owlcollab / owlcollab/owltools
Handling of obo namespaces in golr loads
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@hdietze is already working on this.
Since Apr 27, 2015.
- Dominant language
- Java
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Description
Ontologies are not well behaved in populating the obo format 'namespace' tag with meaningful, concise values (important note: obo namespaces != owl/xml namespace. See obo specs).
We should ditch the namespace field in favor of a more useful category field. This would cause a bit of churn. We can instead overload the namespace field and overwrite it with useful info.
Mapping from ID space (CL, GO, etc) to value:
- GO: use existing obo namespace field
- MA: 'mouse anatomy'
- CL: 'cell'
- UBERON: animal anatomy
- EMAP: 'embryonic mouse'
- CHEBI: chemical
- Anything else:
uc(IDspace)
last step: s/[\-_]/ /g; (for amigo facet purposes)
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