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[bioontology-support] Extended GO file

Jane Lomax jane at ebi.ac.uk
Wed May 26 05:46:26 PDT 2010


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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