Phenotypes and the proteins that affect them

[Jim McCusker]

I'm trying to figure out how to model the relationship between a phenotype and a protein that may affect it. I could set up an anonymous process where the protein is the participant and the phenotype is the target, but I wasn't sure if that's actually accurate in SIO.

Right now I'm modeling it this way:

<x> a :OMIMPhenotypeInfluence;

     sio:'has participant' <${protein}>;

     sio:'has target' <${phenotype}>.

  

     <${phenotype}> a sio:phenotype.

(those are genshi-based template variables for URIs, for the folks keeping score at home).

But is there a proper sio:process subclass for x?

Thanks,

Jim

[Michel Dumontier]

Right. so normally, we attribute the phenotype to an organism that has a particular perturbation 

e.g. <phenotype> sio:is-attribute-of some (sio:organism that sio:has-part some (sio:variant-of some :protein))

if you just want to report an association, then

<x> a sio:association;  // currently there is a gene-disease association. we could add others.

  sio:refers-to :protein;

  sio:refers-to :phenotype;

.

m.

 

Michel Dumontier

Associate Professor of Medicine (Biomedical Informatics), Stanford University

Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group

http://dumontierlab.com

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