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[bioontology-support] Extended GO file

Chris Mungall cjm at berkeleybop.org
Wed May 26 08:48:51 PDT 2010


Hi Pradip

You should treat these just the same way you treat equivalence axioms  
to intersection constructs in OWL. GO has the inferred links  
materialized. SO is available in two versions, one with the inferred  
links materialized.


On May 26, 2010, at 5:46 AM, Jane Lomax wrote:

> Hi Pradip - it's probably best not to show the intersection_of  
> information in the visualization. Currently in GO the intersection  
> info is usually redundant with the asserted relationships - this can  
> mean the genus term is the same as the is_a, or that the genus term  
> is much more general than the is_a - either way it would be  
> potentially confusing to visualize both in the same graph. Not sure  
> if the OLS developer is aware of this - he's here at EBI so I'll  
> check next time I see him.
>
> Jane
>
> Kanjamala, Pradip P. wrote:
>>
>> Hi Jane,
>> I was investigating how the intersection_of gets represented on the
>> Ontology Lookup service to see if there were other ways of  
>> representing
>> the information.
>> I found the sequence ontology (SO) also has intersection_of used  
>> within
>> the ontology. The term SO:0000034 has an intersection_of defined  
>> for it.
>> It looks like this in the OBO file:
>>
>> [Term]
>> id: SO:0000034
>> name: morpholino_oligo
>> def: "Morpholino oligos are synthesized from four different  
>> Morpholino
>> subunits, each of which contains one of the four genetic bases (A,  
>> C, G,
>> T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of
>> these four subunit types are joined in a specific order by non-ionic
>> phosphorodiamidate intersubunit linkages to give a Morpholino."
>> [http://www.gene-tools.com/]
>> synonym: "morpholino oligo" EXACT []
>> is_a: SO:0001247 ! implied link automatically realized !  
>> synthetic_oligo
>> intersection_of: SO:0001247 ! synthetic_oligo
>> intersection_of: has_quality SO:0001183 ! Morpholino
>>
>> The visualization is
>> http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=SO&termId=SO%3A00
>> 00034&termName=morpholino_oligo
>>
>> Would it be fine if we represented the information in a similar  
>> fashion
>> ie,
>> We would define the relations
>> SO:0000034 is_a SO:0001247
>> SO:0000034 has_quality SO:0001183
>>
>> Regards,
>> Pradip
>>
>> -----Original Message-----
>> From: Jane Lomax [mailto:jane at ebi.ac.uk]
>> Sent: Thursday, May 20, 2010 4:44 AM
>> To: Trish Whetzel
>> Cc: Kanjamala, Pradip P.; support
>> Subject: Re: Extended GO file
>>
>> Hi Trish and Pradip -
>>
>> The term details panel looks fine.
>>
>> For the visualization, I would only ever show the asserted links (in
>> this example the isa and regulates links) rather than the  
>> intersection
>> links, if that makes sense. So in the fact the visualization you  
>> have it
>>
>> here:
>> http://stage.bioontology.org/visualize/42780/?conceptid=GO%3A0080050#vis
>> ualization
>>
>> thanks,
>>
>> Jane
>>
>> Trish Whetzel wrote:
>>
>>> Hi Jane,
>>>
>>> The ontology loader is now updated and the cross-product information
>>> is displayed in the term details panel:
>>> http://stage.bioontology.org/visualize/42780/?conceptid=GO 
>>> %3A0080050.
>>>
>>
>>
>>> I included Pradip, the developer working on this, in the email  
>>> thread
>>> to help fast-track discussions.
>>>
>>> One question that came up was what to display for the visualization
>>> panel
>>>
>>>
>> (http://stage.bioontology.org/visualize/42780/?conceptid=GO%3A0080050#vi
>> sualization)
>>
>>> if a user clicks on "biological regulation AND regulates SOME seed
>>> development" and selects "Show Hierarchy to Root".
>>>
>>> Trish
>>>
>>>
>>> On May 4, 2010, at 5:15 AM, Jane Lomax wrote:
>>>
>>>
>>>> Hi Trish - sorry, my mistake, I had it set to 'show hierarchy to
>>>> root' rather than 'neighbourhood network'. That display looks spot
>>>>
>> on.
>>
>>>> There are another set of tags  - intersection_of - in the GO ext  
>>>> file
>>>>
>>
>>
>>>> that may be of interest for display. These comprise the formal
>>>> definition of the term (we call them cross-products - I think it
>>>> means the same as intersectionOf in OWL). Not all GO terms have  
>>>> these
>>>>
>>
>>
>>>> tags yet - at the moment it's only the regulation terms - but I  
>>>> think
>>>>
>>
>>
>>>> people would be pretty interested to see them if there's a suitable
>>>> way of displaying them. Here's an example stanza:
>>>>
>>>> [Term]
>>>> id: GO:0010029
>>>> name: regulation of seed germination
>>>> namespace: biological_process
>>>> def: "Any process that modulates the frequency, rate or extent of
>>>> seed germination." [GOC:sm]
>>>> is_a: GO:0048580 ! regulation of post-embryonic development
>>>> intersection_of: GO:0065007 ! biological regulation
>>>> intersection_of: regulates GO:0009845 ! seed germination
>>>> relationship: regulates GO:0009845 ! seed germination
>>>>
>>>> cheers,
>>>>
>>>> Jane
>>>>
>>>> Trish Whetzel wrote:
>>>>
>>>>> Hi Jane,
>>>>>
>>>>> For the term GO:0071013, I do see 'has_part' in both the term
>>>>> details and visualization tabs (screenshots attached).  Do you  
>>>>> have
>>>>> an image of how you expected this to be displayed?
>>>>>
>>>>> I have reported the error in display of 'Equivalent Class' and  
>>>>> that
>>>>> the regulates relationships are missing. However, they are  
>>>>> displayed
>>>>>
>>
>>
>>>>> in the production version using the regular file:
>>>>>
>>>>>
>> http://bioportal.bioontology.org/visualize/42733/?conceptid=GO%3A0031341
>> .
>>
>>>>> Trish
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Apr 30, 2010, at 4:57 AM, Jane Lomax wrote:
>>>>>
>>>>>
>>>>>> Hi Trish - it doesn't seem to be showing any of the has_part
>>>>>> relations, e.g GO:0071013 has_part GO:0000974 isn't appearing
>>>>>>
>>>>>> Actually, it doesn't seem to be showing the regulates  
>>>>>> relationships
>>>>>>
>>
>>
>>>>>> either and they're just in the regular file e.g. GO:0031341
>>>>>> regulates GO:0001906
>>>>>>
>>>>>> As an aside, what does Equivalent Class mean?
>>>>>>
>>>>>> thanks,
>>>>>>
>>>>>> Jane
>>>>>>
>>>>>>
>>>>>>
>>>>>> Trish Whetzel wrote:
>>>>>>
>>>>>>> Hi Jane,
>>>>>>>
>>>>>>> We have loaded the extended GO file to the Staging server of
>>>>>>> BioPortal. Would you mind reviewing and providing comments? It  
>>>>>>> can
>>>>>>>
>>
>>
>>>>>>> be viewed at: http://stage.bioontology.org/visualize/42684
>>>>>>>
>>>>>>> Trish
>>>>>>>
>>>>>>>
>>>>>> -- 
>>>>>> Dr Jane Lomax
>>>>>> GO Editorial Office
>>>>>> EMBL-EBI
>>>>>> Wellcome Trust Genome Campus
>>>>>> Hinxton
>>>>>> Cambridgeshire, UK
>>>>>> CB10 1SD
>>>>>>
>>>>>> p: +44 1223 492516
>>>>>> f: +44 1223 494468
>>>>>>
>>>>>>
>>>> -- 
>>>> Dr Jane Lomax
>>>> GO Editorial Office
>>>> EMBL-EBI
>>>> Wellcome Trust Genome Campus
>>>> Hinxton
>>>> Cambridgeshire, UK
>>>> CB10 1SD
>>>>
>>>> p: +44 1223 492516
>>>> f: +44 1223 494468
>>>>
>>>>
>>
>>
>>
>
>
> -- 
> Dr Jane Lomax
> GO Editorial Office
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridgeshire, UK
> CB10 1SD
>
> p: +44 1223 492516
> f: +44 1223 494468




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