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README.md

mzIdentML validator - Semantic validation of mzIdentML 1.1 and 1.2 files

General

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.

Download link

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)

Literature

More details about the mapping file mechanism and the validator are described in the following publications: