Merge remote-tracking branch 'upstream/master' into add-web-ui

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"