Biology Reference
In-Depth Information
Fig.
2
Schematic workfl ow of the MIAPE Extractor and MIAPE Generator tools
.
MIAPE information is automati-
cally extracted from mzML, mzIdentML, X!Tandem xml output fi le and PRIDE xml fi les, and it is stored in the
ProteoRed MIAPE repository. This MIAPE information can then be manually checked and edited using the
online MIAPE Generator tool which can generate MIAPE compliant reports that can serve as materials and
methods section or as supplementary material in a manuscript for publication
5.2.1 The MIAPE
Extractor
The
MIAPE extractor
tool provides automation to the PMWTK. It
is a Java
®
stand-alone application that allows, in a fully automatic
way, to extract MIAPE information from fi les such as PRIDE
XML, mzML, or mzIdentML, and stores it in the ProteoRed
MIAPE repository. So, the user can automatically generate MIAPE
MS and MSI compliant reports from his proteomics data and then
he can easily add missing MIAPE information by completing the
corresponding Web forms from the MIAPE Generator tool.
Additionally, the MIAPE Extractor tool is able to export MIAPE
MS and/or MSI documents from the repository to a PRIDE XML
fi le that will be MIAPE-compliant in case of these MIAPE reports
were complete, and that can be sent to the PRIDE public reposi-
tory for publication (Fig.
2
).
The MIAPE Extractor tool is developed using the ProteoRed Java
MIAPE API, an Application Programming Interface (API) coded
in Java that provides a data model for representing MIAPE GE,
GI, MS and MSI documents; it includes a set of functionalities to
extract MIAPE information from standard proteomics fi les; it also
offers several programmatic ways to manage and store MIAPE
information. This API licensed under an open-source license, is the
unique programmatic resource that allows the development of
tools managing MIAPE information.
5.2.2 The ProteoRed
Java MIAPE-API
