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Diffstat (limited to 'bh20sequploader/bh20seq-schema.yml')
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 210 |
1 files changed, 210 insertions, 0 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml new file mode 100644 index 0000000..81a7f22 --- /dev/null +++ b/bh20sequploader/bh20seq-schema.yml @@ -0,0 +1,210 @@ +$base: http://biohackathon.org/bh20-seq-schema +$namespaces: + sch: https://schema.org/ + efo: http://www.ebi.ac.uk/efo/ + obo: http://purl.obolibrary.org/obo/ + sio: http://semanticscience.org/resource/ + edam: http://edamontology.org/ + evs: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl# + +$graph: + +- name: hostSchema + type: record + fields: + host_species: + ## autocomplete # NCBITAXON + doc: Host species as defined in NCBITaxon (e.g. http://purl.obolibrary.org/obo/NCBITaxon_9606 for Homo sapiens) + type: string + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0000532 + host_id: + doc: Identifer for the host. If you submit multiple samples from the same host, use the same host_id for those samples + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 + host_common_name: + doc: Text label for the host species (e.g. homo sapiens) + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NOMEN_0000037 + host_sex: + doc: Sex of the host as define in NCIT, IRI expected (http://purl.obolibrary.org/obo/C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female) or unkown (http://purl.obolibrary.org/obo/NCIT_C17998)) + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/PATO_0000047 + host_age: + doc: Age of the host as number (e.g. 50) + type: int? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/PATO_0000011 + host_age_unit: + doc: Unit of host age.... this field is unstable as of now (might be removed) + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/UO_0000036 + host_health_status: + doc: A condition or state at a particular time + type: string? + jsonldPredicate: http://purl.obolibrary.org/obo/NCIT_C25688 + host_treatment: + doc: Process in which the act is intended to modify or alter + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0000727 + host_vaccination: + doc: Field is unstable + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/VO_0000001 + additional_host_information: + doc: Field for additional host information + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + +- name: sampleSchema + type: record + fields: + collector_name: + doc: Name of the person that took the sample + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001895 + collecting_institution: + doc: Institute that was responsible of sampeling + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + specimen_source: + doc: A specimen that derives from an anatomical part or substance arising from an organism, e.g. tissue, organ + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001479 + collection_date: + doc: Date when the sample was taken + type: string? + jsonldPredicate: + _id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164 + collection_location: + doc: Geographical location where the sample was collected as Gazetteer (https://www.ebi.ac.uk/ols/ontologies/gaz) reference, e.g. http://purl.obolibrary.org/obo/GAZ_00002845 (China) + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/GAZ_00000448 + sample_storage_conditions: + doc: Information aboout storage of a specified type, e.g. frozen specimen, paraffin, fresh .... + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0001472 + additional_collection_information: + doc: Add additional comment about the circumstances that a sample was taken + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_001167 + sample_id: + doc: Id of the sample as defined by the submitter + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 + source_database_accession: + doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here + type: string? + jsonldPredicate: + _id: http://edamontology.org/data_2091 + +- name: virusSchema + type: record + fields: + virus_species: + doc: The name of a taxon from the NCBI taxonomy database + type: string? + jsonldPredicate: + _id: http://edamontology.org/data_1875 + virus_strain: + doc: Name of the virus strain + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_010055 + +- name: technologySchema + type: record + fields: + sample_sequencing_technology: + doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION) + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0600047 + sequence_assembly_method: + doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0002699 + sequencing_coverage: + doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. 100x) + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/FLU_0000848 + +- name: submitterSchema + type: record + fields: + submitter_name: + doc: Name of the submitter + type: string + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000116 + submitter_address: + doc: Address of the submitter + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000172 + originating_lab: + doc: Name of the laboratory that took the sample + type: string + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C37984 + lab_address: + doc: Address of the laboratory where the sample was taken + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/OBI_0600047 + provider_sample_id: + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C37900 + submitter_sample_id: + type: string? + jsonldPredicate: + _id: http://www.ebi.ac.uk/efo/EFO_0001741 + authors: + doc: Name of the author(s) + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C42781 + publication: + doc: Reference to publication of this sample (e.g. DOI, pubmed ID, ...) + type: string? + jsonldPredicate: + _id: http://purl.obolibrary.org/obo/NCIT_C19026 + submitter_orchid: + doc: ORCHID of the submitter + type: string? + jsonldPredicate: + _id: http://semanticscience.org/resource/SIO_000115 + +- name: MainSchema + type: record + documentRoot: true + fields: + host: hostSchema + sample: sampleSchema + virus: virusSchema? + technology: technologySchema + submitter: submitterSchema + id: + doc: The subject (eg the fasta/fastq file) that the metadata describes + type: string + jsonldPredicate: + _id: "@id" + _type: "@id" + noLinkCheck: true |