web services

a web service is a software component for application-to-application communication, typically based on SOAP and XML for message format and communicating protocol, respectively.

web services provided by the gmd

Warning: As this site must be considered as beta, all services offered here are subject to change at any time.

All functionality presented on the ms analysis page is implemented using the web services given below. Although a direct communication to the database would save roundtrips to the webserver, hence increase performance by reducing server load and communication time, this pattern is used to demonstrate both flexibility and openess of this application. In general, the library search and the sub-group prediction could be included in any MS annotation software capable of using web services.

• wsPrediction.asmx; see BioCatalogue Web Services Registry
• wsLibrarySearch.asmx; see BioCatalogue Web Services Registry
• wsGoBioSpace.asmx; see BioCatalogue Web Services Registry

Prediction Sample client

You can download a very simple client featuring a Microsoft Excel® spreadsheet. Given a Spectrum, an Retention Index (RI) value and an Mining Model identifier (here, Mining Model is an equivalent term to Decision Tree) the user defined function PredictSingle(ri, spectrum, MiningModelId, [optional property]) establishes a connection to GMD web site and invokes the prediction web service for potentially hundereds/thousends of mass spectra and Decisoin Trees, depending on your patience. The opional parameter property can be used to extract specific details from the predcition, i.e. PredictionGroupIsPresent, Probability, AdjustedProbability, Support, or NodeId. However, you have to have to enable macros to use the functionality. Feedback and bug reports are highly appreciated!

identifier mapping services

• convert name to MapMan GetXRefs.ashx?q=alanine&o=MapMan
• convert name to KEGG GetXRefs.ashx?q=alanine&o=KEGG
• convert name to ChEBI GetXRefs.ashx?q=alanine&o=ChEBI

other general services

• Send your spectrum (using a link) to the GMD website for searching against the library. Viewing the results is enabled in the normal manner via the GMD web interface. This link supports five parameters:
  • autoStart (true, false) indicating whether or not to start the search automatically
  • ri (numeric value) for the retention index
  • riWindow (numeric value) for the retention index window size
  • AlkaneRetentionIndexGcColumnComposition (none, VAR5 or MDN35) what a confusing name to distinguish the supported GC variants
  • spectrum white space delimitted string of mass and intensity pairs
  (many thanks to Adam Carroll for this feature request)
• GMD Spectrum News Feed 
• exporting spectra
  • in NIST MSP format
    • a single spectrum by ID and Column, column is requested for retention index (RI) output onlySpectrumMsp.ashx?id=b26abb69-7f9c-4313-87d8-ffb94b1ba856&column=MDN35
  • in JCAMP-DX format
    • a single spectrum by ID SpectrumJcampDx.ashx?id=bb0be0dd-be45-45d2-af7c-0437f672184d
    • two spectra, bottom one given by ID, top one given as BASE64 encoded string of floats JCAMP-DX with a north south plot (many thanks to Robert Lancashire for enabling this feature in the JCAMP file format)