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authorlltommy2020-04-20 10:13:16 +0200
committerlltommy2020-04-20 10:13:16 +0200
commita1a5b2db96c315c784a8a77d8b2ce0db4c009f89 (patch)
treed9ede1baa4bc8e5bd5382f8941b2be9d2a9d703c
parentfdbaeeb5ed29f6a2b1a9de466cb62e6fd6849b85 (diff)
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Making collection date and collection location MANDATORY fields, turning orcid into IRI
-rw-r--r--bh20sequploader/bh20seq-schema.yml6
-rw-r--r--example/metadata.yaml2
-rw-r--r--example/minimal_example.yaml2
3 files changed, 7 insertions, 3 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 5000f08..64008f2 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -87,12 +87,12 @@ $graph:
_type: "@id"
collection_date:
doc: Date when the sample was taken
- type: string?
+ type: string
jsonldPredicate:
_id: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25164
collection_location:
doc: Geographical location where the sample was collected as wikidata reference, e.g. http://www.wikidata.org/entity/Q148 (China)
- type: string?
+ type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/GAZ_00000448
_type: "@id"
@@ -214,6 +214,8 @@ $graph:
type: string?
jsonldPredicate:
_id: http://semanticscience.org/resource/SIO_000115
+ _type: "@id"
+ noLinkCheck: true
- name: MainSchema
type: record
diff --git a/example/metadata.yaml b/example/metadata.yaml
index 1e7f29c..8bbf980 100644
--- a/example/metadata.yaml
+++ b/example/metadata.yaml
@@ -17,7 +17,7 @@ sample:
collecting_institution: Institute that was responsible of sampeling
specimen_source: http://purl.obolibrary.org/obo/NCIT_C155831
specimen_source2: http://purl.obolibrary.org/obo/NCIT_C155835
- collection_date: Date when the sample was taken
+ collection_date: 2020-01-01
collection_location: http://www.wikidata.org/entity/Q148
sample_storage_conditions: XXX
additional_collection_information: XXX
diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml
index f4118d1..ed578e2 100644
--- a/example/minimal_example.yaml
+++ b/example/minimal_example.yaml
@@ -8,6 +8,8 @@ sample:
sample_id: XX
collector_name: John Doe
collecting_institution: Doe university
+ collection_date: 2020-01
+ collection_location: http://www.wikidata.org/entity/Q148
virus:
virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049