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[bioontology-support] Extended GO file

Kanjamala, Pradip P. Kanjamala.Pradip at mayo.edu
Thu May 20 09:46:19 PDT 2010


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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