[Go] 'binding issues' item listed on the GO Consortium meetingagenda
D'Eustachio, Peter
Peter.D'Eustachio at nyumc.org
Mon Mar 23 15:21:44 PDT 2009
I looked. Glucose is_a_function_parent of glucose 6-phosphate. The only
is_a parent is glucopyranose (which is OK, I think), so Chris gets is_a
ontology navigation AND Harold gets chemical sanity, this time.
-----Original Message-----
From: go-bounces at genome.stanford.edu
[mailto:go-bounces at genome.stanford.edu] On Behalf Of Chris Mungall
Sent: Monday, March 23, 2009 6:08 PM
To: hjd at informatics.jax.org
Cc: GO LIST
Subject: Re: [Go] 'binding issues' item listed on the GO Consortium
meetingagenda
On Mar 23, 2009, at 2:25 PM, Harold Drabkin wrote:
> From one of Jim's earlier comments, I think a big problem is
> parentage: if Chebi has a relationship between, say glucose-6
> phosphate and glucose (child parent or something) , and we have a
> protein that binds glucose-6-phosphate, we don't want to imply any
> binding to glucose ( it might, but it might not).
I think it's very important to mention the relationship type here. If
the relation is is_a, then I disagree
If CHEBI says X is_a Y
Then we are *forced* to accept that X binding is_a Y binding. If we
don't like this we can always request CHEBI change the relation.
As I mentioned previously, with CHEBI's other relations all bets are
off. It is simplest to ignore these for now (in future we will want to
tackle how binding works in combination with part_of relations, but we
don't need to complicate the picture for now)
This is extremely important. We should be working with CHEBI, not
making redundant conflicting statements.
> Chebi may have relationships between, for example, for ATP, ADP,
> and AMP, but a protein may bind very specifically to one of them.
If P binds specifically to X, and X is_a Y, then P binds specifically
to Y. this is built in to the is_a relation, there is absolutely no
getting around this.
Fortunately CHEBI does not make an is_a relation directly between any
of these terms. Instead they are all is_a children of "adenosine 5'
phosphate"
http://obofoundry.org/obo/CHEBI:15422+CHEBI:16761+CHEBI:16027.png
(CHEBI calls this by the plural "adenosine 5' phosphate*s*", which is
wrong and will need to be changed in CHEBI. They are open to this)
This means that if P binds to an ATP molecule, it is also the case
that P binds to an adenosine 5' phosphate molecule. Does this seem
reasonable?
> And I suppose there are many cases where a protein can bind related
> chemicals with different non-zero affinities, so that if one
> annotated binding to one there may be a good chance it would bind
> another. Should there be a rule in how one interprets the annotation
> line so as to not read any relationships among things in the target
> ontology to the actual single term designated as the target for the
> GO annotation? (hope this is clear).fcc
I think that so long as the is_a relations in the external ontology
are correct, there is no danger of inferring false positives.
This conservative approach means that we may have false negatives, but
that's always the case with GO.
>
> Harold
>
>
>
> Chris Mungall wrote:
>> I have added this example to the col16 page:
>>
http://wiki.geneontology.org/index.php/Annotation_Cross_Products#Binding
>>
>> I think the use of CHEBI in annotation-time cross-products poses
>> specific problems
>>
>> * It's often not clear (to me anyway) which CHEBI term to use.
>> Jim's example (linked to in the above page) has "PEP binding".
>> CHEBI has two terms in which PEP is a RELATED synonym:
>> "phosphoenolpyruvic acid" and "phosphoenolpyruvate". neither of
>> these are defined in the traditional OBO sense. It's not clear if
>> the InChi strings count as they are under RELATED synonym too.
>>
>> (Jim/Debbie - since you provided this example can you comment on
>> this, I'm too lazy to read the PMID, thanks!)
>>
>> * Many CHEBI terms do not have is_a parents. It's extremely
>> important for there to be correct is_a parentage. For example, if
>> the post-composed term is "phosphoenolpyruvic acid binding" then
>> this can be inferred to be a subtype of GO:0042301 ! phosphate
>> binding, based on is_a parentage in CHEBI.
>>
>> * CHEBI has other relations, but their semantics are unclear
>>
>> This gives me reason for caution. However, I am optimistic - CHEBI
>> are willing to fix these things in their ontology.
>>
>> In particular I would propose the following guidelines for use of
>> CHEBI in annotation time cross-products
>>
>> * The CHEBI term *should* preferably have a definition. The GO
>> annotator who uses a CHEBI ID in col 16 should propose a definition
>> on the CHEBI tracker
>> * The CHEBI term *must* have is_a ancestry to CHEBI:24431 !
>> molecular structure. If a GO annotator wishes to use a CHEBI ID in
>> col 16, and there is no such ancestry, the annotator should send a
>> request on the CHEBI tracker
>> * The CHEBI term *should* have the correct synonym assignment. For
>> example, if the GO curator thinks the correct post-composed term is
>> "PEP binding" then PEP *must* be either an EXACT synonym or a
>> primary term name.
>>
>> On Mar 18, 2009, at 7:53 AM, Jim Hu wrote:
>>
>>> Hi Pascale,
>>>
>>> I think this is also potentially related to the discussion of
>>> whether/how the cross-product system can/should be used for post-
>>> composition of binding annotations.
>>>
>>> Jim
>>>
>>> On Mar 18, 2009, at 8:46 AM, Pascale Gaudet wrote:
>>>
>>>> Hi Emily,
>>>>
>>>> I am attaching the summary Debby Siegele put together about some
>>>> of the issues we've been having with substrate binding. (This was
>>>> sent to the ref genome list).
>>>>
>>>> Pascale
>>>>
>>>> Emily Dimmer wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I noticed that the GO Consortium meeting agenda for Monday 30th
>>>>> March has a item entitled 'binding issues'. However there is no
>>>>> indication of who added this topic.Could someone please give a
>>>>> bit more detail about why this item has been added?
>>>>>
>>>>> I do agree that it is an area that is probably worth discussing
>>>>> (particularly with regards ISSing 'protein binding'
>>>>> annotations). Its just that I feel that agenda items which deal
>>>>> with annotation issues are more easily resolved when the meeting
>>>>> participants have had advanced notice as to the background of
>>>>> the discussion topic, so to be able to review their database's
>>>>> annotation sets/collect their thoughts!
>>>>>
>>>>> Thanks,
>>>>> Emily
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------
>>>>> Emily Dimmer Ph.D.
>>>>> GOA Coordinator
>>>>> EMBL-EBI
>>>>> Wellcome Trust Genome Campus
>>>>> Hinxton
>>>>> Cambridge CB10 1SD, U.K.
>>>>> Tel: +44 1223 494654
>>>>> Fax: +44 1223 494468
>>>>> email: edimmer at ebi.ac.uk
>>>>> URL: http://www.ebi.ac.uk/goa
>>>>>
>>>>> _______________________________________________
>>>>> Go mailing list
>>>>> Go at geneontology.org
>>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>>>
>>>>>
>>>> <
>>>> BindingTermDocumentation
>>>> .doc>_______________________________________________
>>>> Go mailing list
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>>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>> =====================================
>>> Jim Hu
>>> Associate Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>>
>>>
>>> _______________________________________________
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>>
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