be one of: Direct DNA stain, Indirect DNA stain, Broth and agar culture, PCR, Nested PCR, ELISA, Autoradiography, Immunostaining, Cell-based assay, or Microbiological assay. | |
| mycoplasma_testing_results | Whether the biomaterial passed or failed the mycoplasma test. | string | no | Mycoplasma testing results | pass, fail | Should be one of: pass, or fail. | |
| drug_treatment | Description of drugs added to the growth medium. | string | no | Drug treatment | 100 ug/mL ampicillin; 15 ug/mL tetracycline | ||
| feeder_layer_type | Type of feeder layer cells on which biomaterial was grown. | string | no | Feeder layer type | feeder-free, feeder-dependent, JK1 feeder cells, feeder-dependent, SNL 76/7 feeder cells, feeder-dependent, human marrow stromal cells, feeder-dependent, bovine embryonic fibroblast cells, feeder-dependent, mouse embryonic fibroblast cells, feeder-dependent, mouse fibroblast STO cells, feeder-dependent, mouse bone marrow stromal cells, feeder-dependent, mouse yolk sac-derived endothelial cells, feeder-dependent, human foreskin fibroblast cells, feeder-dependent, human newborn fibroblast cells, feeder-dependent, human fetal lung fibroblast cells, feeder-dependent, human uterine endometrial cells, feeder-dependent, human breast parenchymal cells, feeder-dependent, human embryonic fibroblast cells, feeder-dependent, human adipose stromal cells, feeder-dependent, human amniotic epithelial cells, feeder-dependent, human placental fibroblast cells, feeder-dependent, human umbilical cord stromal cells, feeder-dependent, human fetal muscle cells, feeder-dependent, human fetal skin cells, feeder-dependent, human fetal liver stromal cells, feeder-dependent, human fallopian tubal epithelial cells, feeder-dependent, human amniotic mesenchymal cells | feeder-free; feeder-dependent, mouse embryonic fibroblast cells |
Information about the medical tests performed on the individual.
Location: module/biomaterial/medical_tests.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| pft_method | Indicate which Pulmonary Function Testings (PFTs) methods were performed. Please indicate all tests performed. | array | no | Pulmonary Function Testing method | spirometry, plethysmography, DLCO_KCO_test | spirometry; plethysmography; DLCO_KCO_test | |
| pft_age | Indicate the age of the subject at the time point of Pulmonary Function Testing (PFT) in years, if known. | number | no | Age at Pulmonary Function Test | 10; 34; 68 | ||
| pft_time_point | Indicate at which date the Pulmonary Function Testing (PFT) were recorded as YYYY-MM-DD if available. If this information is not shareable, please indicate 'not_shareable'. | string | no | Date at Pulmonary Function Test | 2024-11-14; 2019-01-31; not_shareable | ||
| pft_relative_time_point | If timepoint of sample collection (time of collection) and/or timepoint of PFT recording (pft_time_point) is not available, indicate how many days prior or after sample collection the pulmonary function parameters were assessed if available. | integer | no | Days between collection and Pulmonary Function Test | -5; 2; 0 | ||
| fev1_predicted | Indicate the predicted Forced Expiratory Volume in 1 second (FEV1) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | FEV1 predicted | 3500; 4200; 2800 | ||
| fev1_prebd | Indicate the measured FEV1 in milliliters before the administration of a bronchodilator if available. | number | no | FEV1 before bronchodilator | 3000; 3800; 2600 | ||
| fev1_postbd | Indicate the measured FEV1 in milliliters after the administration of a bronchodilator if available. | number | no | FEV1 after bronchodilator | 3200; 4000; 2700 | ||
| fev1_prebd_predicted_percent | Indicate the percentage of the predicted FEV1 achieved before bronchodilator administration if available. | number | no | FEV1 before bronchodilator percent of predicted | 86; 90; 78 | ||
| fev1_postbd_predicted_percent | Indicate the percentage of the predicted FEV1 achieved after bronchodilator administration if available. | number | no | FEV1 after bronchodilator percent of predicted | 91; 95; 82 | ||
| fvc_predicted | Indicate the predicted Forced Vital Capacity (FVC) in milliliters, based on patient age, sex, height, and ethnicity, if available. | number | no | FVC predicted | 4500; 5000; 3800 | ||
| fvc_prebd | Indicate the measured FVC in milliliters before bronchodilator administration if available. | number | no | FVC before bronchodilator | 4000; 4800; 3600 | ||
| fvc_postbd | Indicate the measured FVC in milliliters after bronchodilator administration if available. | number | no | FVC after bronchodilator | 4200; 5000; 3700 | ||
| fvc_prebd_predicted_percent | Indicate the percentage of the predicted FVC achieved before bronchodilator administration if available. | number | no | FVC before bronchodilator percent of predicted | 89; 96; 95 | ||
| fvc_postbd_predicted_percent | Indicate the percentage of the predicted FVC achieved after bronchodilator administration if available. | number | no | FVC after bronchodilator percent of predicted | 93; 100; 97 | ||
| fev1_fvc_ratio_prebd | Indicate the ratio of FEV1 to FVC before bronchodilator administration if available. | number | no | FEV1 to FVC ratio before bronchodilator | 0.75; 0.79; 0.72 | ||
| fev1_fvc_ratio_postbd | Indicate the ratio of FEV1 to FVC after bronchodilator administration if available. | number | no | FEV1 to FVC ratio after bronchodilator | 0.76; 0.80; 0.73 | ||
| frc_abs | Indicate the Functional Residual Capacity (FRC) in absolute milliliters if available. | number | no | FRC absolute | 3000; 3500; 2700 | ||
| frc_predicted_percent | Indicate the percentage of the predicted FRC, based on patient demographics, if available. | number | no | FRC percent of predicted | 95; 88; 102 | ||
| rv | Indicate the Residual Volume (RV) in milliliters if available. | number | no | RV | 1500; 1800; 1400 | ||
| rv_predicted_percent | Indicate the percentage of the predicted RV, based on patient demographics, if available. | number | no | RV percent of predicted | 80; 90; 85 | ||
| ic | Indicate the Inspiratory Capacity (IC) in milliliters if available. | number | no | IC | 3500; 4000; 3200 | ||
| ic_predicted_percent | Indicate the percentage of the predicted IC, based on patient demographics, if available. | number | no | IC percent of predicted | 92; 85; 97 | ||
| dlco | Indicate the Diffusing Capacity of the Lung for Carbon Monoxide (DLCO) in milliliters if available. | number | no | DLCO | 25; 30; 22 | ||
| dlco_predicted_percent | Indicate the percentage of the predicted DLCO, based on patient demographics, if available. | number | no | DLCO percent of predicted | 88; 95; 82 | ||
| kco | Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in mmol/min/kPa/L if available. | number | no | KCO | 5; 6; 4.5 | ||
| kco_predicted_percent | Indicate the percentage of the predicted KCO, based on patient demographics, if available. | number | no | KCO percent of predicted | 90; 98; 85 |
Information about collection institute location.
Location: module/biomaterial/collection_institute.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| name | Name of the institute where the biomaterial was collected on. | string | yes | Collection institute name | institute_1; Addenbrooke's Hospital; University of California, San Francisco | ||
| latitude | Latitute of the institute where the biomaterial was collected on, in decimal degrees. | string | no | Collection institute latitude | 52.1; -0.127541; 38.045956 | ||
| longitude | Longitude of the institute where the biomaterial was collected on, in decimal degrees. | string | no | Collection institute longitude | 0.1; -84.512016; 23.792138 |
Information about specific diseases profile of the individual.
Location: module/biomaterial/disease_profile.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| copd_gold_stage | Indicate the current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease). | integer | no | GOLD stage | 1, 2, 3, 4 | 1; 2; 3; 4 | |
| copd_mmrc_grade | Indicate the Modified British Medical Research Council (mMRC) dyspnea scale grade. | integer | no | mMRC grade | 0, 1, 2, 3, 4 | 0, 1; 2; 3; 4 | |
| copd_cat_score | Indicate the COPD Assessment Test (CAT) score. | integer | no | CAT score | 2; 5; 37 | ||
| copd_gold_abe_assessment | Indicate the Global Initiative for Chronic Obstructive Lung Disease (GOLD) A, B, C, D assessment group if available. | string | no | GOLD ABE assessment | A, B, E | A; B; E | |
| copd_phenotype | Indicate the COPD disease phenotype(s) of donor. Please indicate all applicable phenotypes of donor. | array | no | COPD phenotype | COPD not otherwise specified, COPD with emphysema, COPD with bronchitis, COPD with history of asthma, COPD with >300 eos in blood, COPD with allergy, COPD with Chronic Mucus Hypersecretion, COPD with frequent exacerbations | COPD with bronchitis; COPD with history of asthma; COPD with emphysema | |
| copd_emphysema_percentage | Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan. | number | no | Percentage of emphysema | |||
| PUCAI_score | Indicate the Pediatric Ulcerative Colitis Activity Index (PUCAI) score if available. | number | no | PUCAI score | |||
| PCDAI_score | Indicate the Pediatric Crohn’s Disease Activity Index (PCDAI) score if available. | number | no | PCDAI score | |||
| wPCDAI_score | Indicate the weighted Pediatric Crohn’s Disease Activity Index (wPCDAI) score if available. | number | no | wPCDAI score |
Reproductive history of the donor.
Location: module/biomaterial/reproductive_history.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| menarche_age | Age at menarche, rounded to nearest whole number. | integer | no | Menarche age | 13; 12; 16 | ||
| menstrual_cycle_stage | Menstrual cycle stage of donor at the time of collection. | string | no | Menstrual cycle stage | follicular phase, ovulation, luteal phase, menstruation | follicular phase; ovulation; luteal phase; menstruation | |
| menopause_status | Menopausal status of donor at time of sample collection. | string | no | Menopause status | pre-menopausal, peri-menopausal, post-menopausal, post-menopausal (induced) | pre-menopausal; peri-menopausal; post-menopausal; post-menopausal (induced) | |
| parity | Number of children (full-term pregnancies) the donor has given birth to at time of sample collection. | integer | no | Full term pregnancy - parity | 0; 2; 3 | ||
| gravidity | Number of pregnancies the donor has had at time of sample collection. | integer | no | Pregnancy - gravidity | 2; 3; 5 |
Information relating to how a biomaterial was preserved and/or stored over a period of time.
Location: module/biomaterial/preservation_storage.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| storage_method | The method by which a biomaterial was stored after preservation or before another protocol was used. | string | no | Storage method | ambient temperature, cut slide, fresh, frozen at -70C, frozen at -80C, frozen at -150C, frozen in liquid nitrogen, frozen in vapor phase, paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C | frozen in liquid nitrogen; fresh | |
| storage_time | Length of time the biomaterial was stored for in Storage time units. | number | no | Storage time | 5 | ||
| storage_time_unit | The unit in which Storage time is expressed. | object | no | See module time_unit_ontology | Storage time unit | ||
| preservation_method | The method by which a biomaterial was preserved through the use of chemicals, cold, or other means to prevent or retard biological or physical deterioration. | string | no | Preservation method | cryopreservation in liquid nitrogen (dead tissue), cryopreservation in dry ice (dead tissue), cryopreservation of live cells in liquid nitrogen, cryopreservation, other, formalin fixed, unbuffered, formalin fixed, buffered, formalin fixed and paraffin embedded, hypothermic preservation media at 2-8C, fresh | cryopreservation in liquid nitrogen (dead tissue); fresh |
Lifestyle and habits of the donor.
Location: module/biomaterial/lifestyle.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| physical_activity | The habitual level of physical activity and regular physical activities. | string | no | Physical activity | active - football, tennis; sedentary |
Information relating to the death of an organism.
Location: module/biomaterial/death.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| cause_of_death | Conditions resulting in death. | string | yes | Cause of death | Hypoxic brain damage; Sudden cardiac arrest | ||
| cold_perfused | Whether perfusion with cold fluid was used to help preserve tissues before heart stopped. | boolean | no | Cold perfused | Should be one of: yes, no. | ||
| days_on_ventilator | Number of days on ventilator before death occurred. | number | no | Number of days on ventilator | 4 | ||
| hardy_scale | Value on 4-point Hardy scale cause of death classification. | integer | no | Value on Hardy scale | 0 | ||
| time_of_death | Date and time when death was declared. | string | no | Time of death | 2016-01-21T00:00:00Z; 2016-03 | ||
| organ_donation_death_type | Type of death preceding organ donation. | string | no | Organ donation death type | Donation after circulatory death (DCD), Donation after brainstem death (DBD) | Should be one of: Donation after circulatory death (DCD), or Donation after brainstem death (DBD). | |
| normothermic_regional_perfusion | Whether entire body was perfused with warm oxygenated blood. | string | no | Normothermic regional perfusion | yes, no, unknown | Should be one of: yes, no, or unknown. |
Information about other organisms that this organism is related to.
Location: module/biomaterial/familial_relationship.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| parent | The individual's parent. | string | no | Parent | |||
| child | The individual's child. | string | no | Child | |||
| sibling | The individual's sibling. | string | no | Sibling |
Information about the medical history of a donor.
Location: module/biomaterial/medical_history.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| alcohol_status | Whether the individual is actively consuming, has formerly consumed or has never consumed alcohol beverages | string | no | Alcohol status | active, former, never | Should be one of: active, former, never. | |
| alcohol_type | Types of alcoholic beverages the donor consumed. | array | no | Alcohol type | beer; liquor; wine | ||
| alcohol_units | Alcohol consumption of donor in alcohol units per week (strength (ABV) x volume (ml) ÷ 1,000). | number | no | Alcohol units | 2.5; 15.2; 23 | ||
| alcohol_usage_duration | Number of years in which the donor consumed alcohol. | integer | no | Alcohol usage duration | 5 | ||
| medication | Medication(s) the individual was taking at time of biomaterial collection. | array | no | See module medication_ontology | Medication | ||
| smoking_status | Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc. | string | no | Smoking status | active, former, never | Should be one of: active, former, never. | |
| smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking. | number | no | Smoking pack years | 4.55 | ||
| years_since_smoking_cessation | If smoking status is 'former', specify the number of years since smoking cessation. | integer | no | Years since smoking cessation | 12 | ||
| household_smoking_exposure | If the donor is exposed to passive smoking in their household or not (excluding if they are the ones smoking). | boolean | no | Household smoking exposure | Should be one of: yes; no. | ||
| vaping_status | Whether the individual is actively, was formerly or never vaped. | string | no | Vaping status | active, former, never | Should be one of: active, former, never. | |
| marijuana_inhaled_status | Whether the individual is actively, was formerly or never inhaled/smoked marijuana. | string | no | Inhaled marijuana status | active, former, never | Should be one of: active, former, never. | |
| nutritional_state | Nutritional state of individual at time of biomaterial collection. | string | no | Nutritional state | normal, fasting, feeding tube removed | Should be one of: normal, fasting, or feeding tube removed. | |
| fasting_time | Duration of the donor's fasting period (in hours) prior to sample collection. | integer | no | Fasting time | 2; 5; 8 | ||
| diet_meat_consumption | Dietary patterns of donor - meat (chicken, seafood, fish, pork, lamb, beef, etc.) consumption versus meat-free diet - at time of sample collection. Fill yes if donor consumes meat or no if donor does not consumes meat. | boolean | no | Meat consumption | Should be one of: yes; no. | ||
| reproductive_history | Reproductive history of the donor at the time of collection. | object | no | See module reproductive_history | Reproductive history | ||
| blood_test | Results from blood tests performed on the individual. | object | no | See module blood_test | Blood tests | ||
| test_results | Results from medical tests performed on the individual. | string | no | Test results | lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative | ||
| treatment | Treatments the individual has undergone prior to biomaterial collection. | string | no | Treatments | Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer | ||
| previous_surgeries | Previous surgeries the individual has undergone prior to biomaterial collection. | string | no | Previous surgeries | Appendectomy; Coleostomy; Vaginoplasty; LASIK; Abdominal surgery | ||
| defined_diet | Whether the individual was following a defined diet at the time of biomaterial collection. | boolean | no | Defined diet | yes; no | ||
| diet_specific | Defined diet the donor was on at the time of biomaterial collection. | array | no | Diet Specific | vegan, vegetarian, omnivore, gluten_free, fodmap, baby_formula, breastfeeding, elimination, keto, paleo | gluten_free; fodmap; baby_formula; breastfeeding; elimination; keto; paleo |
Blood test results of the donor.
Location: module/biomaterial/blood_test.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| androstenedione | Androstenedione in the last blood test of the donor before collection. | number | no | Androstenedione | 0.7; 3.4; 2.41 | ||
| androstenedione_unit | Androstenedione unit. | string | no | Androstenedione unit | ng/dL, nmol/L | ng/dL; nmol/L | |
| dhea | Dehydroepiandrosterone (DHEA) in the last blood test of the donor before collection. | number | no | DHEA | 240; 3500; 1500 | ||
| dhea_unit | DHEA unit. | string | no | DHEA unit | ng/dL, nmol/L | ng/dL; nmol/L | |
| estrogen | Estrogen in the last blood test of the donor before collection. | number | no | Estrogen | 10; 150; 120 | ||
| estrogen_unit | Estrogen unit. | string | no | Estrogen unit | pg/mL, pmol/L | pg/mL; pmol/L | |
| fasting_glucose | Fasting glucose levels from the donor's last blood test after at least 8 hours of fasting, prior to the biopsy collection. | number | no | Fasting glucose | 70; 125; 90.2 | ||
| fasting_glucose_unit | Fasting glucose unit. | string | no | Fasting glucose unit | mg/dL, mmol/L | mg/dL; mmol/L | |
| fasting_insulin | Fasting insulin levels from the donor's last blood test after at least 8 hours of fasting, prior to the biopsy collection. | number | no | Fasting insulin | 2; 20; 14 | ||
| fasting_insulin_unit | Fasting insulin unit. | string | no | Fasting insulin unit | μU/mL, pmol/L | μU/mL; pmol/L | |
| free_fatty_acid | Free Fatty Acid (FFA) in the last blood test of the donor before collection. | number | no | FFA | 0.1; 0.6; 0.24 | ||
| free_fatty_acid_unit | Free Fatty Acid (FFA) unit. | string | no | FFA unit | mmol/L | mmol/L | |
| haematocrit | Percentage of red blood cells in whole blood from the donor's last blood test prior to biopsy collection. | number | no | Haematocrit | 36; 54; 45 | ||
| haematocrit_unit | Haematocrit unit. | string | no | Haematocrit unit | percentage (%) | % | |
| haemoglobin | Concentration of haemoglobin in whole blood from the donor's last blood test prior to biopsy collection. | number | no | Haemoglobin | 12; 17.5; 14.2 | ||
| haemoglobin_unit | Haemoglobin unit. | string | no | Haemoglobin unit | g/dL, mmol/L | g/dL; mmol/L | |
| hba1c | Concentration of glycated hemoglobin (HbA1c) from the donor's last blood test prior to biopsy collection. | number | no | HbA1c | 42; 58; 53.3 | ||
| hba1c_unit | HbA1c unit. | string | no | HbA1c unit | mmol/mol, % | mmol/mol; % | |
| hdl | High-density lipoprotein cholesterol (HDL) in the last blood test of the donor before collection. | number | no | HDL | 40; 60; 92 | ||
| hdl_unit | HDL unit. | string | no | HDL unit | mg/dL, mmol/L | mg/dL; mmol/L | |
| homa_ir | Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) in the last blood test of the donor before collection. | number | no | HOMA-IR | 0.4; 1.2; 0.94 | ||
| ldl | Low-density lipoprotein cholesterol (LDL) in the last blood test of the donor before collection. | number | no | LDL | 160; 133 | ||
| ldl_unit | LDL unit. | string | no | LDL unit | mg/dL, mmol/L | mg/dL; mmol/L | |
| platelet_count | Measurement of platelets per unit volume of blood from the donor's last blood test prior to biopsy collection | number | no | Platelet count | 240; 124; 110 | ||
| platelet_count_unit | Platelet count unit. | string | no | Platelet count unit | 10^9/L, cells/μL | 10^9/L; cells/μL | |
| shbg | Sex hormone binding globulin (SHBG) in the last blood test of the donor before collection. | number | no | SHBG | 10; 140; 72 | ||
| shbg_unit | SHBG unit. | string | no | SHBG unit | nmol/L | nmol/L | |
| testosterone | Testosterone in the last blood test of the donor before collection. | number | no | Testosterone | 15; 1000; 420 | ||
| testosterone_unit | Testosterone unit. | string | no | Testosterone unit | nmol/L, ng/dL | nmol/L; ng/dL | |
| triglycerides | Triglycerides levels from the donor's last blood test after at least 9-12 hours of fasting, prior to the biopsy collection. | number | no | Triglycerides | 160; 133; 140 | ||
| triglycerides_unit | Triglycerides unit. | string | no | Triglycerides unit | mg/dL, mmol/L | mg/dL; mmol/L | |
| white_blood_cell_count | Measurement of total white blood cells per unit volume of blood from the donor's last blood test prior to biopsy collection. | number | no | White cell count | 4.5; 11; 9.24 | ||
| white_blood_cell_count_unit | White cell count unit. | string | no | White cell count unit | 10^9/L, cells/μL | 10^9/L; cells/μL | |
| bloodtest_time_offset | Time between the test and the collection of the sample, in days. | number | no | Blood test time offset | 12; 42; 98 |
Donor's residence location information.
Location: module/biomaterial/residence.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| country_territory | Country or territory of donor's residence. | string | no | Country | Afghanistan, Albania, Algeria, American Samoa, Andorra, Angola, Anguilla, Antarctica, Antigua and Barbuda, Argentina, Armenia, Aruba, Ashmore and Cartier Islands, Australia, Austria, Azerbaijan, Bahamas, Bahrain, Baker Island, Bangladesh, Barbados, Bassas da India, Belarus, Belgium, Belize, Benin, Bermuda, Bhutan, Bolivia, Borneo, Bosnia and Herzegovina, Botswana, Bouvet Island, Brazil, British Virgin Islands, Brunei, Bulgaria, Burkina Faso, Burundi, Cambodia, Cameroon, Canada, Cape Verde, Cayman Islands, Central African Republic, Chad, Chile, China, Christmas Island, Clipperton Island, Cocos Islands, Colombia, Comoros, Cook Islands, Coral Sea Islands, Costa Rica, Cote d'Ivoire, Croatia, Cuba, Curacao, Cyprus, Czechia, Democratic Republic of the Congo, Denmark, Djibouti, Dominica, Dominican Republic, Ecuador, Egypt, El Salvador, Equatorial Guinea, Eritrea, Estonia, Eswatini, Ethiopia, Europa Island, Falkland Islands (Islas Malvinas), Faroe Islands, Fiji, Finland, France, French Guiana, French Polynesia, French Southern and Antarctic Lands, Gabon, Gambia, Gaza Strip, Georgia, Germany, Ghana, Gibraltar, Glorioso Islands, Greece, Greenland, Grenada, Guadeloupe, Guam, Guatemala, Guernsey, Guinea, Guinea-Bissau, Guyana, Haiti, Heard Island and McDonald Islands, Honduras, Hong Kong, Howland Island, Hungary, Iceland, India, Indonesia, Iran, Iraq, Ireland, Isle of Man, Israel, Italy, Jamaica, Jan Mayen, Japan, Jarvis Island, Jersey, Johnston Atoll, Jordan, Juan de Nova Island, Kazakhstan, Kenya, Kerguelen Archipelago, Kingman Reef, Kiribati, Kosovo, Kuwait, Kyrgyzstan, Laos, Latvia, Lebanon, Lesotho, Liberia, Libya, Liechtenstein, Line Islands, Lithuania, Luxembourg, Macau, Madagascar, Malawi, Malaysia, Maldives, Mali, Malta, Marshall Islands, Martinique, Mauritania, Mauritius, Mayotte, Mexico, Micronesia, Federated States of, Midway Islands, Moldova, Monaco, Mongolia, Montenegro, Montserrat, Morocco, Mozambique, Myanmar, Namibia, Nauru, Navassa Island, Nepal, Netherlands, New Caledonia, New Zealand, Nicaragua, Niger, Nigeria, Niue, Norfolk Island, North Korea, North Macedonia, Northern Mariana Islands, Norway, Oman, Pakistan, Palau, Palmyra Atoll, Panama, Papua New Guinea, Paracel Islands, Paraguay, Peru, Philippines, Pitcairn Islands, Poland, Portugal, Puerto Rico, Qatar, Republic of the Congo, Reunion, Romania, Russia, Rwanda, Saint Barthelemy, Saint Helena, Saint Kitts and Nevis, Saint Lucia, Saint Martin, Saint Pierre and Miquelon, Saint Vincent and the Grenadines, Samoa, San Marino, Sao Tome and Principe, Saudi Arabia, Senegal, Serbia, Seychelles, Sierra Leone, Singapore, Sint Maarten, Slovakia, Slovenia, Solomon Islands, Somalia, South Africa, South Georgia and the South Sandwich Islands, South Korea, South Sudan, Spain, Spratly Islands, Sri Lanka, State of Palestine, Sudan, Suriname, Svalbard, Sweden, Switzerland, Syria, Taiwan, Tajikistan, Tanzania, Thailand, Timor-Leste, Togo, Tokelau, Tonga, Trinidad and Tobago, Tromelin Island, Tunisia, Turkey, Turkmenistan, Turks and Caicos Islands, Tuvalu, Uganda, Ukraine, United Arab Emirates, United Kingdom, Uruguay, USA, Uzbekistan, Vanuatu, Venezuela, Viet Nam, Virgin Islands, Wake Island, Wallis and Futuna, West Bank, Western Sahara, Yemen, Zambia, Zimbabwe | Singapore; United Kingdom; Brazil; Australia; Nigeria | |
| region | Region of donor's residence. | string | no | Region | Massachusetts; Catalonia; Ondo; Ontario | ||
| locality | Nearest city, town, or village to location of donor's residence. | string | no | Locality | Singapore; Cambridge; Boston; Kingston | ||
| duration | Duration of residence, in years, rounded up to the nearest whole number. | string | no | Duration of residence | 20; 37; 45-65 | ||
| area_type | Urban, suburban, or rural descriptor of residence. | string | no | Area type of residence | urban, suburban, rural | urban; suburban; rural |
Information relating to pathological and morphological features of cells.
Location: module/biomaterial/cell_morphology.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| cell_morphology | General description of the morphology of cells. | string | no | Cell morphology | adherent cells; form single layer colonies | ||
| cell_size | Size of cells in Cell size unit. | string | no | Cell size | 15; 20-30 | ||
| cell_size_unit | The unit in which the Cell size is expressed. | object | no | See module length_unit_ontology | Cell size unit | ||
| percent_cell_viability | Percent of cells determined to be viable. | number | no | Percent cell viability | 98.7 | ||
| cell_viability_method | The method by which cell viability was determined. | string | no | Cell viability method | Fluorescein diacetate hydrolysis; ATP test | ||
| cell_viability_result | Result of the cell viability test. | string | no | Cell viability result | pass, fail | Should be one of: pass, fail | |
| percent_necrosis | Percent of cells identified to be necrotic. | number | no | Percent necrotic cells | 10 |
State of specimen at time of collection.
Location: module/biomaterial/state_of_specimen.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| autolysis_score | State of tissue breakdown due to self-digestion. | string | no | Autolysis score | none, mild, moderate | Should be one of: none, mild, or moderate. | |
| gross_description | Color, size, and other aspects of specimen as visible to naked eye. | string | no | Gross description | focal wedge shaped region of tan-orange discoloration; cystic | ||
| gross_images | List of filenames of photographs of specimen without magnification. | array | no | Gross image | my_gross_image_file.jpg | ||
| ischemic_temperature | Whether specimen experienced warm or cold ischemia. | string | no | Ischemic temperature | warm, cold | Should be one of: warm, or cold. | |
| ischemic_time | Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. | integer | no | Ischemic time | 7200 | ||
| microscopic_description | How the specimen looks under the microscope and how it compares with normal cells. | string | no | Microscopic description | Mixture of different cell sizes apparent; Dead cells are quite faint on microscope | ||
| microscopic_images | List of filenames of photographs of specimen under microscope. | array | no | Microscopic image | my_microscopic_image_file.jpg | ||
| postmortem_interval | Duration of time between when death was declared and when the specimen was preserved or processed. | integer | no | Post-mortem interval | 2400 |
Information relating to a timecourse.
Location: module/biomaterial/timecourse.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| value | The numerical value in Timecourse unit associated with a time interval used in the experiment. | string | yes | Timecourse value | 2; 5.5-10.5 | ||
| unit | The unit in which the Timecourse value is expressed. | object | yes | See module time_unit_ontology | Timecourse unit | ||
| relevance | Relevance of the Timecourse value/unit to the experiment. | string | no | Timecourse relevance | Collection after tumor cells injected into the mammary gland; Time tissue underwent liberase digestion |
Information specific to an organism that is a mouse (Mus musculus).
Location: module/biomaterial/mouse_specific.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| strain | The name of the mouse strain. | array | no | See module strain_ontology | Mouse strain |
Information describing purchased kits or reagents used in a protocol.
Location: module/process/purchased_reagents.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| retail_name | The retail name of the kit/reagent. | string | no | Retail name | SureCell WTA 3' Library Prep Kit; CytoTune iPS 2.0 Sendai Reprogramming Kit | ||
| catalog_number | The catalog number of the kit/reagent. | string | no | Catalog number | 20014279 | ||
| manufacturer | The manufacturer of the kit/reagent. | string | no | Manufacturer | Illumina; ThermoFisher Scientific | ||
| lot_number | The batch or lot number of the kit/reagent. | string | no | Batch/lot number | 10001A | ||
| expiry_date | The date of expiration for the kit/reagent. | string | no | Expiry date | 2018-01-31; 2018-01 | ||
| kit_titer | Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. | string | no | Titer | 3.0x10^7 |
Information relating to an INSDC experiment.
Location: module/process/sequencing/insdc_experiment.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| insdc_experiment_accession | An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession. | string | yes | INSDC experiment accession | SRX0000000 |
Information about barcodes used in a protocol.
Location: module/process/sequencing/barcode.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| barcode_read | The read in which the barcode is found. | string | yes | Barcode-containing read | Read 1, Read 2, Read 3, Read 4, i7 Index, i5 Index | Should be one of: Read 1, Read 2, i7 Index, or i5 Index. | |
| barcode_offset | The 0-based offset of start of barcode in read. | integer | yes | Barcode offset | 0 | ||
| barcode_length | Length of barcode in nucleotides. | integer | yes | Barcode length | 28 | ||
| white_list_file | Name of file containing legitimate barcode sequences. | string | no | White list barcode file | barcode_whitelist_file.txt |
Information specific to 10x experiments.
Location: module/process/sequencing/10x.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| fastq_method | Method used for the generation of fastq files from bcl files. | string | no | Fastq creation method | Cellranger mkfastq; bcl2fastq2 | ||
| fastq_method_version | Version of the program used for fastq generation. | string | no | Fastq creation method version | Cellranger 2.1.1; v2.20 | ||
| pooled_channels | The number of channels pooled within a sequencing lane. | number | no | Pooled channels | 4 | ||
| drop_uniformity | Whether drop uniformity was achieved as a result of visual inspection of emulsion after a 10x run. | boolean | no | Drop uniformity | Should be one of: yes, or no. |
Information specific to plate-based sequencing experiments.
Location: module/process/sequencing/plate_based_sequencing.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| plate_label | A label or name for the plate on which the well is located. | string | yes | Plate label | 2217 | ||
| well_label | A label or name for the well in which the cell is located. | string | no | Well label | A1 | ||
| well_quality | Quality of well if imaged before sequencing. | string | no | Well quality | OK, control, 2-cell well, control, empty well, low quality cell | Should be one of: 'OK', 'control, 2-cell well', 'control, empty well', or 'low quality cell'. |