Biology Reference
In-Depth Information
Fig.
3
Schematic workfl ow of the semantic validators. Standard data fi les are submitted to the validator
software. If the fi le is MIAPE compliant, that is, it is semantically valid and contains all the data required by
MIAPE guidelines, the validator will show a validation report confi rming the MIAPE compliance of the fi le.
However, if the fi le is not valid, the validation report will contain some error messages explaining which infor-
mation is missing or missed placed in the fi le
Additionally, the bioinformatics working group of ProteoRed
is also providing a set of Web-services that offers interaction with
the ProteoRed MIAPE repository. So, it provides a remote and
secure access to stored MIAPE documents, as well as a way to
remotely store new MIAPE documents. The MIAPE Extractor
tool uses these Web-services to interact with the ProteoRed MIAPE
repository.
Together with the proteomics data representation schemas, a sys-
tem for validating standard data fi les has been developed by
HUPO-PSI. The called PSI semantic validator framework [
21
] not
only checks the XML syntax but it also enforces rules regarding the
use of an ontology class or Controlled Vocabulary (CV) terms by
checking that the terms exist in the resource and that they are used
in the correct location of a document. Moreover, this framework is
extremely fast, even on sizable data fi les, and fl exible, as it can be
adapted to any standard by customizing the parameters it requires:
an XML Schema Defi nition, one or more CVs or ontologies, and a
mapping fi le describing in a formal way how the semantic resources
and the format are interrelated. As such, the validator provides a
general solution to the common problem in data exchange: how to
validate the correct usage of a data standard beyond simple XML
schema defi nition validation. It also tackles the issue of checking
that experimental data reported using a specifi c format, CVs and
public bio-ontologies (e.g., Gene Ontology, NCBI taxonomy) are
compliant with the MIAPE recommendations. So, implementing
the PSI semantic validator framework for each standard data for-
mat, HUPO-PSI provides a tool able to validate all the standard
fi les (Fig.
3
).
5.2.3 Semantic
Validators
