From d7498093d0f5e0db052ef88815d57c2648d09425 Mon Sep 17 00:00:00 2001
From: lltommy
Date: Thu, 9 Apr 2020 14:34:54 +0200
Subject: Updating schema and examples. This is still work in progress but we
 get there

---
 example/metadata.yaml        | 49 +++++++++++++++++++++++++++++++-------------
 example/minimal_example.yaml | 14 +++++++++++++
 2 files changed, 49 insertions(+), 14 deletions(-)
 create mode 100644 example/minimal_example.yaml

(limited to 'example')

diff --git a/example/metadata.yaml b/example/metadata.yaml
index 587d0be..8a93379 100644
--- a/example/metadata.yaml
+++ b/example/metadata.yaml
@@ -1,17 +1,38 @@
-sampleInformation:
-  location: "USA"
-  host : "Homo Sapiens"
-  sequenceTechnology: "Sanger"
-  assemblyMethod: "CLC Genomics"
+host:
+    host_id: XX1
+    host_species: string
+    host_common_name: string
+    host_sex: string
+    host_age: 20
+    host_age_unit: string
+    host_health_status: string
+    host_treatment: string
+    additional_host_information: string
 
-InstituteInformation:
-  OriginatingLab: "Erik's kitchen"
-  SubmittingLab: "National Institute for Viral Disease Control and Prevention, China CDC"
+sample:
+    collector_name: XXX
+    collecting_institution: XXX
+    specimen_source: XXX
+    collection_date: XXX
+    collection_location: XXX
+    sample_storage_conditions: XXX
+    additional_collection_information: XXX
 
-SubmitterInformation:
-  Submitter: "National Institute for Viral Disease Control and Prevention, China CDC"
-  submissionDate: "04-04-2020"
+virus:
+    virus_species: XX
+    virus_strain: XX
 
-VirusDetail:
-  VirusName: "hCoV-19/USA/identifer/2020"
-  AccessionId: "EPI_ISL_Random"
+technology:
+    sample_sequencing_technology: XX
+    sequence_assembly_method: XX
+    sequencing_coverage: 70x
+
+submitter:
+    submitter_name: tester
+    submitter_address: testerAdd
+    originating_lab: testLab
+    lab_address: labAdd
+    provider_sample_id: string
+    submitter_sample_id: string
+    authors: testAuthor
+    submitter_id: X12
\ No newline at end of file
diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml
new file mode 100644
index 0000000..201b080
--- /dev/null
+++ b/example/minimal_example.yaml
@@ -0,0 +1,14 @@
+host:
+    host_id: XX
+    host_species: string
+
+sample:
+    collector_name: XXX
+    collecting_institution: XXX
+
+technology:
+    sample_sequencing_technology: XX
+
+submitter:
+    submitter_name: tester
+    originating_lab: testLab
\ No newline at end of file
-- 
cgit v1.2.3


From dbe094a150d6c969b3d69f112b3538e6a87a74a2 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Thu, 9 Apr 2020 15:59:46 -0400
Subject: Add "sequencefile" for the metadata subject.

---
 bh20sequploader/bh20seq-schema.yml | 13 ++++++++++++-
 example/metadata.yaml              |  2 +-
 2 files changed, 13 insertions(+), 2 deletions(-)

(limited to 'example')

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index fd9e854..5c962d1 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -1,3 +1,8 @@
+$base: http://biohackathon.org/bh20-seq-schema
+$namespaces:
+  sch: https://schema.org/
+  efo: http://www.ebi.ac.uk/efo/
+  obo: http://purl.obolibrary.org/obo/
 $graph:
 
 - name: hostSchema
@@ -75,4 +80,10 @@ $graph:
     sample: sampleSchema
     virus: virusSchema?
     technology: technologySchema
-    submitter: submitterSchema
\ No newline at end of file
+    submitter: submitterSchema
+    sequencefile:
+      doc: The subject (eg the fasta/fastq file) that this metadata describes
+      type: string?
+      jsonldPredicate:
+        _id: "@id"
+        _type: "@id"
diff --git a/example/metadata.yaml b/example/metadata.yaml
index 8a93379..41ff93e 100644
--- a/example/metadata.yaml
+++ b/example/metadata.yaml
@@ -35,4 +35,4 @@ submitter:
     provider_sample_id: string
     submitter_sample_id: string
     authors: testAuthor
-    submitter_id: X12
\ No newline at end of file
+    submitter_id: X12
-- 
cgit v1.2.3