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Instability in representation of deprecation status in obographs JSON #70
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@cmungall - any idea why this might be the case? |
So when you say 'recently' has there been a change to the obographs library you're using? |
I'm not using directly. It comes through re-use in OWL-API. @cmungall would know if/when there have been changes there. Note - it could be that there's some subtle difference is source (OWL/OBO) files that is causing the change. If so, not obvious what that might be. |
It's probably more likely that's the case as the obographs library hasn't been changed in a long while. There is a new version in the immutables branch, but this should produce identical output. |
What ontology are you using? Simply loading # example of a deprecated class
- id: "http://purl.obolibrary.org/obo/VT_0000009"
lbl: "red blood cell quantity"
type: "CLASS"
meta:
definition:
val: "OBSOLETE: Replace with VT:00001586, erythrocyte quantity."
xrefs:
- "VTO:CP"
basicPropertyValues:
- pred: "http://www.geneontology.org/formats/oboInOwl#created_by"
val: "mshimoyama"
- pred: "http://www.geneontology.org/formats/oboInOwl#creation_date"
val: "2011-06-14T03:01:56Z"
- pred: "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"
val: "Trait.ontology"
deprecated: true
# however your class doesn't appear to have all the information as shown in protege
- id: "http://purl.obolibrary.org/obo/FBbt_00050127"
lbl: "Drosophila neuroblast AOTUv3"
type: "CLASS" |
http://purl.obolibrary.org.obo/fbbt.owl
|
How is the AP mapping for the deprecated key specified?
Schema has deprecated as a primary key under meta:
https://github.com/geneontology/obographs/blob/master/schema/subschemas/obographs-meta-schema.json#L123
I have code that relies on this when parsing obographs JSON, but recently this not been showing up in translations, instead ending up only as a
pred
val
pair underbasicPropertyValues
, e.g. -{'id': 'http://purl.obolibrary.org/obo/FBbt_00050127',
'meta': {'definition': {'val': '.',
'xrefs': ['FlyBase:FBrf0221412', 'FlyBase:FBrf0221438']},
'basicPropertyValues': [{'pred': 'http://purl.obolibrary.org/obo/IAO_0100001',
'val': 'FBbt:00100545'},
{'pred': 'http://www.w3.org/2002/07/owl#deprecated', 'val': 'true'},
{'pred': 'http://www.geneontology.org/formats/oboInOwl#hasOBONamespace',
'val': 'fly_anatomy.ontology'},
{'pred': 'http://www.w3.org/2000/01/rdf-schema#comment',
'val': 'Obsoleted due to equivalence with neuroblast DALcl1 (Omoto et al., 2018 - FBrf0240929).'}]},
'type': 'CLASS',
'lbl': 'neuroblast AOTUv3'}
from
(note also - boolean cast to string!)
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