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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:
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"
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
# Removed_common_name. Not necessary since we turned species into IRI
# 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 defined in NCIT, IRI expected (http://purl.obolibrary.org/obo/NCIT_C20197 (Male), http://purl.obolibrary.org/obo/NCIT_C27993 (Female), http://purl.obolibrary.org/obo/NCIT_C45908 (Intersex), or http://purl.obolibrary.org/obo/NCIT_C17998 (Unknown))
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/PATO_0000047
_type: "@id"
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"
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: List of vaccines given to the host
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/VO_0000002
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
_type: "@id"
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
_type: "@id"
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: int?
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_orcid:
doc: ORCID of the submitter as a full URI, e.g. https://orcid.org/0000-0002-1825-0097
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
|
