Validation of mzQC Files

Here we give a brief overview of syntactic and semantic validation requirements of mzQC files. Full validation is implemented in the mzqc-pylib reference implementation.

Syntactic Validation

With the help of the mzQC JSON schema, mzQC instances can be readily checked for syntactic schema compliance. There are a number of JSON schema implementations for use in various programming languages that also support validation of JSON schema draft-07 from which the mzQC schema is designed.

Semantic Validation

Due to the advanced design of the mzQC JSON schema, many aspects of a valid mzQC file can already be verified via syntactic validation without the need of explicit semantic validation. There are, however, a few additional semantic rules that need to be followed to create fully compliant mzQC files.

• All used controlledVocabulary elements MUST reference a valid ontology.
• All used CV terms (including the quality metrics) must be present in one of the controlled vocabularies listed in the files controlledVocabularies element, matching in name and accession.
• All qualityMetric elements MUST be unique within their runQuality or setQuality parent.
• The value type of qualityMetric elements MUST match the specification in the CV (i.e. single value, n-tuple, matrix, or table).
• The value of qualityMetric MUST match its unit definition (and type implicitly).
• All columns of table qualityMetric elements MUST have the same length.
• label attributes in the metadata elements MUST be unique within its mzQC file.
• All inputFile elements MUST have a unique location attribute within their runQuality or setQuality element.

Additionally, more detailed checks might be performed to assess the validity of specific metric values on a case-by-case basis (e.g., percentages should sum to 100%).

Find out about more details on the validator page itself.

Online Validation

mzQC is web-native, and integrates nicely with modern applications and websites. You can find one example on this website if you visit the Validator.

We have several alternatives for validation, however. For these, have a look at the respective projects.

• jmzqc: Java library to create, process, and validate mzQC files.
• pymzqc: Python library to create, process, and validate mzQC files.