Question: Mapping Drug/Chemical Names To Cas Number
2
gravatar for Nims
5.6 years ago by
Nims90
India
Nims90 wrote:

I would like to know it there is any way to map a list of drug/chemical names to their corresponding CAS RN, if only names of drug/chemicals are known.

drug target • 3.9k views
ADD COMMENTlink modified 5.6 years ago by SimonCB765150 • written 5.6 years ago by Nims90
1

Singh, what numbers are you talking about and what do you want to do with the CAS RNs when youve got them ?

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by cdsouthan1.8k
1
gravatar for cdsouthan
5.6 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

PubChem have these in the CID synonym lists. They are somewhat noisy because the name and RN mappings done by different secondary sources (in the SIDs) are not necessarily concordant with SciFinder direct (salt-parent cross-overs are common in fact) But why not use InChIKey ? these are openly provenanced.

You can get some background here http://www.slideshare.net/cdsouthan/southan-bio-it2012drugnames

ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by cdsouthan1.8k

To be more specific, examine this file: ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/CID-Synonym-unfiltered.gz

ADD REPLYlink written 5.6 years ago by Malachi Griffith17k

So to be more precise - I have only drug/chemical names and nothing else. And I want to fins their corresponding CAS number.

ADD REPLYlink written 5.6 years ago by Nims90

You can use MGs list, exept you might choose "filtered". If you only have names (from where?) your mapping results will be noisy but there is actually no way to resolve these cleanly.

ADD REPLYlink written 5.6 years ago by cdsouthan1.8k
1
gravatar for SimonCB765
5.6 years ago by
SimonCB765150
SimonCB765150 wrote:

If your drug is in the Therapeutic Target Database, then you can use their file of cross-references to get the CAS number (along with other identifiers).

ADD COMMENTlink written 5.6 years ago by SimonCB765150

Thanks a ton.I just missed the file you pointed out. Is there also something that could co-relate TTD targets to corresponding NCBI gene (I could only see UniProt IDs)?

ADD REPLYlink written 5.6 years ago by Nims90

Unfortunately, I never found anything that did that. I ended up using UniProt accessions as my 'true' ID, and mapped TTD target IDs and NCBI gene IDs to UniProt accessions (along with all other IDs I needed). Not perfect, but going between UniProt and NCBI gene IDs was relatively simple.

ADD REPLYlink written 5.6 years ago by SimonCB765150

So if I am not wrong - you are getting NCBI gene ID indirectly from UniProt, probably mapping first to a UniProt record and then NCBI gene ID.

ADD REPLYlink written 5.6 years ago by Nims90

The question is which mapping you trust more/has greater coverage. Do you trust UniProt to record the NCBI IDs more accurately and completely, or NCBI to record the UniProt accession more accurately and completely. The way I did it was to go from all my sources to UniProt. In the case of NCBI gene IDs I believe I used the gene2accession file (ftp://ftp.ncbi.nih.gov/gene/DATA/) to map from Gene IDs to UniProt accessions.

ADD REPLYlink written 5.6 years ago by SimonCB765150
0
gravatar for Egon Willighagen
5.6 years ago by
Maastricht
Egon Willighagen5.2k wrote:

One good source is WikiPedia, which has been working with Chemical Abstracts, resulting in the http://commonchemistry.org/ project.

ADD COMMENTlink written 5.6 years ago by Egon Willighagen5.2k
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