Use case

IspIder

Reference	Userreq.IspIder
High-level reqs	ComplexEvents GenericShimReplacement
Proposed by	Simon Hubbard

	Taverna 1.3	Taverna 2.0
Priority

Overview

To develop an integrated platform of proteomic data resources enabled as Grid and Web services for the storage, dissemination and management of proteomic data, using existing standards from proteomics, bioinformatics and e-Science.

Overall Goals

The objective of the scenario is to specify and implement a workflow application for identifying and classifying proteins. To do this, the workflow combines the capabilities of mass spectrometric techniques with protein classification tools. Pepmapper, a peptide mass fingerprinting tool, is used to identify a peptide digest molecular mass. This mass is used to map to databases (swissprot) and other resources (GO and Interpro) to identify and characterise the protein.

Required services

swissprot,

pepmapper,

GO,

interpro2GO

Workflow outline

The workflow takes as input the name of the peptide masses, the name of the database used for identifying the protein, the identification error, and the mapping database that associates SwissProt^? entries to Interpro entries. In response, it replies with the name of the identified protein, the associated GO identifier, GO name and classification. Furthermore, it specifies the name of the associated GO term parents with respect to the GO ontology.

Appendix

Reference: http://www.ispider.man.ac.uk/