How to associate enzymatic reactoins with metabolic pathways? #1035
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Dear Biolink team, Let me start by thanking all your colleagues who do such a wonderful job. I work on metabolic pathways and that's why I'm very interested in Biolink Model, and I considered it a brilliant approach! I'm trying to understand how to link Biolink Model's vocabularies to the different participants in metabolic pathways. We have a pathway
Now I want to link
All these associations do not directly link reactions to pathways: we have to go down to the molecular level (gene or enzyme). Is there any association of type
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Replies: 4 comments 1 reply
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Hi Min, thank you for your interest in Biolink Model! We will get back to you soon with some answers. You happen to have contacted us during a week when we have an all-week all-hands meeting for the Translator project, so all the Biolink Model architects and developers are super-busy right now. Hopefully someone will get back to you next week. |
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Hi Min, thanks so much for reaching out and for such a well crafted discussion topic! Adding a |
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Thank you very much for your quick answers despite being very busy. And I am glad you are going to add this "reaction-pathway" association (can't wait!). Let me ask you one more questions. |
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do your superpathways have the same semantics as biocyc superpathways?
…On Thu, Jun 9, 2022 at 5:29 AM Min ***@***.***> wrote:
Thank you very much for your quick answers despite being very busy. And I
am glad you are going to add this "reaction-pathway" association (can't
wait!).
Let me ask you one more questions.
I would like to group the pathways into super-pathways. I have seen that
there is Relation: superclass_of
<https://biolink.github.io/biolink-model/docs/superclass_of.html#relation-superclass_of>
but not all pathways participate in super-pathways. So it would be better
to use Relation: subclass_of
<https://biolink.github.io/biolink-model/docs/subclass_of.html#relation-subclass_of>
in the other direction? Or do you have any other advice?
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Hi Min, thanks so much for reaching out and for such a well crafted discussion topic! Adding a
biolink:MolecularActivity to biolink:Pathway association
makes sense to me. PR: #1036 edit: spoke to Chris M offline, and he agrees. Let's add it! :)