#1184 Question about MF filter in OBO Edit 2.3

closed-works-for-me
nobody
OBO-Edit (934)
5
2012-10-15
2012-10-12
No

Hi all,
I want to do MF filter with OBO Edit
v2.3 like this mail shows:
https://mailman.stanford.edu/pipermail/go-helpdesk/2011-December/004790.html
and im not succeding. Have you got any idea of making MF filter on this new
version? Thanks in advanced,
Antonela

Discussion

1 2 > >> (Page 1 of 2)
  • Heiko Dietze
    Heiko Dietze
    2012-10-12

    Hello,

    The v2.3 beta release should not behave differently to 2.2.
    Could you please describe which part of the MF filter approach does not work for you or where it fails? Are there any exceptions in the OBO-Edit log file (oboedit_config/log)?

    Thank you.

     
  • Heiko Dietze
    Heiko Dietze
    2012-10-12

    • labels: 844902 --> OBO-Edit
    • milestone: 898738 -->
     
  • Ive downloaded this ontology from The Gene Ontology website: http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo
    I tried to load it in oboEdit and i found this error:
    Load Error, line 20063 Expected ".
    org.obo.dataadapter.OBOParseEngine.translateException(OBOParseEngine.java:1451)
    org.obo.dataadapter.OBOParseEngine.translateAndThrow(OBOParseEngine.java:1443)
    org.obo.dataadapter.OBOParseEngine.doParse(OBOParseEngine.java:407)
    org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:48)
    org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:72)
    org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270)
    org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43)
    org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60)
    org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137)
    org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79

    Thanks so much,
    Antonela

     
  • Also i tried with the file i attach here, that file i loaded without problems, but when i made the step in the email i said before, nothings happens, the MF filter was not made. Thanks you a lot.

     
  • I couldnt upload the file, too heavy. If you have an email address ill send it to you.

     
  • Heiko Dietze
    Heiko Dietze
    2012-10-13

    Hello,

    I just tested the behavior (see original link to e-mail archive). For the current GeneOntology, it worked perfectly fine. So I can only guess whats going wrong:

    * The correct file adapter to load the gene_ontology_ext.obo is the 'OBO Flat file adapter' with default settings
    * If there is a syntax error, try re-downloading the file and try again.
    * The filter panel is only available in the 'Save As' Advanced Panel
    * Did you select an output file?

    * gene_ontology_ext.obo: This is the extended version of the GeneOntology. It contains more relationships, than the 'normal' GO release file. This simpler GO file is available here:
    http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo

    Using the simpler GO, the description on how to extract the MF branch in OBO-Edit works fine.

    If you use the extended GO, you need to modify the link filter so that it excludes any link that isn't of Type is_a.

     
  • Thanks for the link to the simpler ontology. Ive download and loaded it without problem, but, again, when i do the steps in the email, the ontology graph remanins the same, it shows the 3 branches instead of only 1: MF. What's wrong?? Thank you a lot.

     
  • Heiko Dietze
    Heiko Dietze
    2012-10-13

    Hello,

    the filter manipulates, what is written during the 'save as' operation. It does not change the currently loaded ontology in OBO-Edit. For practical reasons you should save this filtered ontology in a different file, than the original (e.g. mf.obo).

    Does your filtered 'Save as' operation create such a file?

     
  • Perfect! I saved the profile, and loaded it , and it showed only the branch of MF. Thank you so much for your dedication and answer!

     
  • Heiko Dietze
    Heiko Dietze
    2012-10-15

    The user has successfully created the new ontology file containing the requested subset.

     
1 2 > >> (Page 1 of 2)