Document Detail


The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.
MedLine Citation:
PMID:  19834897     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
The Human Proteome Organization's Proteomics Standards Initiative (PSI) promotes the development of exchange standards to improve data integration and interoperability. PSI specifies the suitable level of detail required when reporting a proteomics experiment (via the Minimum Information About a Proteomics Experiment), and provides extensible markup language (XML) exchange formats and dedicated controlled vocabularies (CVs) that must be combined to generate a standard compliant document. The framework presented here tackles the issue of checking that experimental data reported using a specific format, CVs and public bio-ontologies (e.g. Gene Ontology, NCBI taxonomy) are compliant with the Minimum Information About a Proteomics Experiment recommendations. The semantic validator not only checks the XML syntax but it also enforces rules regarding the use of an ontology class or CV terms by checking that the terms exist in the resource and that they are used in the correct location of a document. Moreover, this framework is extremely fast, even on sizable data files, and flexible, as it can be adapted to any standard by customizing the parameters it requires: an XML Schema Definition, one or more CVs or ontologies, and a mapping file describing in a formal way how the semantic resources and the format are interrelated. As such, the validator provides a general solution to the common problem in data exchange: how to validate the correct usage of a data standard beyond simple XML Schema Definition validation. The framework source code and its various applications can be found at http://psidev.info/validator.
Authors:
Luisa Montecchi-Palazzi; Samuel Kerrien; Florian Reisinger; Bruno Aranda; Andrew R Jones; Lennart Martens; Henning Hermjakob
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Proteomics     Volume:  9     ISSN:  1615-9861     ISO Abbreviation:  Proteomics     Publication Date:  2009 Nov 
Date Detail:
Created Date:  2009-11-25     Completed Date:  2010-02-22     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101092707     Medline TA:  Proteomics     Country:  Germany    
Other Details:
Languages:  eng     Pagination:  5112-9     Citation Subset:  IM    
Affiliation:
European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK. luisa@ebi.ac.uk
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MeSH Terms
Descriptor/Qualifier:
Computational Biology / methods*
Humans
Proteomics / standards*
Reproducibility of Results
Grant Support
ID/Acronym/Agency:
WT085949MA//Wellcome Trust

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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