[Ontology-editors] [Software-group] obo2obo failing

Tue Feb 10 10:27:36 PST 2009

Hi Tanya,

In the brave new world with tags, we don't have to put the suggested terms 
in comments at all any more. Instead, we set 'consider' and 'replaced_by' 
terms in OE (works in OE1 or OE2, as long as you save in OBO format 
version 1.2, which we all do anyway). Drag a 'live' term and drop it onto 
an obsolete term, and a little menu pops up with just the 'set consider 
term' and 'set replacement term' options.

The OBO format 1.0 files still use text comments, but they're generated by 
obo2obo magic.

I can demo sometime if that's still all confusing.

m

On Tue, 10 Feb 2009, Tanya Berardini wrote:

> Hi Midori,
>
> Thanks for fixing the documentation.  I'm still confused about how to add
> the comments to the file.  Can one do this in OE1?  If so, how?  Or is this
> a new feature of OE2?  If so, how does one do it there?  Or does this
> involve editing the flat file?
>
> Thanks,
>
> Tanya
>
> On Tue, Feb 10, 2009 at 3:37 AM, Midori Harris <midori at ebi.ac.uk> wrote:
>
>> I've fixed the go_write file (will commit later today, probably by the time
>> you get to email) and updated the documentation. Can't help with the innards
>> of obo2obo, unfortunately!
>>
>> m
>>
>>
>> On Mon, 9 Feb 2009, Chris Mungall wrote:
>>
>>
>>> OK, but I think we need to fix the obo file too. Can we do this with
>>> obo2obo or shall I write a perl script? Should be a 2-liner
>>>
>>> I'm thinking that perhaps the comments issue is not linked to obo2obo
>>> failing on production, as I can't reproduce Mike's error:
>>>
>>>  /Applications/OBO-Edit1/obo2obo -formatversion OBO_1_0
>>>> obo_format_1_2/gene_ontology.1_2.obo -writecomments -o
>>>> /tmp/gene_ontology.1_0.obo -runscript
>>>> ~/Eclipse/workspace/OBO-Edit/docs/examplescripts/strip_disjoint_and_replaced_by_tags.osl
>>>>
>>>> args[0] = |-formatversion|
>>>> args[1] = |OBO_1_0|
>>>> args[2] = |obo_format_1_2/gene_ontology.1_2.obo|
>>>> args[3] = |-writecomments|
>>>> args[4] = |-o|
>>>> args[5] = |/tmp/gene_ontology.1_0.obo|
>>>> args[6] = |-runscript|
>>>> args[7] =
>>>> |/Users/cjm/Eclipse/workspace/OBO-Edit/docs/examplescripts/strip_disjoint_and_replaced_by_tags.osl|
>>>> Allowdangling = false
>>>> Parse Done!
>>>> About to write files..., session object count = 28093
>>>> writePath = null
>>>> savePath = [/tmp/gene_ontology.1_0.obo]
>>>>
>>>
>>> This is on revision 1.188 of the file
>>>
>>> This is running the release version of obo2obo from OE1.1, using the osl
>>> script from svn head (the same script did not seem to be distributed with
>>> OE1). This is on OS X so I have a file
>>>        more /Applications/OBO-Edit1/obo2obo.vmoptions
>>>         -Xmx512M
>>>
>>> I believe this is OS X specific, I think for running obo2obo on linux the
>>> best thing to do is edit the obo2obo file and set -Xmx
>>>
>>> ...but I have a feeling we did this previously for obo2obo on
>>> production..?
>>>
>>> Might be an idea to check the actual version used into cvs
>>>
>>> On Feb 9, 2009, at 10:50 AM, Midori Harris wrote:
>>>
>>>  Oh crud -- that page is out of date. The only comments we type in
>>>> nowadays are the first, i.e. "this term was made obsolete because we didn't
>>>> like the look of it", kind; the others have been superseded in the OBO
>>>> format 1.2 files by the 'consider' and 'replaced_by' tags. For the 1.0
>>>> format files, comments are created by the obo2obo utility as Mike's cronjob
>>>> runs it.
>>>>
>>>> I'm on my way out now, but will work on that doc page tomorrow.
>>>>
>>>> m
>>>>
>>>> On Mon, 9 Feb 2009, Tanya Berardini wrote:
>>>>
>>>>  Is there something I could be doing to help sort this out?  I did
>>>>> several
>>>>> term obsoletions on both Thursday and Friday, following the protocol and
>>>>> format outlined in http://geneontology.org/GO.usage.shtml#obs.  I was
>>>>> editing and saving in OE1.101.
>>>>>
>>>>> Cheers,
>>>>>
>>>>> Tanya
>>>>>
>>>>> On Mon, Feb 9, 2009 at 9:19 AM, Chris Mungall <cjm at berkeleybop.org>
>>>>> wrote:
>>>>>
>>>>>
>>>>>> one possibility is that we have just gone over some kind of size
>>>>>> threshold.
>>>>>> If so we have to up the memory. This can be done directly in the
>>>>>> obo2obo
>>>>>> script
>>>>>>
>>>>>> however, I have a suspicion this may be some oddity to do with the
>>>>>> -writecomments required for 1.2 to 1.0. On friday some obsoletions in
>>>>>> the
>>>>>> ontology were accidentally made 1.0-style, this may be confusing
>>>>>> obo2obo.
>>>>>> Let's sort that out first and see if that works
>>>>>>
>>>>>> On Feb 9, 2009, at 9:12 AM, Mike Cherry wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>>>
>>>>>>> the obo2obo command is failing.  It worked last week, specifically it
>>>>>>> worked on version 1.185 of the gene_ontology.1_2.obo file.  With
>>>>>>> version
>>>>>>> 1.188 it doesn't work.
>>>>>>>
>>>>>>> Here is the command.
>>>>>>>
>>>>>>> obo2obo -formatversion OBO_1_0 /tmp/gene_ontology.1_2.obo
>>>>>>> -writecomments
>>>>>>> -o /tmp/gene_ontology.1_0.obo -runscript
>>>>>>>
>>>>>>> /share/go/bin/oboedit/current/docs/examplescripts/strip_disjoint_and_replaced_by_tags.osl
>>>>>>> ;
>>>>>>>
>>>>>>> The error message on failng is just:
>>>>>>>
>>>>>>> Exception in thread "main" java.lang.StackOverflowError
>>>>>>>
>>>>>>> It there something wrong with that OBO file?
>>>>>>>
>>>>>>> -Mike
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Software-group mailing list
>>>>>>> Software-group at geneontology.org
>>>>>>> http://fafner.stanford.edu/mailman/listinfo/software-group
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>
>
>
>