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Metadata

Reference file

A reference file used by a secondary reference pipeline.

View JSON source: reference_filedoneShow required fields only

Properties

Genome assembly typeRequiredreference_file.assembly_typecopy (string enum) The assembly type of the genome reference file. Should be one of: "primary assembly", "complete assembly" or "patch assembly".
NCBI taxon IDRequiredreference_file.ncbi_taxon_idcopy (integer) A taxonomy ID (taxonID) from NCBI. For example "9606" or "10090".
Reference typeRequiredreference_file.reference_typecopy (string enum) The type of the reference file. Should be one of: "genome sequence", "transcriptome sequence", "annotation reference", "transcriptome index" or "genome sequence index".
Reference versionRequiredreference_file.reference_versioncopy (string) The genome version of the reference file. For example "GencodeV27" or "Ensembl 87".
Reference file>Genus speciesRequired (species_ontology object) The scientific binomial name for the species of this reference.
Species ontology IDreference_file.genus_species.ontologycopy (string from species_ontology) An ontology term identifier in the form prefix:accession. For example "NCBITaxon:9606" or "NCBITaxon:10090".Graph restriction: Subclasses of OBI:0100026, NCBITaxon:2759 from obo:efo or obo:NCBITaxon.
Species ontology labelreference_file.genus_species.ontology_labelcopy (string from species_ontology) 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. For example "Homo sapiens" or "Mus musculus".
SpeciesRequiredreference_file.genus_species.textcopy (string from species_ontology) The name of the species to which the organism belongs. For example "Homo sapiens" or "Mus musculus".
Reference file>File coreRequired (file_core object) Core file-level information.
Checksumreference_file.file_core.checksumcopy (string from file_core) MD5 checksum of the file. For example "e09a986c2e630130b1849d4bf9a94c06".
File nameRequiredreference_file.file_core.file_namecopy (string from file_core) The name of the file. For example "R1.fastq.gz" or "codebook.json".
File sourcereference_file.file_core.file_sourcecopy (string enum from file_core) The source of the file. This is typically an organisation, repository, person or dedicated process. Should be one of: "DCP/2 Analysis", "Contributor", "ArrayExpress", "HCA Release", "GEO", "SCEA", "SCP", "DCP/1 Matrix Service", "LungMAP", "Zenodo" or "Publication".
File formatRequiredreference_file.file_core.formatcopy (string from file_core) The format of the file. For example "fastq.gz" or "tif".
Reference file>File core>Content description (file_content_ontology array) General description of the contents of the file.
Content description ontology IDreference_file.file_core.content_description.ontologycopy (string from file_content_ontology) An ontology term identifier in the form prefix:accession. For example "data:3497" or "data:0863".Graph restriction: Subclasses of data:0006 from obo:edam.
Content description ontology labelreference_file.file_core.content_description.ontology_labelcopy (string from file_content_ontology) 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. For example "DNA sequence (raw)" or "Sequence alignment".
Content descriptionRequiredreference_file.file_core.content_description.textcopy (string from file_content_ontology) General description of the contents of the file. For example "DNA sequence (raw)" or "Sequence alignment".
Reference file>provenance (provenance object) Provenance information provided by the system.
Accessionreference_file.provenance.accessioncopy (string from provenance) A unique accession for this entity, provided by the broker.
Document IDRequiredreference_file.provenance.document_idcopy (string from provenance) Identifier for document.
Schema major versionreference_file.provenance.schema_major_versioncopy (integer from provenance) The major version number of the schema. For example "4" or "10".
Schema minor versionreference_file.provenance.schema_minor_versioncopy (integer from provenance) The minor version number of the schema. For example "6" or "15".
Submission dateRequiredreference_file.provenance.submission_datecopy (string from provenance) When project was first submitted to database.
Submitter IDreference_file.provenance.submitter_idcopy (string from provenance) ID of individual who first submitted project.
Update datereference_file.provenance.update_datecopy (string from provenance) When project was last updated.
Updater IDreference_file.provenance.updater_idcopy (string from provenance) ID of individual who last updated project.