[Obo-format] add xml data to obo format

[Savas]

Dear Obo-discuss,

I am msc student at iyte. in my thesis, I need add xml data (
http://proteowizard.sourceforge.net/example_data/tiny.pwiz.1.1.mzML )
to psi-ms.obo (http://psidev.sourceforge.net/mi/psi-mi.obo) by obo
format library

I don't find way how to add xml data. if you help me, I am very happy.

Note : I attached needed files.

regards,

Savaş TAKAN
Research Assistant at İzmir Institute of Technology
Computer Engineer

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[Chris Mungall]

Hi Savaş

I'm not sure I understand the question. What do you mean by add xml to psi-ms.obo?

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[Savaş TAKAN]

I want to use obo for storage purpose ( storing xml data). for doing this, I think that instance  is suitable for this and obo have such as facility ( http://oboformat.googlecode.com/svn/branches/2011-11-29/doc/obo-syntax.html  ).

I want to use obo because of readability (turtle and rdf/xml are not good readable.) 

I changed obo format library for creating instance by  BNF and also solved xref problem ( i think it is bug).

but obo format don't have validation, reasoner. I need to solve these. do you have any suggestion ?

Savaş TAKAN
Research Assistant at İzmir Institute of Technology

Computer Engineer 

2012/2/14 Chris Mungall <cjmu...@lbl.gov>

[Chris Mungall]

Hi Savs,

It' still not clear what you mean by store xml data - do you want to just encode a big blob of xml - or do you want to take what is being modeled in that xml and model it directly in obo?

Regarding validation - you can syntatically validate your obo-format file using the reference obo2owl translator (http://oboformat.org)

For semantic validation, every obo file is an owl ontology, you can use any owl reasoner.

If you've found bugs in the spec or implementation can you post them to the tracker (or send the patches to me) thanks!