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[bioontology-support] Extended GO file

Jane Lomax jane at ebi.ac.uk
Thu Jun 10 04:43:29 PDT 2010


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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