dictyBase / Modware-Loader

Various data munging and loading scripts for genome database

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Loading obo with terms from other ontology #163

Closed cybersiddhu closed 8 years ago

cybersiddhu commented 8 years ago

And obo file may contain terms imported from other ontologies. Those imported terms will conflict/break the loader when those ontologies are going to be loaded separately. They cannot co-exist in chado. The possible solution is to identify those imported terms and filter them during the load. However, the question is how to identify them ?

162

cybersiddhu commented 8 years ago

Ideas

Run owltools for owl2obo conversion and selectively do not import the ontologies.
During the loading, skip any terms from imported ontology.

cybersiddhu commented 8 years ago

A SPARQL command to list imported term.

PREFIX obo-term: <http://purl.obolibrary.org/obo/>
SELECT ?s ?subclass ?label
FROM <http://purl.obolibrary.org/obo/merged/RO>
{
?s a owl:Class .
?s rdfs:subClassOf ?subclass .
?s rdfs:label ?label .
 FILTER regex(?s, "(PATO|GO|CARO|ENVO|CL)")
}

Executed in ontobee

cybersiddhu commented 8 years ago

There is nothing much that needed to be done with the Modware-loader itself. It can be fixed by running owltools with correct set of options. For the fix with RO the commit is here