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 WorkgroupFormatStandardValidator Web ApplicationSource codeConfiguration files
Molecular InteractionMIF25MIMIxMIMIx validatorcontact

MI-mapping   MI-CvSourceList

 MIF25IMEx  IMEx validator  contactMI-mapping-Imex
 MIF25PAR  PAR validator  contactPAR-mapping
PAR-CvSourceList
Mass SpectrometrymzMLMIAPE-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 validatorscode in C++ 
Proteomics InformaticsmzIdentML 1.1.1MIAPE-MSI

Java mzIdentML validator

 

Java code here

mzid-mapping

miape-msi-rules

object-rules

miape-object-rules

Protein SeparationGelML (version 1.1 candidate)MIAPE-GEGelML validator Available hereGelML-mapping (draft)

 

 


 

 

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