Hi,
Could you please provide the Broad IDs of the 32 drugs from the previous challenge? The names you provided are hard to find in other databases because slightly different names are being used whereas the Broad IDs seem more unique/reliable.
Thank you,
Denise
Created by Denise Duma denise.duma Glad it helped! Thank you, that was useful, I didn't think about looking up these names on DepMap! ...yeah, I know it's really shameful to not be able to figure out everything by oneself! Interesting, thanks for that information. A cursory google search suggests there is no master dataset of BRD IDs that is publicly accessible (or at least easily so). The closest I found was the the clue.io Repurposing related drug annotations dataset, but it's two years old and also missing some compounds.
Manually searching by compound on the depmap.org portal (https://depmap.org/portal) shows BRD ids for 3 of the compounds you listed, and then for the fourth (varlitinib) under a different name for the same drug (ARRY334543).
It's not clear to me, however, how accurate or comprehensive this search is. It looks like there can sometimes be multiple BRD-ids for a given chemical entity (probably due to specific lots/vendors of a compound used in screening?)
Sorry I can't be of more help; perhaps reaching out to the depmap folks you could acquire a more comprehensive map file.
These are the names for which I cannot find BRD IDs: icotinib, bafetinib, varlitinib, and crenolanib. Sorry, I'm not familiar with these naming conventions myself, but I'm trying to look up these drugs in CTRP which also uses BRD IDs. Thanks for the information. I've seen the BRD-XXX IDs a lot but didn't know the name for that identifier!
To clarify, when I call it the "standard InChI" - that's just the name of the identifier, I'm not claiming it is more standard or less standard than other identifiers. :)
Can you let me know where you are looking for the BRD IDs and which compounds you are not finding them for? Broad ID are also quite standard, for instance, the Broad ID for the drug named AEE-788 from the previous challenge is BRD-K40718343. However, I'm not able to find these IDs for all 32 drugs and I prefer using the Broad IDs rather than the actual names because they're less messy. Hi @denise.duma,
I'm not sure what Broad ID you are referring to, but for compound mapping purposes the InChIKey and standard InChI tend to be the most reliable and interoperable.
I went to the [PubChem Identifier Exchange Service](https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi) and plugged in the compound names from the Drug Activity challenge to get InChIKey and standard InChI maps:
* [InChIKey map](syn22105925)
* [standard InChI map](syn22105927)
I have not verified the accuracy of these particular PubChem ID exchange values, so, caveat emptor. But this service has been very accurate and useful for me in the past.
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