From bc62d3f4c9ed8d94e536d2dd67fedf40b3e011ab Mon Sep 17 00:00:00 2001
From: lltommy
Date: Mon, 13 Apr 2020 02:36:18 +0200
Subject: Starting to turn values into IRIs ...

---
 bh20sequploader/bh20seq-schema.yml | 10 +++++++---
 example/metadata.yaml              | 10 +++++-----
 example/minimal_example.yaml       |  4 ++--
 3 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 81a7f22..2d2e4c9 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -13,11 +13,11 @@ $graph:
   type: record
   fields:
     host_species:
-        ## autocomplete # NCBITAXON
         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
@@ -33,16 +33,18 @@ $graph:
         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.... this field is unstable as of now (might be removed)
+        doc: Unit of host age e.g. http://purl.obolibrary.org/obo/UO_0000036
         type: string?
         jsonldPredicate:
-          _id: http://purl.obolibrary.org/obo/UO_0000036
+          _id: http://purl.obolibrary.org/obo/NCIT_C42574
+          _type: "@id"
     host_health_status:
         doc: A condition or state at a particular time
         type: string?
@@ -91,6 +93,7 @@ $graph:
       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?
@@ -120,6 +123,7 @@ $graph:
       type: string?
       jsonldPredicate:
           _id: http://edamontology.org/data_1875
+          _type: "@id"
     virus_strain:
       doc: Name of the virus strain
       type: string?
diff --git a/example/metadata.yaml b/example/metadata.yaml
index d9e8e92..15e4e44 100644
--- a/example/metadata.yaml
+++ b/example/metadata.yaml
@@ -2,11 +2,11 @@ id: placeholder
 
 host:
     host_id: XX1
-    host_species: string
+    host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
     host_common_name: string
-    host_sex: string
+    host_sex: http://purl.obolibrary.org/obo/NCIT_C27993
     host_age: 20
-    host_age_unit: string
+    host_age_unit: http://purl.obolibrary.org/obo/UO_0000036
     host_health_status: string
     host_treatment: string
     additional_host_information: string
@@ -17,12 +17,12 @@ sample:
     collecting_institution: XXX
     specimen_source: XXX
     collection_date: XXX
-    collection_location: XXX
+    collection_location: http://purl.obolibrary.org/obo/NCIT_C16428
     sample_storage_conditions: XXX
     additional_collection_information: XXX
 
 virus:
-    virus_species: XX
+    virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
     virus_strain: XX
 
 technology:
diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml
index 160d1d4..43adfa8 100644
--- a/example/minimal_example.yaml
+++ b/example/minimal_example.yaml
@@ -2,8 +2,8 @@ id: placeholder
 
 host:
     host_id: XX
-    host_species: string
-    host_sex: string
+    host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
+    host_sex: http://purl.obolibrary.org/obo/NCIT_C20197
 
 sample:
     sample_id: XXX
-- 
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