Question: Get all chemical compounds interacted with target
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gravatar for emanismail.92
16 months ago by
emanismail.920 wrote:

I want to get all Pubchem Chemical compounds (CID) interacted with a given uniprot target. I need it to study relation between Chemical compounds and Targets

Thanks in advance

uniprot cid interaction • 730 views
ADD COMMENTlink modified 16 months ago by Denise - Open Targets5.0k • written 16 months ago by emanismail.920

What have you tried?

ADD REPLYlink written 16 months ago by RamRS25k

I tried pubchem pug rest api, but can't reach such service

ADD REPLYlink written 16 months ago by emanismail.920

What do you mean by can't reach such service? What location are you based out of? Is the website blocked there?

ADD REPLYlink written 16 months ago by RamRS25k

Why are you interested in PubChem, that contains compounds linked to < 1,000 targets? Have you thought in exploring ChEMBL that a much larger proportion of active compounds identified using dose–response assays and linked to > 4,000 targets (see Gauton et al. 2012 for the stats and more details on PubChem and ChEMBL).

Because some of the PubChem data is available in ChEMBL, you could perhaps give the Open Targets Platform a go and get the (ChEMBL) drug compounds (with known mechanism of action) that modulate a target (as UniProt IDs or Ensembl gene IDs).

Drug information is also available via the Open Targets batch search or the REST API. Check this short animation to see how easy is to run (and interpret) the batch search too. Or read the post on Open Targets and programmatic access. If REST is the way for you, this endpoint is one example on how to get the evidence used to link ENSG00000145335 and diseases when filtering for drug information (from ChEMBL).

https://api.opentargets.io/v3/platform/public/evidence/filter?target=ENSG00000145335&datasource=chembl.

This is how one can visualise the associated diseases in the user interface.

If you are not interested in associations with these diseases, I'd recommend you exploring the ChEMBL web services API documentation.

ADD REPLYlink modified 16 months ago • written 16 months ago by Denise - Open Targets5.0k

Thanks alot for your reply. I need pubchem CID for each chemical compound. If I use CHEMBL, Is there any way to get Pubchem CID from Chembl ID

ADD REPLYlink written 16 months ago by emanismail.920

There is the PubChem Identifier Exchange Service. If you have a list of ChEMBL IDs, select the option "synonyms' and as output CIDs (or vice-versa). I've tried ChEMBL1000 aka CETIRIZINE, which gives me PubChem CID 2678.

Check more on the theme of Converting between drug identifier formats here on Biostars, as another tool (Cactvs Cheminformatics Toolkit) has been mentioned as well.

I will check with ChEMBL if they have a web interface toolkit (or plan to release one) since they have already all cross-referenced anyway. Perhaps their web services could also do the converting.

And at last but not least, I also recommend you to check Pierre Lindenbaum's comments ;-)

ADD REPLYlink written 16 months ago by Denise - Open Targets5.0k
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