-
Notifications
You must be signed in to change notification settings - Fork 3
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
gene decreases chemical rules and data #267
Comments
One option is to just modify the rule to be what we think it should be by reversing the directions of the chemical/gene edges. It might be that if the TMKP edges were in the data correctly that we would have found that rule. |
We want to try removing TMKP. This will involve adding TMKP to the deny list for increases/decreases edges... |
@cbizon here's an example query with the {
"message": {
"query_graph": {
"edges": {
"e0": {
"predicates": [
"biolink:treats"
],
"subject": "n0",
"object": "n1",
"provided_by": {
"denylist": [
"infores:tmkp"
]
}
}
},
"nodes": {
"n0": {
"ids": [
"MONDO:0004979"
],
"is_set": false
},
"n1": {
"categories": [
"biolink:SmallMolecule"
],
"is_set": false
}
}
}
}
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Starting from NCATSTranslator/Feedback#879
The rule is
(chemical a)<- decreases - (gene g) -decreases-> (chemical b) -treats-> (disease d)
The rule is coming from our mining. But it does produce odd results like the one listed above.
Some of the problem here seems to be that TMKP has a lot of its edges reversed. So if a paper says "chemical decreases gene' then it gets into TMKP and robokop as "gene decreases chemical". To what effect this causes the rule to exist, I am unsure, but it is in there. It may not be the relevant feature, as there are other similar rules that are for sure driven by CTD.
Interestingly, we don't have a rule going the other direction, which I think would be much more easily supportable from a meaning standpoint if not from the statistics...
The text was updated successfully, but these errors were encountered: