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

[Pankaj Jaiswal (OSU)]

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.

Pankaj