rDGIdb package inconsistency with web interface
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Last seen 4 months 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.

  test <- queryDGIdb(c("RPS3A"),
       sourceDatabases = NULL,
       geneCategories = NULL,
       interactionTypes = NULL)
rDGIdb • 431 views
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Last seen 1 hour 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.

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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" } ] } ] } ] } } }

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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.

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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.

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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.

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.

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