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

[Midori Harris]

Oh crud -- that page is out of date.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the look of it", kind; the others have been superseded in the OBO format 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
>>>
>>>
>>
>
>
>