owlcollab / owlcollab/owltools

Handling of obo namespaces in golr loads

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#118 1 comment 0 reactions 1 assignee View on GitHub

@hdietze is already working on this.

Since Apr 27, 2015.

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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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