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authorlltommy2020-04-13 02:36:18 +0200
committerlltommy2020-04-13 02:36:18 +0200
commitbc62d3f4c9ed8d94e536d2dd67fedf40b3e011ab (patch)
tree45087b43c880dc459ea05793005ae8377306d98e
parent31686ba2e1b2edec29229ab5adb28b366893f17b (diff)
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Starting to turn values into IRIs ...
-rw-r--r--bh20sequploader/bh20seq-schema.yml10
-rw-r--r--example/metadata.yaml10
-rw-r--r--example/minimal_example.yaml4
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