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 file produced from any process.
Location: core/file/file_core.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| file_name | The name of the file. | string | yes | File name | R1.fastq.gz; codebook.json | ||
| format | The format of the file. | string | yes | File format | fastq.gz; tif | ||
| content_description | General description of the contents of the file. | array | no | See module file_content_ontology | Content description | ||
| checksum | MD5 checksum of the file. | string | no | Checksum | e09a986c2e630130b1849d4bf9a94c06 | ||
| file_source | The source of the file. This is typically an organisation, repository, person or dedicated process. | string | no | File source | DCP/2 Analysis, Contributor, ArrayExpress, HCA Release, GEO, SCEA, SCP, DCP/1 Matrix Service, LungMAP, Zenodo, Publication, DCP/2 Ingest | GEO; Contributor |
Information about an intended protocol that was followed in the project.
Location: core/protocol/protocol_core.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| protocol_id | A unique ID for the protocol. | string | yes | Protocol ID | |||
| protocol_name | A short name for the protocol. | string | no | Protocol name | |||
| protocol_description | A general description of the protocol. | string | no | Protocol description | |||
| publication_doi | The publication digital object identifier (doi) for the protocol. | string | no | Publication DOI | 10.1101/193219 | ||
| protocols_io_doi | The protocols.io digital object identifier (doi) for the protocol. | string | no | protocols.io DOI | 10.17504/protocols.io.mgjc3un | ||
| document | A filename of a PDF document containing the details of the protocol. | string | no | Document filename | my_cool_protocol.pdf |
Information about the project.
Location: core/project/project_core.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| project_short_name | A short name for the project. | string | yes | Project label | CoolOrganProject. | ||
| project_title | An official title for the project. | string | yes | Project title | Study of single cells in the human body. | ||
| project_description | A longer description of the project which includes research goals and experimental approach. | string | yes | Project description |
Information about any biological material that was generated/used in the project including everything from a whole organism to subcellular components.
Location: core/biomaterial/biomaterial_core.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| biomaterial_id | A unique ID for the biomaterial. | string | yes | Biomaterial ID | |||
| biomaterial_name | A short, descriptive name for the biomaterial that need not be unique. | string | no | Biomaterial name | |||
| biomaterial_description | A general description of the biomaterial. | string | no | Biomaterial description | |||
| ncbi_taxon_id | A taxonomy ID (taxonID) from NCBI. | array | yes | NCBI taxon ID | 9606 | ||
| genotype | Genotype of the biomaterial. | string | no | Genotype | DRB1 0401 protective allele; HLA-B*3901 allele | ||
| supplementary_files | A list of filenames of biomaterial-level supplementary files. | array | no | Supplementary files | sample_site_image.jpg | ||
| biosamples_accession | A BioSamples accession. | string | no | BioSamples accession | SAMN00000000 | ||
| insdc_sample_accession | An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. | string | no | INSDC sample accession | SRS0000000 | ||
| HDBR_accession | A Human Developmental Biology Resource (HDBR) sample accession. | string | no | HDBR accession | 34526; 14758, 2, liver | ||
| timecourse | Information relating to a timecourse associated with this biomaterial. | object | no | See module timecourse | Timecourse |
Information relevant to how a biomaterial or file was converted into another biomaterial or file.
Location: core/process/process_core.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| process_id | A unique ID for the process. | string | yes | Process ID | |||
| process_name | A short, descriptive name for the process that need not be unique. | string | no | Process name | |||
| process_description | A general description of the process. | string | no | Process description | |||
| location | Location where the process took place. | string | no | Location | Wellcome Trust Sanger Institute; Cancer Institute Stanford University | ||
| operators | Identifier for individual(s) who executed the process. | array | no | Operator(s) | Technician 1; JD; John Doe |