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Re: Problem with cycles when transforming an *.obo file to rdf or owl.

From: Balhoff, Jim <balhoff@renci.org>
Date: Thu, 27 May 2021 14:18:56 +0000
To: Luis Gasco Sanchez <luisgascosanchez@gmail.com>
CC: "semantic-web@w3.org" <semantic-web@w3.org>
Message-ID: <48E42563-91FC-49C9-B038-231BFDF50788@renci.org>
Hi Luis,

This doesn’t address your question about cycles, but you can convert from .obo to any other OWL format using the ROBOT command line tool (http://robot.obolibrary.org) (I am a developer). Or you can open directly in Protege and save as a different format.

Best regards,
Jim


On May 27, 2021, at 9:48 AM, Luis Gasco Sanchez <luisgascosanchez@gmail.com<mailto:luisgascosanchez@gmail.com>> wrote:

Dear semwebers,

I am currently working with semantic similarity measures from rdf or owl files.

Due to project requirements, we are trying to transform an *.obo file to rdf or owl format. To do this we are reading the file with the python networkx library, and we have discovered that it has cycles (it is not an acyclic graph).

We have been thinking for a while about how to detect where there are cycles within the ontology, to try to remove them, and change the file format, without success. I was wondering if any of the experts in this semantic web network would know if there is a tool that allows us to easily detect where these cycles occur and try to fix them.

In case it is of interest, I attach the link where you can download the .obo file we are working with (https://zenodo.org/record/4722925#.YK-h1agzaUk).


Thanks in advance for your time!

Best regards,

Luis Gascó
Text Mining Research Engineer @TeMU
Barcelona Supercomputing Center (Spain)



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