[Ontology-editors] cross products

[David Hill]

Hi Chris,

Just for clarity. Tanya and I are currently trying to change all the 
'during' terms to 'involved in' terms if there really is a part_of 
relationship. There are some cases in the GO where 'during' really means 
during. In those cases, the term means that the 2 processes just occur 
at the same time, but otherwise are unrelated. So the 'during' rule 
might not be such a good one.

We need to clean up these 'during' terms as well as 'by' terms and 'via' 
terms.

David
**
Chris Mungall wrote:
>
> The answer is it's a mix, depending on the xp set. *Ultimately* the 
> goal is to never have to parse a term again and to create xp defs 
> prospectively rather than retrospectively (we can still use obol for 
> *generation* of names, defs and synonyms, based on the newly created 
> xp def). We're nearer this goal with some xp sets rather than others.
>
> For example, the inter-organism regulation ones are quite hard, and we 
> probably have a few iterations to go. These iterations are quite 
> useful besides improving the grammar, as they clarify many parts of 
> the ontology, and also consistency of naming.
>
> The bp_xp_self which you are working on is a special case. There is a 
> long tail of terms that can be trivially parsed; for example "X during 
> Y" is translated to "an X that part_of Y". These have a high accuracy. 
> But there are other terms in your set for which I liberally applied 
> grammatical rules I knew to be less accurate. One such rule involved 
> using a relational adjective to guess an xp def, resulting in
>
> GO:0048007 ! antigen processing and presentation, exogenous lipid 
> antigen via MHC class Ib
> synonym: "exogenous lipid antigen processing and presentation via MHC 
> class Ib" ==>
> intersection_of: GO:0048003 ! antigen processing and presentation of 
> lipid antigen via MHC class Ib
> intersection_of: part_of GO:0042638 ! exogen
>
> (currently in the vetted file)
>
> This is quite obviously wrong!! I knew there would be many incorrect 
> ones in the bp_xp_self set from the outset, I did a first pass filter 
> myself, but probably not a good enough job. So in some ways your set 
> is the hardest as it has the highest ratio of nonsense. We should 
> perhaps invert the procedure for you, such that everything starts off 
> unvetted and must be explicitly vetted.
>
> The goal in this case is not to improve the obol rule: it's simply not 
> possible to get a 100% accurate xp def from terms such as this. Obol 
> is really for the low hanging fruit (LHF), the trivially composable 
> terms.
>
> We'll probably revisit the example above when we return to do 
> bp_xp_pro. For now, just delete erroneous xp defs such as the one above
>
> On Apr 6, 2009, at 5:27 AM, Jennifer Deegan (nee Clark) wrote:
>
>> Hi,
>>
>> David and I were editing some of my cross products together on Friday 
>> and we realised that we had different ideas of what we were meant to 
>> do.  I just wanted to check that we are on the right lines now, and 
>> Chris asked me to do it on list so we are all up to date on the 
>> correct scheme.
>>
>> I had assumed that the intersection files that Chris generated with 
>> obol  were a one-off, and that we were to hand edit the stanzas and 
>> put the resulting corrected intersection tags into the vetted file.
>>
>> David thought that the plan was for us to correct the live GO and 
>> feed back on obol's rules so that autogeneration would work correctly 
>> for all future runs.
>>
>> Which one is right?
>>
>> Thanks,
>>
>> Jen
>>
>>
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>
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-- 
David P. Hill, Ph.D.
Bioinformatics Scientist: Ontology Development
Gene Ontology Consortium
The Jackson Laboratory
www.geneontology.org
www.informatics.jax.org
tel:207-288-6430