PubChem Identifier Exchange Service

PubChem released a Identifier Exchange Service enabling users to convert identifiers of different databases from one into the other. This is perfect, as PubChem is the central chemical structure oriented resource capable to convert identifiers based on the structure! In contrast, the services I implemented for the Golm Metabolome Database is just to small and is definitely not a global resource. The Chemical Translation Service is also not perfect, as it relies on text-matching and use PubChem downloads to build up the dictionary. The PubChem Identifier Exchange Service has the potential to save Bioinformaticians (especially in metabolomics) a lot of work, because converting identifiers is one of the major problems here.
But still PubChem's Service is not perfect as it is limited by the asynchronous FTP based Power User Gateway (PUG). Don't get me wrong, I love asynchronous programming! But is there any client application implemented initialising a http request, polling for results which are finally fetched via FTP?

calling a web service from Excel

Recently I evaluated the possibility to call a web service from Excel. The call is encapsulated within a function which can be used as a formula from within Excel.

Chebi web services returns multiple hits

Today I tried the getStructureSearch() method from EMBL-EBI to resolve some of the structures with in the GMD into Chebi identifiers. Strangly some of the compounds resultet in multiple hits even with search set to IDENTITY.

...
ChebiWebServicePortTypeClient ChebiClient = new ChebiWebServicePortTypeClient();
ChebiClient.getStructureSearchCompleted += new EventHandler(ChebiClient_getStructureSearchCompleted);

getStructureSearch structure = new getStructureSearch();
structure.structure = mymolfile; //here goes the molFile structure
structure.type = StructureType.MOLFILE;
structure.structureSearchCategory = StructureSearchCategory.IDENTITY;
structure.totalResults = 1;
structure.tanimotoCutoff = 0.5f;

ChebiClient.getStructureSearchAsync(structure, null);
...



For a structure of Glucose 4 results are returned:

• http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17234
• http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:42758
• http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:17634
• http://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:584174

Strange enough I setted totalResults = 1 and still get more than one result...

Any ideas out there?



Update:

Janna Hastings from ChEBI acknowledge that I have picked up on a bug in the ChEBI
webservice implementation of the structure search. This was resolved in the release July 7th.

on the air

Greetings folks!
I will blog here about my daily problems, tasks and thoughts with respect to the Golm Metabolome Database, GoBioSpace or any other mass spec related program I developed.

use the source!
luke