aboutsummaryrefslogtreecommitdiff
path: root/bh20sequploader/bh20seq-schema.yml
diff options
context:
space:
mode:
authorPjotr Prins2020-04-09 15:34:06 -0500
committerPjotr Prins2020-04-09 15:34:06 -0500
commit0670ac0644c1e7366952e254bdee2db62e673275 (patch)
treeaed056a1ca4208cf30993da3e96bbb4fb08dbe52 /bh20sequploader/bh20seq-schema.yml
parent146cf2f5d1be9a5dd9d6cd65ce9c760853d014f8 (diff)
parentdbe094a150d6c969b3d69f112b3538e6a87a74a2 (diff)
downloadbh20-seq-resource-0670ac0644c1e7366952e254bdee2db62e673275.tar.gz
bh20-seq-resource-0670ac0644c1e7366952e254bdee2db62e673275.tar.lz
bh20-seq-resource-0670ac0644c1e7366952e254bdee2db62e673275.zip
Merge branch 'master' of github.com:arvados/bh20-seq-resource
Diffstat (limited to 'bh20sequploader/bh20seq-schema.yml')
-rw-r--r--bh20sequploader/bh20seq-schema.yml89
1 files changed, 89 insertions, 0 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
new file mode 100644
index 0000000..5c962d1
--- /dev/null
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -0,0 +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: hostSchema
+ type: record
+ fields:
+ 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: sampleSchema
+ type: record
+ fields:
+ 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: virusSchema
+ type: record
+ fields:
+ virus_species: string?
+ virus_strain: string?
+
+- name: technologySchema
+ type: record
+ fields:
+ 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:
+ 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"