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authorPjotr Prins2020-04-12 12:49:06 -0500
committerGitHub2020-04-12 12:49:06 -0500
commit23722a63682fdffe51efca55b40573fa27370973 (patch)
tree7628ccda2671fe9a3e9ff204918c965d4bb9e257 /bh20sequploader/bh20seq-schema.yml
parent10ccb97cab69cb704c154387d544a74cd38d3cdf (diff)
parent92e1608b2d8b21f2001d7bf480301d314337fdc0 (diff)
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+$base: http://biohackathon.org/bh20-seq-schema
+$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