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[bioontology-support] Extended GO file

Trish Whetzel whetzel at stanford.edu
Fri Jun 11 23:49:11 PDT 2010


Ok, Pradip can you load this into production?

Thanks,
Trish


On Jun 10, 2010, at 4:43 AM, Jane Lomax wrote:

> Nope, think it looks okay now. Thanks!
>
> Jane
>
> Trish Whetzel wrote:
>> 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
>>>
>
>
> -- 
> 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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