rDGIdb package inconsistency with web interface
1
0
Entering edit mode
@66fdce6a
Last seen 9 weeks ago
United Kingdom

Searching for the gene "RPS3A" directly in the dgidb.org site gives a few gene-drug interactions. Whereas the below code gives a blank dataframe suggested no drug-gene interactions are present. If the package just interacts with the API why am I seeing this behaviour?

Any help would be much appreciated.

   library(rDGIdb)
  test <- queryDGIdb(c("RPS3A"),
       sourceDatabases = NULL,
       geneCategories = NULL,
       interactionTypes = NULL)
  detailedResults(test)
rDGIdb • 355 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 37 minutes ago
United States

It doesn't appear to be inconsistent. Here is the API call result. And the query on the old version. Although as you may be noting, the beta version has different results.

0
Entering edit mode

I went on https://www.dgidb.org/api and searched "RPS3A" and got the below result. Not sure how you got something different. There is certainly inconsistency... I've used the package for a fair amount of analyses, of which I'm now not confident on/

{ "data": { "genes": { "nodes": [ { "interactions": [ { "drug": { "name": "MT-3724", "conceptId": "chembl:CHEMBL4297789" }, "interactionScore": 0.1456297627063282, "interactionTypes": [ { "type": "inhibitor", "directionality": "INHIBITORY" } ], "interactionAttributes": [ { "name": "Mechanism of Action", "value": "80S Ribosome inhibitor" }, { "name": "Direct Interaction", "value": "true" } ], "publications": [], "sources": [ { "sourceDbName": "ChEMBL" } ] }, { "drug": { "name": "EXALUREN", "conceptId": "ncit:C174918" }, "interactionScore": 0.1474501347401574, "interactionTypes": [ { "type": "modulator", "directionality": null } ], "interactionAttributes": [ { "name": "Direct Interaction", "value": "true" }, { "name": "Mechanism of Action", "value": "80S Ribosome modulator" } ], "publications": [], "sources": [ { "sourceDbName": "ChEMBL" } ] }, { "drug": { "name": "ATALUREN", "conceptId": "ncit:C169791" }, "interactionScore": 0.1438537899903974, "interactionTypes": [ { "type": "modulator", "directionality": null } ], "interactionAttributes": [ { "name": "Direct Interaction", "value": "true" }, { "name": "Mechanism of Action", "value": "80S Ribosome modulator" } ], "publications": [], "sources": [ { "sourceDbName": "ChEMBL" } ] }, { "drug": { "name": "DORLIMOMAB ARITOX", "conceptId": "chembl:CHEMBL2109124" }, "interactionScore": 0.1474501347401574, "interactionTypes": [ { "type": "inhibitor", "directionality": "INHIBITORY" } ], "interactionAttributes": [ { "name": "Direct Interaction", "value": "true" }, { "name": "Mechanism of Action", "value": "80S Ribosome inhibitor" } ], "publications": [], "sources": [ { "sourceDbName": "ChEMBL" } ] }, { "drug": { "name": "CYCLOHEXIMIDE", "conceptId": "ncit:C171712" }, "interactionScore": 0.125489476374602, "interactionTypes": [ { "type": "inhibitor", "directionality": "INHIBITORY" } ], "interactionAttributes": [ { "name": "Direct Interaction", "value": "true" }, { "name": "Mechanism of Action", "value": "80S Ribosome inhibitor" } ], "publications": [], "sources": [ { "sourceDbName": "ChEMBL" } ] } ] } ] } } }

0
Entering edit mode

Yes. You went on the beta version and got different results than I (and the package) get when using the existing version. Was that not clear from my previous post? I mean the link you provide says 'The previous version of DGIdb can be found at old.dgidb.org until June 1st, 2024.' right at the top.

There are two versions, and they give different results for the same gene. That's got nothing to do with the package, really, other than the fact that it is still querying the non-beta version.

ADD REPLY
0
Entering edit mode

The address I linked (https://www.dgidb.org/api) does not state 'The previous version of DGIdb can be found at old.dgidb.org until June 1st, 2024.. The address https://beta.dgidb.org/api does however.

There seems to be three versions/addresses

I'm assuming what your saying is the package queries the old "https://old.dgidb.org/api" address, which is inconsistent with both the beta address (https://beta.dgidb.org/api), and the standard https://www.dgidb.org/api, which is neither beta nor old. Surely the maintainers should configure the package to interact with this address (https://www.dgidb.org/api), which would give users a more updated list of interactions.

0
Entering edit mode

This is what I see when I go to the link you provide.

enter image description here

But anyway, I cannot speak for the maintainers, and since I don't use the package have no opinion as to how it should work. You could

A.) Get the sources, make the changes you think should be made, and send them a PR to update their package. This may not be possible, as the GitHub that you have already posted an issue on is ancient and hasn't been touched since they first added it.

B.) Contact them directly and ask for them to update the package. They are supposed to follow their package tag on this support site, but there's no enforcement mechanism for that. The maintainer hasn't responded to any of the posts, so they might not know there is an issue.

C.) Get the sources, make the changes, have your own version that does what you want.

ADD REPLY
0
Entering edit mode

That is strange as I only see that previous version message when I go on the https://beta.dgidb.org/api version.

I did contact the writer of the package and he suggested to contact his old lab as he's not involved in it's maintenance anymore. I think getting the sources and making the changes myself might be a bit out of my reach. Will have a look into it though!

Thank you for all the advice James.

Login before adding your answer.

Traffic: 831 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6