Re: [Obo-discuss] -simple vs -basic

[Chris M. <cjm...@lb...>]

On Jun 10, 2013, at 9:05 AM, David Osumi-Sutherland wrote:

> Hi Chris,
> 
> Didn't realise the OBO 1.4 spec had this doc.  Much clearer to me now.  Looks like generating -basic.obo versions will always involve some ontology-dependent spec.
> 
> I think it is worth generating -basic.obo versions of Drosophila ontologies in addition to the -simple ones we generate right now.   I can probably do this simply by filtering out disjoints + certain relationship types from the -simple.obo version.   Easy enough to write my own code for this, but do you have any code used in generation of the go-basic.obo version you can share?

I wouldn't recommend using or adapting it:
http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/software/utilities/filter-obo-for-standard-release.pl

This script will eventually be replaced by code that uses the OWLAPI and associated tooling. (We have managed to eliminate a lot of dependencies on obo format within the internal GO infrastructure, but there still ad-hoc scripts that have to be replaced)

There is a convenience wrapper for this in the OWLTools command line. You can do something like this:

	owltools fbbt-simple.owl --make-subset-by-properties [OBJECT PROPERTY LIST] //  -o -f fbbt-basic.obo

For a general guide on how to use owltools to do ontology processing on the command line:

	http://code.google.com/p/owltools/wiki/CommandLineExamples

> 
> Cheers,
> David
> 
> 
> On 10 Jun 2013, at 16:46, Chris Mungall wrote:
> 
>> 
>> Hi David
>> 
>> The reason Oort uses a different suffix than "basic" is that in obo-format "obo-basic" is reserved as a name for a very restricted subset of obo-format
>> 
>> 	http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#6.2
>> 
>> This is the subset that is implicitly expected by what is probably the majority of tools used to do things with GO, as well as tools such as the current version of the OLS.
>> 
>> The simplification step that Oort performs is not guaranteed to produce an ontology that conforms to "obo basic". Custom processing steps need to be added. For example, with GO "has part" is removed to ensure the DAG formed by all relationships is acyclic.   This is also removed because for GO the basic file is further simplified such that annotation propagation is meaningful.
>> 
>> This is not idea from the point of view of users using the Obo ontology release tool (Oort) to make ontology releases, more on this later.
>> 
>> On Jun 10, 2013, at 4:18 AM, David Osumi-Sutherland wrote:
>> 
>>> Hi all,
>>> 
>>> Quick question about the naming of derivative release files.
>>> 
>>> I'm in the process of setting up new repos for the various Drosophila related ontologies and working on PURL redirects for the various flavours of release file.  I'd like the nomenclature to follow the system that oort uses so that I can easily automate generation of releases.   Oort currently rolls a vanilla, pre-reasoned OBO file lacking imports called <foundry_namespace>-simple.obo  (e.g. fbbt-simple.obo).  But I gather GO plans to call their release file GO-basic.obo and I've noticed that the cell ontology have also moved to this naming scheme (https://cell-ontology.googlecode.com/svn/trunk/src/ontology/cl-basic.obo).
>>> 
>>> I'm happy to use this naming system instead, but I'd like a decision on a standard ASAP + centralised documentation of this and other standard flavours.  I'm finishing up a couple of papers right now on Drosophila related ontologies and it is important that these file names are standardised before they are submitted (deadline 21st June).
>>> 
>>> Cheers,
>>> David
>>> 
>>> 
>>> David Osumi-Sutherland, PhD
>>> Ontologist at FlyBase & Virtual Fly Brain
>>> Department of Genetics, University of Cambridge,
>>> Downing Street, Cambridge, CB2 3EH, UK
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>>> http://www.virtualflybrain.org
>>> 
>>> 
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