Psidev-gps-dev -- HUPO PSI: GPS -- Announce / Discuss


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This list caters specifically to the HUPO PSI: GPS workgroup's activities, providing a central organising point for announcements and discussion.

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The HUPO PSI General Proteomics Standards workgroup (GPS) is tasked to provide standards with relevance to the whole of proteomics; we are developing solutions in several areas:

=> Minimum reporting requirements -- the Minimum Information About a Proteomics Experiment (MIAPE) documents contain guidelines on how to fully report a proteomics experiment. It is expected that these guidelines will ultimately be enforced by journals, compliant repositories and funders (cf. MIAME).

=> XML format for data exchange -- derived from the GPS proteomics workflow/data object model, PSI-OM, this markup language (known as PSI-ML) is designed to become the standard format for exchanging data between researchers, and submission to repositories or journals. We will also provide a generic SQL implementation, as a reference only. The model and the exchange format will eventually form part of the emerging functional genomics model, which will be part developed by GPS in collaboration with the developers of the MAGE model for transcriptomics. Some development (such as mzData and mzIdent from the MS workgroup) will be on modules that form part of the overall format; GelML is an example of this.

=> Ontologies -- these lists of clearly defined terms are crucial for the construction of unambiguously worded data files. The GPS will contribute terms to the MGED ontology (extended), under the 'psi' namespace. We will also coordinate with the Mass Spec (and Search Engines) working group, whose ontology terms will likely be owned by the American Society for Mass Spectrometry (ASMS).

To see the collection of prior postings to the list, visit the Psidev-gps-dev Archives.

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