Semantic Web process for Glycoproteomics data analysis

The Semantic Web services listed here were developed as components of a scientific workflow that allows the tracking, storing and querying of experimental glycoproteomics data. The system correlates experimental data results with biology and allows for automated data processing using these Semantic Web services. Protocol developed for high throughput glycoproteomics experiment consists of multiple distributed computational resources located on heterogeneous computational platforms. The execution of these Web services to mirror analysis protocols necessitates the deployment of a specific workflow instance. 

This scientific workflow involves the analysis of RAW mass spectrometric files (generated by mass spectrometers) in terms of peptide identification and quantification. This involves conversion of the RAW files into mzXML format [Pedrioli PG et. al. (2004) Nat Biotechnol]. This is followed by processing of these files into peaklist files using two different applications. These processed peaklist files are submitted to the MASCOT search program for identification of peptides. Using ProValt application [Weatherly DB et. al. Mol Cell Proteomics. 2005], the MASCOT results are processed, accumulated and archived for statistical analysis. The peptides from the ProValt are subsequently provided as input to a database as a function of the sample from a biological source.

Semantic Web Services: SAWSDL Files

The components of WSDL file have been annotated using ProPreO ontology . The annotation conforms to the SAWSDL framework which is in the process of becoming a W3C recommendation. SAWSDL conformant annotation was carried out using Radiant, an eclipse plug-in for semantic annotation of Web services, developed by LSDIS Lab for semantic annotation of Web services.

For complementary information on tools and use cases, see METEOR-S' SAWSDL framework.