[Obo-format] add xml data to obo format

4 views
Skip to first unread message

Savas

unread,
Feb 4, 2012, 11:51:56 AM2/4/12
to obo-f...@lists.sourceforge.net
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

------------------------------------------------------------------------------
Virtualization & Cloud Management Using Capacity Planning
Cloud computing makes use of virtualization - but cloud computing
also focuses on allowing computing to be delivered as a service.
http://www.accelacomm.com/jaw/sfnl/114/51521223/
_______________________________________________
Obo-format mailing list
Obo-f...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/obo-format

Chris Mungall

unread,
Feb 13, 2012, 5:43:56 PM2/13/12
to Savas, obo-f...@lists.sourceforge.net
Hi Savaş

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


------------------------------------------------------------------------------
Try before you buy = See our experts in action!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-dev2

Savaş TAKAN

unread,
Feb 15, 2012, 8:30:40 AM2/15/12
to Chris Mungall, obo-f...@lists.sourceforge.net, savas...@iyte.edu.tr
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

unread,
Feb 15, 2012, 11:12:28 AM2/15/12
to Savaş TAKAN, obo-f...@lists.sourceforge.net

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!
Reply all
Reply to author
Forward
0 new messages