[Transport] [Ontology-editors] calcium ion transport question

[Chris Mungall]

On Feb 6, 2009, at 11:47 AM, Pankaj Jaiswal (OSU) wrote:

>
>
> Tanya Berardini wrote:
>> On Fri, Feb 6, 2009 at 11:04 AM, Chris Mungall <cjm at berkeleybop.org  
>> <mailto:cjm at berkeleybop.org>> wrote:
>>        Actually, we already have a term for 'calcium ion transport  
>> into
>>        cytosol' (GO:0060402), which does not have the negative
>>        regulation of sequestering parentage that GO:0051209 has. So
>>        I'll make GO:0060402 an additional parent of GO:0051209.  
>> That's
>>        consistent with everything here and in the ontology.
>>    is_a parent?
>>    That means GO:0060402 will have an only is_a child, which invites
>>    the question, what kinds of GO:0060402 ! calcium ion transport  
>> into
>>    cytosol are not kinds of GO:0051209 ! release of sequestered  
>> calcium
>>    ion into cytosol?
>> Legend:
>> GO:0051209 = release of sequestered calcium ion into cytosol
>> GO:0060402 = calcium ion transport into cytosol
>> GO:0014808 = release of sequestered calcium ion into cytosol by  
>> sarcoplasmic reticulum
>> GO:0051209 refers specifically release from "...endoplasmic  
>> reticulum or mitochondria ...into the cytosolic compartment."    A  
>> sibling for this under 60402 should be 'GO:0014808 release of  
>> sequestered calcium ion into cytosol by sarcoplasmic  
>> reticulum' (Varsha's new term).  I'm not too sure about 14808 being  
>> a child of 51209 since 51209 refers to release from ER or  
>> mitochondria but not SR.
>> Either: rename 51209 to include the ref to ER or mitochondria (not  
>> so satisfactory because of the 'OR') or refine its definition to be  
>> more broad (to include SR) and create child terms specific to  
>> mitochondria and ER.
>> Tanya
>
> This seems to be putting a lot of directionality in the term name,  
> whcih is obviously not scorable in computational analysis. Is there  
> a better semantic way or by introducing new relationship types
>
> -occurs_from
> -occurs_towards
>
> This will allow to simply use the CC terms tagged to generic terms  
> (e.g. Calcium Ion transport.

See:
http://wiki.geneontology.org/index.php/XP:biological_process_xp_cellular_component

>
>
> Pankaj
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