[Ontology-editors] filtering of .obo files for the main release

[Chris Mungall]

done

On Feb 5, 2009, at 4:19 PM, Mike Cherry wrote:

> I'll put it back on you to get someone to update the README to  
> clearly say that gene_ontology_edit.obo, editors/ 
> gene_ontology_write.obo and obo_format_1_2/gene_ontology_ext.obo are  
> the same.
>
> Here is what the README says now.
>
> !version: $Revision: 1.1 $
> !date: $Date: 2006/10/12 04:15:01 $
> go/ontology contents documentation
>
> Gene Ontology - The Ontologies
> ---------------------------------------------
>
> The current format used by the Gene Ontology Consortium (GOC) is
> called OBO v1.2.  The file corresponding to this format is
> gene_ontology_edit.obo.  The specification for OBO v1.2 is provided at
> the following location:
>
>  http://www.geneontology.org/GO.format.obo-1_2.shtml
>
> The other files in this directory contain older formats that were
> previously used by the GOC.  The specifications of the older formats,
> and others used by the GOC, can be found at:
>
>  http://www.geneontology.org/GO.format.shtml
>
> The gene_ontology.obo file is OBO v1.0 format.  It was used by GOC
> from February 14, 2004 to October 11, 2006.  This file is recreated
> daily from the OBO v1.2 file.
>
> The other files represent the original so called "flat file" format
> used by the GOC between June 16, 1999 and February 14, 2004.  The
> ontologies were split into separate files: process.ontology,
> function.ontology, and component.ontology.  The term definitions were
> also in a separate file named GO.defs.  These files are recreated once
> a week from the OBO v1.2 file.
>
> For help please contact the GOC at gohelp at geneontology.org
>
>
>
>
>
>
>
>
> On Feb 5, 2009, at 3:19 PM, Chris Mungall wrote:
>
>> here's the rationale for the 3 files
>>
>>> obo_format_1_2/gene_ontology_ext.obo
>>
>> cutting edge users.
>>
>>>
>>> obo_format_1_2/gene_ontology.1_2.obo
>>
>> the default (safe) file, where most go file consumers should go
>>
>>> obo_format_1_0/gene_ontology.1_0.obo
>>
>>
>> legacy. I wouldn't be sorry to see it go but we should give notice.  
>> Unfortunately this was necessary at the time as 1.2 introduced non- 
>> backwards compatible changes
>>
>> On Feb 5, 2009, at 2:59 PM, Mike Cherry wrote:
>>
>>> Chris,
>>>
>>> The script now runs everyday at 7:30 pm as part of the other  
>>> conversions.  All these commands are in a wrapper script not  
>>> separated into individual cron jobs.  All the errors go to one log  
>>> file.  The new file (obo_format_1_2/gene_ontology_ext.obo) is now  
>>> in CVS, of course for now it is the same as obo_format_1_2/ 
>>> gene_ontology.1_2.obo.
>>>
>>> We have three OBO1.2 files that are the same:
>>> gene_ontology_edit.obo
>>> editors/gene_ontology_write.obo
>>> obo_format_1_2/gene_ontology_ext.obo
>>>
>>> One of the reduced OBO 1.2:
>>> obo_format_1_2/gene_ontology.1_2.obo
>>>
>>> And two of the OBO1.0:
>>> gene_ontology.obo
>>> obo_format_1_0/gene_ontology.1_0.obo
>>>
>>> Do we really need all these copies?  Seems we should delete some  
>>> of these.  We can report the deletion to GOFRIENDS and state the  
>>> change in the README file in each directory.  For me the big  
>>> concern is all the files have difference CVS versions.  Some one  
>>> looking for a file will be very confused.
>>>
>>> -Mike
>>>
>>>
>>>
>>> On Feb 4, 2009, at 6:05 PM, Chris Mungall wrote:
>>>
>>>>
>>>> I have moved this script to the main GO cvs and renamed it:
>>>> 	./software/utilities/filter-obo-for-standard-release.pl
>>>>
>>>> I have tested it and it seems fine.
>>>>
>>>> Updated the docs:
>>>> 	http://wiki.geneontology.org/index.php/Ontology_publishing_pipeline_2009
>>>>
>>>> So we can make the switch any time prior to the links going live.
>>>>
>>>> I can't see the crontab but I imagine it's just a change from  
>>>> something like
>>>>
>>>> 	cp ontology/editors/gene_ontology_write.obo ontology/ 
>>>> obo_format_1_2/gene_ontology.1_2.obo
>>>> 	...
>>>>
>>>> to
>>>>
>>>> 	cp ontology/editors/gene_ontology_write.obo ontology/ 
>>>> obo_format_1_2/gene_ontology_ext.obo
>>>> 	filter-obo-for-standard-release.pl ontology/obo_format_1_2/ 
>>>> gene_ontology_ext.obo > ontology/obo_format_1_2/gene_ontology. 
>>>> 1_2.obo
>>>>
>>>> it's a little chatty on STDERR, we can pipe it to a file or /dev/ 
>>>> null, doesn't really matter
>>>> 	
>>>>
>>>> On Jan 27, 2009, at 1:48 PM, Mike Cherry wrote:
>>>>
>>>>> Looks fine.  The current cron job running at 7:30 pm.
>>>>>
>>>>> -Mike
>>>>>
>>>>> On Jan 27, 2009, at 11:40 AM, Chris Mungall wrote:
>>>>>
>>>>>> Hi Mike
>>>>>>
>>>>>> The other week Ben, David and Tanya discussed a change to the  
>>>>>> obo publishing pipeline, introducing a filtering step to shield  
>>>>>> the majority of users from certain extensions to the GO, whilst  
>>>>>> at the same time allowing power-users a means of accessing the  
>>>>>> extended GO outside the editors space.
>>>>>>
>>>>>> We will probably discuss this tomorrow, but we will also need  
>>>>>> to coordinate on the cron changes required. I have written up  
>>>>>> the proposed flow here:
>>>>>> http://wiki.geneontology.org/index.php/Ontology_publishing_pipeline_2009
>>>>>
>>>>>
>>>
>>>
>
>