A couple of papers from here at Newcastle University have appeared over the past couple of weeks. Here's a summary of them both.
- Data Standards
From "An Update on Data Standards for Gel Electrophoresis" in Practical Proteomics Issue 1, September 2007, and by Andrew R. Jones and Frank Gibson.
From the abstract: "We report on standards development by the Gel Analysis Workgroup of the
Proteomics Standards Initiative. The workgroup develops reporting
requirements, data formats and controlled vocabularies for experimental
gel electrophoresis, and informatics performed on gel images. We
present a tutorial on how such resources can be used and how the
community should get involved with the on-going projects. Finally, we
present a roadmap for future developments in this area."
Provides a summary of ongoing work in the Gel electrophoresis and Gel informatics fields in terms of data and metadata standardization. This includes work on MIAPE GE and MIAPE GI, two checklists for minimal information required on these types of experiments and analyses. For both GE and GI, there are data formats (GelML and GelInfoML, respectively, both extensions of FuGE) and a suggested controlled vocabulary (sepCV). More information can be found on http://www.psidev.info.
Frank works in the CARMEN neuroscience project here at Newcastle, and Andy is in Liverpool and works on, among other things, FuGE. CARMEN collaborates with the SyMBA project, which was originally developed by me and a few others within Neil Wipat's Integrative Bioinformatics Group here at Newcastle but which is now a sourceforge project at http://symba.sf.net. Andy Jones is a co-author with me, Neil Wipat, Matt Pocock and Olly Shaw on an upcoming SyMBA paper.
- Semantic Data Integration
A paper that was presented at the Integrative Bioinformatics Conference 2007 by me and my co-authors, Matt Pocock and Neil Wipat, is now available from the Journal of Integrative Bioinformatics website.
Allyson L. Lister, Matthew Pocock, Anil Wipat. Integration of
constraints documented in SBML, SBO, and the SBML Manual facilitates
validation of biological models. Journal of Integrative Bioinformatics,