Question: How To Parse Data From An Owl File
3
gravatar for halo22
8.8 years ago by
halo22180
Indianapolis, IN
halo22180 wrote:

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 • 4.5k views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 8.8 years ago by halo22180
1

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

ADD REPLYlink written 8.8 years ago by Pierre Lindenbaum133k

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

ADD REPLYlink written 8.8 years ago by halo22180
1
gravatar for Michael Schubert
8.7 years ago by
Cambridge, UK
Michael Schubert7.0k wrote:

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 COMMENTlink written 8.7 years ago by Michael Schubert7.0k
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