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[bioontology-support] Extended GO file

Trish Whetzel whetzel at stanford.edu
Wed Jun 9 14:08:59 PDT 2010


Hi all,

Are there any additional changes needed before loading GO Extended to  
the production version of BioPortal?

Trish


On May 26, 2010, at 8:48 AM, Chris Mungall wrote:

> 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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