Fiehnlab in Nature journal feature
How to Querry Metabolites against Various Databases
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Various database stored many information about the compounds studying in metabolomics experiments. Batch mode query is a desired way to get these information.
Metabolite can be represent by various Ids (KEGG, Chebi, Pubchem, CAS, SMILES, Biocyc etc). There is no central service which can convert one Id into another however we can use various index and filters of pubchem for creating binary relationship between various Ids. Batch mode query is one of desired service by a good database to make easy the getting of information.
- Pubchem : Convert CID String into XXXX[CID] OR YYYY[CID] OR .... . Apply filter of various sourceid filter to get more information in various database.
- Metacyc :- Metacyc allow batch query in form of comma separate format. We can use KEGG IDs, Pubchem IDs, CAS number and Name of the Compounds. Be sure that you dont have any comma in compound name.
- KEGG batch mode : If you want to get information about a list of KEGG IDs. Use Kegg Lingand in Bget mode by space separated KEGG Ids. Use KEGG Identifier Service (Paste the Space separated KEGG Ids). Kegg Brite in Accession mode to Get the classification information of the Metabolite.
- Metlin :At Metlin Advance Search mode, Copy Kegg Id or CAS number as comma separated String.
- MMDB : Madison Metabolomics Consortium Database. Save the KEGG IDs, KEGG IDs or Pubchem Ids in a text file and query here.
- Chebi : Type the string as Space Separate format. you can query Kegg Ids, Chebi Ids and Name.
- Reactome : Use Chebi Identifier, Kegg IDs in Reactome Skypainter.
Created by
dinesh
Last modified 2008-02-09 10:13 PM
Last modified 2008-02-09 10:13 PM
