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Dear GO team, First of all, I would like to thank all your colleagues who are doing a great job. I work on metabolic pathways by diving into the world of ontology. That's why I'm very interested in GO-CAM, and I found the idea brilliant! The ttl file downloadable from the official website does not contain details on reactions and metabolites. And I saw on the FAQ that
My understanding from reading the papers and documentation in your GitHub repositories is that you aim to integrate metabolic pathways such as Reactome using Pathways2GO and complete catalytic reactions (enzymes, metabolites ...etc) using on Rhea. For example, the reactome-go-cams shows how to build GO-CAM from Reactome pathways. But the ttl files do not reflect 100% of what is observed on Noctua. For Rhea, I found go-rhea-boom but I have the impression that the json files do not contain the metabolites (the biochemical equation is annotated in the label). Considering all these, here are my questions:
For the last question, I ran some queries described on Pathways2GO. For example get_chemicals.rq: this query works on Gene Ontology SPARQL endpoint but not locally. I guess it' s because the ttl file only contains GO-CAM models? I apologize for overwhelming you with so many questions. Regards, |
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@0m1n0 sorry for the slow response.
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@0m1n0 sorry for the slow response.
In order to completely interpret a GO-CAM OWL file, you must import the ontologies from which the classes mentioned in the GO-CAM come from. We publish a large merged ontology which provides the vocabulary used within GO-CAMs:
http://purl.obolibrary.org/obo/go/extensions/go-lego.owl
This ontology links many GO terms to chemical inputs and outputs, as well as anatomical structures, etc.
I don't think we have a great diagram available like that. We do have a schema for GO-CAMs in the ShEx language here: https://github.com/geneontology/go-shapes/blob/master/shapes/go-cam-shapes.shex
I can't check Ontobee right now, since there seems to be a problem w…