[Biopython-dev] OBO2OWL parser / converter

[Ed Cannon]

Hi Hilmar,

My OBO2OWL parser is implemented based on Tirmizi & Miranker’s paper titled:
“OBO2OWL: Roundtrip between OBO and OWL” (
www.cs.utexas.edu/~hamid/pub/tirmizi-obo2owl-tr-06-47.pdf<http://www.cs.utexas.edu/%7Ehamid/pub/tirmizi-obo2owl-tr-06-47.pdf>
)1.

After having looked at the link you sent me to the OBO2OWL mappings google
spreadsheet, it appears that there are some differences, which I’m looking
into at the minute.

Ref:

1. Syed Hamid Tirmizi and Daniel P Miranker. (2006). OBO2OWL: Roundtrip
between OBO and OWL. The University of Texas at Austin, Department of
Computer Sciences, Technical Report TR-06-47, October 2, 16 pages.


Cheers,

Ed

2009/8/31 Hilmar Lapp <hlapp at gmx.net>

> Hi Ed -
>
> is your converter operating in a way that is congruent with (or even
> utilizing) the mapping and the converter provided by the NCBO and Berkeley
> Ontology projects?
>
> http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page
>
> If not, I'm not sure how beneficial it is for users to have multiple and
> possibly conflicting mappings.
>
>        -hilmar
>
>
> On Aug 30, 2009, at 3:33 PM, Ed Cannon wrote:
>
>  Hi All,
>>
>> I would like to thank you guys for all your hard work and effort in making
>> biopython a great piece of open software.
>>
>> I would also like to introduce myself, my name is Ed Cannon, I am a
>> postdoc
>> at Cambridge University working in the fields of  chemo/bioinformatics and
>> semantic web technologies in the group of Peter Murray-Rust.
>>
>> Since a fair amount of my work involves ontologies, I have written an open
>> biomedical ontology (.obo) to web ontology language (.owl) converter. The
>> resultant file can be loaded and used from Protege. I was wondering if
>> this
>> software would be of any interest to  the biopython community? I have just
>> sent a pull request to biopython on github. The code is located at my
>> branch
>> on my account: http://github.com/eoc21/biopython/tree/eoc21Branch.
>>
>> Thanks,
>>
>> Ed
>> _______________________________________________
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>> Biopython-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biopython-dev
>>
>
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>