Is there any way to obtain PubChem CID using IUPAC name ( via eutils ncbi )

Question

[dobule]

Hi all, I am new to ncbi entrez eutility and got stuck with a problem, whenever i am trying a search:

eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<db_name>&term=<term_name>

I am getting a whole lot of uid's but, i want only a particular id (i.e. of <term_name>)

Is there any way to achieve that.

[5heikki]

Check Entrez Direct: http://www.ncbi.nlm.nih.gov/books/NBK179288/ It's eutils in a more usable package.

[Neilfws]

Would help to show an example term and output. Depending on the precise search term, getting "a whole lot of uids" is a common and expected result.

[dobule]

In my case i need to get a cid (for eg. phenol "CID:996") and then link that id programatically to other db's.

but if I do:

eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pccompound&term=phenol

I'm getting a whole lot of uid's but I only need a particular id (i.e CID:996) and not all other id's as that'll be an overhead.

So, is there any way to get id for the exact term(here:phenol) using eutils[just one id].

[Neilfws]

You can use qualifiers in the term. For example:

term=phenol[UPAC] 

to search by IUPAC Name. However in this case (and many others), that will still not result in a 1:1 mapping to UIDs. Looks from your comment like you found a good solution.

[dobule]

Yes, even IUPAC field provides a bunch of id's.

Wonder if it can be done via eutils.

Answer 1

[wdiwdi]

You can script this easily with the Cactvs Cheminformatics Toolkit (free academic versions at www.xemistry.com/academic)

Here an example for aspirin, Tcl version:

---snip--

echo [ens get "2-acetyloxybenzoic acid" E_CID"]

---snip--

Python version:

---snip--

print(Ens("2-acetyloxybenzoic acid").E_CID)

---snip---

Please be aware that the name resolution is not 100% reliable, and that above script retrieves the structure with most references - the case with multiple CIDs cited above is not an error, but an indication of limitations in name generation, structure standardization, etc.

[dobule]

Thanks,

but I manage to get cid using iupac name with the help of NCBI PUG REST using:

http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/phenol/

and then parse the cid (I don't know if it is the right way to do)

but my main q is to get a particular id for the "exact" term using eutils.

[wdiwdi]

Well, internally the toolkit uses EUtils and PUG to communicate with PubChem. But if the method is more important to you than the result, this may of course not be the right solution.