Semantic Validation

The PSI Validator generic framework

The PSI semantic validator tackle the issue of automatically checking that experimental data reported using a specific format and various semantic resources are indeed compliant with the MIAPE recommendations. The semantic validator not only check the XML syntax but it enforces many rules as to how controlled vocabulary terms classes are used, it verifies that the terms mentioned exist in its source CV (and it is not just a random string reported in the XML document), and more importantly that the correct terms are used in the correct location of a document. Moreover the semantic validator framework is extremely flexible and it can be adapted to any PSI workgroup standard just by customizing the three input files:

  1. a list of ontologies or CVs necessary to annotate exchanged data in a MIAPE compliant way

  2. a mapping file formalizing how the necessary CVs and an exchange format are interrelated ( see documentation)

  3. a list of object rules to be run by the validator.

The Java source code can be accessed here. The generic framework and dependencies can be downloaded from here.

A tutorial has been made available to guide users writing their own validator. 


Current implementations of the PSI validator in specific workgroups


PSI Workgroup Format Standard Validator Web Application Source code Configuration files
Molecular Interaction MIF25 MIMIx MIMIx validator contact

MI-mapping   MI-CvSourceList

  MIF25 IMEx   IMEx validator   contact MI-mapping-Imex
  MIF25 PAR   PAR validator   contact PAR-mapping
Mass Spectrometry mzML MIAPE-MS

MS validator

Java mzML validator (Java Web Start)

Java code available here

MS-mapping MS-CvSourceList MS-ObjectRules

miape-ms-rules miape-object-rules

Beta implementations     draft validators code in C++  
Proteomics Informatics mzIdentML 1.1.1 MIAPE-MSI

Java mzIdentML validator


Java code here





Protein Separation GelML (version 1.1 candidate) MIAPE-GE GelML validator  Available here GelML-mapping (draft)