Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

Gene Ontology Parsing

John Day-Richter john.richter at aya.yale.edu
Mon Apr 17 12:58:47 PDT 2006


A note for the world about OBO file parsing...

The OBO-Edit source code contains a Java API for parsing OBO files. The 
OBO parsing API uses event-based parsers (like an XML SAX parser), so 
you don't even need to use the OBO-Edit datamodels. Of course, you can 
if you want to.

The OBO-Edit source is available in our CVS repository. For more 
information, go to http://sourceforge.net/projects/geneontology and 
click the CVS link.

	-John

On Apr 17, 2006, at 5:00 AM, Michael Moorhouse wrote:

> George,
> We - well, one of my colleagues / ex- Intern students - have been 
> using the API of GQ Zhang, see: http://www.bioinformatics.org/GO4J/ .
> I've seen the sub graphs it has created and I can find classes 
> (methods?) called things like buildSubGraph, getPath2Root, 
> getPath2Node in the Java documentation I recognise from my Perl 
> go-perl API experiences building parts of our prototype.
> Personally all my experience is with Perl & go-perl API though.
> Michael M.
>
>> Hi,
>> My name is George Papachristoudis, I am a student at Electrical and 
>> Computer Engineering Department of Aristotle University, 
>> Thessaloniki, Greece.
>>  I have a problem concerning the parsing of Gene Ontology which is a 
>> part of my undergraduate research.
>>  I am looking for a Java API Package (and its  accompanying help 
>> documentation) in order to parse and edit Gene Ontology .obo or flat 
>> files via Java commands.
>>  In other words, I would like to find all the paths of a GO term up 
>> to the root (one of the three ontologies) as shown in the interfaces 
>> DAG- and OBO-Editor. However, the problem is that I have to do this 
>> job via Java commands (not manually as is done to both editors).
>> So, I have to find a corresponding Java API Package.
>>  Is there anyone who can shed a light upon my problem?
>>  Thank you in advance,
>> George Papachristoudis
>
>
>
> -- 
> -
> =====================================================
> Dr. Michael J Moorhouse
> Department of Virology,
> Office Ee 17.14
> Dr. Molewaterplein 50,
> Erasmus MC
> 3000 DR ROTTERDAM
> The Netherlands
> Tel: +31 10 408 71 02
> Email: m.moorhouse at erasmusmc.nl
> =====================================================
>
>
> --
> This message is from the GOFriends moderated mailing list.  A list of 
> public
> announcements and discussion of the Gene Ontology (GO) project.
> Problems with the list?           E-mail: 
> owner-gofriends at geneontology.org
> Subscribing   send   "subscribe"   to   
> gofriends-request at geneontology.org
> Unsubscribing send   "unsubscribe"  to  
> gofriends-request at geneontology.org
> Web:          http://www.geneontology.org/


--
This message is from the GOFriends moderated mailing list.  A list of public
announcements and discussion of the Gene Ontology (GO) project.
Problems with the list?           E-mail: owner-gofriends at geneontology.org
Subscribing   send   "subscribe"   to   gofriends-request at geneontology.org
Unsubscribing send   "unsubscribe"  to  gofriends-request at geneontology.org
Web:          http://www.geneontology.org/



More information about the go-friends mailing list