Open cthoyt opened 5 years ago
Is there a BEL toolkit for interconverting between these?
presumably another way is
act(p(X), ma(GO:"kinase activity")) -> act(protein(Y))
This would have the most natural mapping to an activity-centric GO-CAM view. Here the semantics are on the occurrent class, and a more general directly activates
relation could be used
@goodb, is the inference of the modifications something that could fall out of the RHEA axiomatization work?
https://docs.google.com/document/d/10xi10oyISribbssR9CYgz6YVgC_rAVR3W2RvSt7Vdqg/edit
I'm not seeing how the RHEA work would impact this, but might be missing something. Could you give a strawman of what you are thinking might be working here - in terms of the GO MF definitions? The RHEA-based axiomitization of catalytic activities will be useful for classification based on the inputs and outputs of a reaction/function. (See https://github.com/geneontology/go-ontology/issues/14984 ).
On Mon, Oct 1, 2018 at 10:58 PM Chris Mungall notifications@github.com wrote:
Is there a BEL toolkit for interconverting between these?
presumably another way is
act(p(X), ma(GO:"kinase activity")) -> act(protein(Y))
This would have the most natural mapping to an activity-centric GO-CAM view. Here the semantics are on the occurrent class, and a more general directly activates relation could be used
@goodb https://github.com/goodb, is the inference of the modifications something that could fall out of the RHEA axiomatization work?
https://docs.google.com/document/d/10xi10oyISribbssR9CYgz6YVgC_rAVR3W2RvSt7Vdqg/edit
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Is this still needed?
This is still unresolved. #522 will hopefully renew interest in this
In BEL, it's common to see chains like:
I apologize if this isn't idiomatic, but I hope it gets the idea across. What would be the best relation / set of relationships to express this using RO?
CC: @cmungall @dexterpratt