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-rw-r--r--bh20sequploader/bh20seq-schema.yml89
1 files changed, 71 insertions, 18 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 6e0973a..5c962d1 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -1,36 +1,89 @@
+$base: http://biohackathon.org/bh20-seq-schema
+$namespaces:
+ sch: https://schema.org/
+ efo: http://www.ebi.ac.uk/efo/
+ obo: http://purl.obolibrary.org/obo/
$graph:
-- name: sampleInformationSchema
+- name: hostSchema
type: record
fields:
- location: string
- host: string
- sequenceTechnology: string
- assemblyMethod: string
+ host_species:
+ type: string
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0000532
+ host_id: string
+ host_common_name: string?
+ host_sex: string?
+ host_age: int?
+ host_age_unit: string?
+ host_health_status: string?
+ host_treatment:
+ type: string?
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0000727
+ additional_host_information: string?
-- name: InstituteInformationSchema
+- name: sampleSchema
type: record
fields:
- OriginatingLab: string
- SubmittingLab: string
+ collector_name: string
+ collecting_institution: string
+ specimen_source: string?
+ collection_date: string?
+ collection_location:
+ type: string?
+ jsonldPredicate:
+ _id: https://schema.org/fromLocation
+ sample_storage_conditions: string?
+ additional_collection_information: string?
-- name: SubmitterInformationSchema
+- name: virusSchema
type: record
fields:
- Submitter: string
- submissionDate: string
+ virus_species: string?
+ virus_strain: string?
-- name: VirusDetailSchema
+- name: technologySchema
type: record
fields:
- VirusName: string
- AccessionId: string
+ sample_sequencing_technology:
+ type: string
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0000532
+ sequence_assembly_method:
+ type: string?
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0002699
+ sequencing_coverage:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/FLU_0000848
+
+- name: submitterSchema
+ type: record
+ fields:
+ submitter_name: string
+ submitter_address: string?
+ originating_lab: string
+ lab_address: string?
+ provider_sample_id: string?
+ submitter_sample_id: string?
+ authors: string?
+ submitter_id: string?
- name: MainSchema
type: record
documentRoot: true
fields:
- sampleInformation: sampleInformationSchema
- InstituteInformation: InstituteInformationSchema
- SubmitterInformation: SubmitterInformationSchema
- VirusDetail: VirusDetailSchema
+ host: hostSchema
+ sample: sampleSchema
+ virus: virusSchema?
+ technology: technologySchema
+ submitter: submitterSchema
+ sequencefile:
+ doc: The subject (eg the fasta/fastq file) that this metadata describes
+ type: string?
+ jsonldPredicate:
+ _id: "@id"
+ _type: "@id"