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$base: http://biohackathon.org/bh20-seq-schema
$namespaces:
cc: https://creativecommons.org/ns#
dc: http://purl.org/metadata/dublin_core_elements#
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: licenseSchema
type: record
fields:
license_type:
doc: License types as defined in https://wiki.creativecommons.org/images/d/d6/Ccrel-1.0.pdf
type: string
jsonldPredicate:
_id: https://creativecommons.org/ns#License
_type: "@id"
noLinkCheck: true
title:
doc: Attribution title related to data license
type: string?
jsonldPredicate:
_id: http://purl.org/metadata/dublin_core_elements#Title
attribution_name:
doc: Attribution NAME related to data license
type: string?
jsonldPredicate:
_id: https://creativecommons.org/ns#attributionName
attribution_url:
doc: Attribution URL related to data license
type: string?
jsonldPredicate:
_id: https://creativecommons.org/ns#attributionURL
_type: "@id"
noLinkCheck: true
attribution_source:
doc: Attribution source URL related to data license
type: string?
jsonldPredicate:
_id: https://creativecommons.org/ns#attributionSource
_type: "@id"
noLinkCheck: true
- name: hostSchema
type: record
fields:
host_species:
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
_type: "@id"
noLinkCheck: true
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_sex:
doc: Sex of the host as defined in PATO, expect Male (http://purl.obolibrary.org/obo/PATO_0000384) or Female (http://purl.obolibrary.org/obo/PATO_0000383) or in Intersex (http://purl.obolibrary.org/obo/PATO_0001340)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000047
_type: "@id"
noLinkCheck: true
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 e.g. http://purl.obolibrary.org/obo/UO_0000036
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C42574
_type: "@id"
noLinkCheck: true
host_health_status:
doc: A condition or state at a particular time, must be one of the following (obo:NCIT_C115935 obo:NCIT_C3833 obo:NCIT_C25269 obo:GENEPIO_0002020 obo:GENEPIO_0001849 obo:NCIT_C28554 obo:NCIT_C37987)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C25688
_type: "@id"
noLinkCheck: true
host_treatment:
doc: Process in which the act is intended to modify or alter host status
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0000727
host_vaccination:
doc: List of vaccines given to the host
type: string[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/VO_0000002
ethnicity:
doc: Ethinicity of the host e.g. http://purl.obolibrary.org/obo/HANCESTRO_0010
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001014
_type: "@id"
noLinkCheck: true
additional_host_information:
doc: Field for additional host information
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
- name: sampleSchema
type: record
fields:
sample_id:
doc: Unique sample identifier as defined by the submitter
type: string
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
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 wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China)
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/GAZ_00000448
_type: "@id"
noLinkCheck: true
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 for sampeling
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C41206
specimen_source:
doc: Method how the specimen was derived as NCIT IRI, e.g. http://purl.obolibrary.org/obo/NCIT_C155831 (=nasopharyngeal swab)
type: string[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001479
_type: "@id"
noLinkCheck: true
sample_storage_conditions:
doc: Information about 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
source_database_accession:
doc: If data is deposit at a public resource (e.g. Genbank, ENA) enter the Accession Id here. Please use a resolveable URL (e.g. http://identifiers.org/insdc/LC522350.1#sequence)
type: string[]?
jsonldPredicate:
_id: http://edamontology.org/data_2091
_type: "@id"
noLinkCheck: true
- name: virusSchema
type: record
fields:
virus_species:
doc: The name of virus species from the NCBI taxonomy database, e.g. http://purl.obolibrary.org/obo/NCBITaxon_2697049 for Severe acute respiratory syndrome coronavirus 2
type: string
jsonldPredicate:
_id: http://edamontology.org/data_1875
_type: "@id"
noLinkCheck: true
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 device that was used to sequence the sample (e.g Sanger, Nanopore MiniION)
type: string[]
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C153598
_type: "@id"
noLinkCheck: true
assembly_method:
doc: Assembly method refers to how the reads were assembled into contigs for which either a de novo (http://purl.obolibrary.org/obo/GENEPIO_0001628) or mapping/reference based (http://purl.obolibrary.org/obo/GENEPIO_0002028) strategy is used.
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/GENEPIO_0000090
_type: "@id"
alignment_protocol:
doc: Protocol which provides detailed instructions to obtain the assembly
type: string?
jsonldPredicate:
_id: http://www.ebi.ac.uk/efo/EFO_0004917
sequencing_coverage:
doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. [100]) - if multiple technologies were used multiple float values can be submitted e.g. [100, 20]
type: double[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
additional_technology_information:
doc: Field for additional technology information
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
- name: submitterSchema
type: record
fields:
authors:
doc: Name(s) of the author(s) of the sequence data in the scientific publication
type: string[]
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C42781
submitter_name:
doc: Name of the submitter(s) of the sequence data
type: string[]?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000116
submitter_address:
doc: Address of the submitter of the sequence data
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000172
originating_lab:
doc: Laboratory name or identifier where the sample to sequence was produced
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C37984
lab_address:
doc: Address of the laboratory where the sample was produced
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C25407
provider:
doc: Name or identifier of the provider of the sample
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C37900
submitter_sample_id:
doc: Identifier given to the sample by the submitter
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C164332
publication:
doc: Reference to the scientifc publication of the sequence (e.g. DOI, pubmed ID, ...)
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/NCIT_C19026
submitter_orcid:
doc: ORCID of the submitter as a full URI, e.g. https://orcid.org/0000-0002-1825-0097
type: string[]?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/APOLLO_SV_00000496
_type: "@id"
noLinkCheck: true
additional_submitter_information:
doc: Field for additional submitter information
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_001167
- name: MainSchema
type: record
documentRoot: true
fields:
host: hostSchema
sample: sampleSchema
virus: virusSchema
technology: technologySchema
submitter: submitterSchema
license: ["null", licenseSchema]
id:
doc: The subject (eg the fasta/fastq file) that the metadata describes
type: string
jsonldPredicate:
_id: "@id"
_type: "@id"
noLinkCheck: true
|
