How To Parse Data From An Owl File
1
3
Entering edit mode
10.1 years ago
halo22 ▴ 280

Hello, I am working on a project and I need to use the cell line ontology(CLO). I tried accessing CLO using protege but faced problems accessing it, I wrote an email to the creator of the cell line ontology to figure out the problem but didn't get any response. I was wondering if there is a way to parse the OWL file using Perl, I tried to convert the OWL to OBO using Perl OWL to OBO converter but couldn't get all the data. Is there a way to parse the OWL based ontology.

perl ontology • 5.4k views
ADD COMMENT
1
Entering edit mode

any XML parser can parse the rdf/xml file. The question is, what do you want to achieve with this ontology ?

ADD REPLY
0
Entering edit mode

@Pierre Lindenbaum: I am try to extract all the cell line names.

ADD REPLY
1
Entering edit mode
10.0 years ago

Protege, as you mentioned, is indeed the standard way to parse OWL files. Perhaps you should tell us the problem you ran into while using it or post it to their mailing list.

If that doesn't work, you can also go a level lower and query the RDF which OWL builds upon. This you usually do with a SPARQL query, that is similar to SQL.

Of course, there is also the possibility of going on even lower levels and using and XML library or direct text parsing. However, I would (1) explain what problem you have using Protege and (2) if that doesn't work query it with using SPARQL.

ADD COMMENT

Login before adding your answer.

Traffic: 2228 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6