Get Accession Numbers For Chemicals? (Database Crossreference Identifiers)

Question

[Lo Sauer]

Dear all,

Chemspider lists an impressive array of ID's for other databases (without specifying which accession-Id belongs to which DB. -> rub it in CS :) )

e.g. Aspririn

Q: What projects are out there that provide, downloadable or otherwise(webservice), the resolution of chemical names into a comprehensive list of accession Id's. Ideally accession IDs for the major webservices out there. Pubchem does so to a limited degree (under the category 'Classification').

PS: My response from Chemspider, specifically inquiring ONLY the accession lists: "We don't make our database available as a download."

Thanks.

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Update 05/05/'12

This service solved the issue - for the field of metabolomics: Chemical ID Resolver

Answer 1

[Chris Evelo]

We have a metabolite database for BridgeDB that contains identifiers based on HMDB and Chebi. You can see what it does and does not link to in WikiPathways since we use it in there. We in fact do have a version with ChemSpider IDs for the same metabolites (so not all the other in ChemSpider), but I am not sure that is part of the released sets yet. If you like it you can install a local webserver instance of BridgeDB or use the Java code.

[Lo Sauer]

A pathway-wiki, great idea. PS: The file named 'metabolites' consists out of HMDB's metabolites+SMILES? Do you offer an SQL Dump?

Answer 2

[Pablacious]

You can use the EBI's ChEBI (Chemical Entities of Biological Interest) Web Service access to do a text search in the fields name and/or synonyms. This will retrieve a list of IDs, for each one of them you can retrieve the complete entity (with various names, synonyms, cross references to other databases, chemical structure, etc). The initial query also has a score associated to the text search, so you could filter by that or choose the top n results.

You can even try the methods in the web page, before deciding if you want to use the SOAP web service.

You can also use the NCI Cactvs Chemical Resolver.

This is a plain HTTP request.

[Lo Sauer]

Thanks, but my intend is to have a local database for xref's. But this seems promising: ftp://ftp.ebi.ac.uk/pub/databases/chebi/generic_dumps/names.sql

Answer 3

[Anon]

Chemical name and chemical structure associations are available on the PubChem FTP site.

You can also get the CID/SID associations on their FTP site.

[Lo Sauer]

Thanks, but could you point me to the pubchem xref-list if available, starting here: ftp://ftp.ncbi.nlm.nih.gov/pubchem/ ...