Convert activity type mapping to log-scale. #272
Conversation
The activity and potency types on Drug Central are log-scaled, so let's add the "p" in front of the activity types to reflect that.
beasleyjonm
added
the
Biological Context QC
|
Let's discuss this in a meeting perhaps, but these mappings correspond to the values in the drugcentral database, so we can't just change them or it will break them all. Also, the output of using these mappings are the predicates, not the values like ic50, so if we want this change to be represented in the graph we'll need to do something else. It also looks like this only alters the comment in the drug central parser, and the actual mappings are in predicates.py |
|
Ah, my mistake. I believe my latest commit fixes the issue correctly. Let's discuss in an upcoming meeting. |
There was a problem hiding this comment.
@eKathleenCarter check to confirm this. Can we make this biolink compliant?
|
This code looks right now. As Kathleen comments, I think this would be a great example of a property that we would really like to be biolink compliant. Last time I looked I didn't see anything in the model that's an obvious fit, but maybe that's changed. Otherwise, we should reach out to the biolink folks and see if we can make a new property. |
|
I went ahead and switched the other parsers with these edge properties to using the constants we set up, so that they're all consistent. As well as adding this kind of property to biolink, we should probably audit the usage of them across the parsers to make sure they're used in the same way. (BINDING-DB, PHAROS, drugcentral, GtoPDB) |
|
Otherwise, I think we can go ahead and merge this in if you are both good with the state of it now. |
The activity and potency types on Drug Central are log-scaled, so let's add the "p" in front of the activity types to reflect that.