mzIdentML validator - Semantic validation of mzIdentML 1.1 and 1.2 files
The mzIdentML validator is based on the [PSI validator generic framework] (http://www.psidev.info/validator) which is described in detail in the following [tutorial] (http://www.psidev.info/validator-tutorial-0).
The mzIdentML validator makes use of mapping files describing at which positions in the data files which CV terms from the [psi-ms.obo ontology] (https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo) are allowed. In addition there are object rules (encoded in Java) for cases where a configuration via the mapping file mechanism is not possible.
All mapping / object rules which are violoated are reported in coloured output encoding the type of violated rule:
A violated MUST rule is reported in red (ERROR message) A violated SHOULD rule is reported in orange (WARNING message) A violated MAY rule is reported in green (INFO message) An Unanticipated CV term (WARNING) message occurs, if there is a CV term is found in the .mzid data file, for which no mapping rule exists in the mapping file. This points to a possibly forgotten CV mapping rule.
The latest version of the mzIdentML validator can be downloaded [here] (https://github.com/HUPO-PSI/mzIdentML/blob/master/validator/mzIdentMLValidator_GUI_v1.4.32-SNAPSHOT.zip)
More details about the mapping file mechanism and the validator are described in the following publications:
Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M. Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):98-107. doi: 10.1016/j.bbapap.2013.02.017. Epub 2013 Feb 19. [pdf] (http://ac.els-cdn.com/S1570963913000800/1-s2.0-S1570963913000800-main.pdf?_tid=fa5771ec-0acb-11e6-90c5-00000aab0f6b&acdnat=1461578367_5d20743396f240fc9fbb9075ed94a4c8)
Ghali F, Krishna R, Lukasse P, Martínez-Bartolomé S, Reisinger F, Hermjakob H, Vizcaíno JA, Jones AR. Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML. Mol Cell Proteomics. 2013 Nov;12(11):3026-35. doi: 10.1074/mcp.O113.029777. Epub 2013 Jun 28. [pdf] (http://www.mcponline.org/cgi/pmidlookup?view=long&pmid=23813117)