[Ontology-editors] cross products

[Tanya Berardini]

And, yes, we promise to put the documentation up on the wiki.

:)

Tanya

On Mon, Apr 6, 2009 at 2:50 PM, David Hill <dph at informatics.jax.org> wrote:

> 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
>
>
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>



-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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