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26
11
2007
The Mass Spectrometry Web Services Interface to ChemSpider
Posted by: Antony Williams in ChemSpider Services, Community BuildingCopyright©2007 Antony Williams
We have previously rolled out a number of web services integrating to ChemSpider (1,2,3). This was recently extended by unveiling the MassSpec API. Details are below.
Return specified compound details.
Get the list of datasources in ChemSpider.
Search ChemSpider compounds by molecular formula. Search within specified datasources (if given).
Search ChemSpider compounds by molecular formula.
Search ChemSpider compounds by mass +/- range. Search within specified datasources (if given).
Search ChemSpider compounds by mass +/- range.
With these web services it is now feasible for mass spectrometrists to integrate their own software systems directly to ChemSpider for their own purposes. If anyone is interested in integrating via the MassSpecAPI please contact us at info|AT|chemspider.com
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November 28th, 2007 at 8:57 am
One problem with the current response of GetCompoundDetails is that the fields are all wrapped in the same element… now I can assume that the SMILES is always the second element, but this is suboptimal.
November 28th, 2007 at 9:00 am
Actually… seems to apply to not just that service. This is the output for GetRecordDetails:
1269250
OORFINRYBCDBEN-IXJKMYCHCG
InChI=1/C9H10O3/c1-12-6-7-2-4-8(5-3-7)9(10)11/h2-5H,6H2,1H3,(H,10,11)/p-1/fC9H9O3/q-1
[O-]C(=O)c1ccc(cc1)COC
November 28th, 2007 at 9:00 am
<ArrayOfAnyType>
<anyType xsi:type=”xsd:int”>1269250</anyType>
<anyType xsi:type=”xsd:string”>OORFINRYBCDBEN-IXJKMYCHCG</anyType>
<anyType xsi:type=”xsd:string”>InChI=1/C9H10O3/c1-12-6-7-2-4-8(5-3-7)9(10)11/h2-5H,6H2,1H3,(H,10,11)/p-1/fC9H9O3/q-1</anyType>
<anyType xsi:type=”xsd:string”>[O-]C(=O)c1ccc(cc1)COC</anyType>
</ArrayOfAnyType>
November 28th, 2007 at 7:34 pm
Egon, this API may change, it was just the first version to let people try it and start getting feedback. How’d you change it?
November 29th, 2007 at 10:48 am
The above example, I’d do something like:
<cid xsi:type=”xsd:int”>1269250</cid>
<inchikey xsi:type=”xsd:int”>OORFINRYBCDBEN-IXJKMYCHCG</inchikey>
Etc. Likewise for the metabolomics services:
<GetCompoundDetailsResponse xmlns=”http://www.chemspider.com/”>
<GetCompoundDetailsResult>
<formula>C_{50}H_{70}O_{2}</string>
<smiles>O=C\2c1c(cccc1)C(=O)/C(=C/2)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CC\C=C(/C)C</smiles>
<accurateMass>702.537581</accurateMass>
etc.
December 12th, 2007 at 3:59 pm
BTW what are the current meanings of the fields? Some are obvious, but others (esp. those which come back blank
are not.
…
C_{19}H_{19}NO_{2}S
O=S(=O)(c3ccc(c2ccc(n2c1ccc(cc1)C)C)cc3)C
InChI=1/C19H19NO2S/c1-14-4-9-17(10-5-14)20-15(2)6-13-19(20)16-7-11-18(12-8-16)23(3,21)22/h4-13H,1-3H3
JULPDIIDMNHGEC-UHFFFAOYAA
325.4247
325.4247
325.113649
325
4.8
2-methyl-5-(4-methylsulfonylphenyl)-1-(p-tolyl)pyrrole
December 12th, 2007 at 8:28 pm
Mitch… This web method:
List GetCompoundDetails(string csid)
Returns the following list of fields:
MF,
SMILES,
InChI,
InChIKey,
Average_Mass,
Molecular_Weight,
Monoisotopic_Mass,
Nominal_Mass,
ALogP,
XLogP,
CommonName
We will be changing the MassSpecAPI soon:
The methods will accept a user token (UUID) to allow us to identify what users are performing what activities so we can help people and monitor usage appropriately
Also, this will report errors back to us
Also we will provide additional capabilities with this procedure.
Are there any improvement requests?
December 13th, 2007 at 5:57 pm
Thanks for the info.
I don’t have any improvement requests of my own, but will second Egon’s suggestion to provide ’self-documenting’ tags.