during the Metabolomics Workshop we got to know
the ISA-Tab format, introduced by Phillipe Rocca-Serra.
ISA-Tab can describe (among others) a set of metabolomics profiling
experiments, users, experiment factors, plants, ...
so it is a perfect match as an input format to MetWare.
The next thing that will be built is a standalone import utility,
which reads the ISA-Tab CSV files, creates MetBeans from the information
(using classes from metbeans.jar and bigmet.jar) and persists them
in the metware database using the save() methods of our metbeans
During the first steps, this ISA-Tab <-> MetWare binding will be done
manually, and for things like "experiment" and "user" the mapping
should be trivial.
Once we have some (likely incomplete) import of ISA-Tab into MetWare,
the next step would be to build a SKOS-ified ISA-Tab, which allows
a mapping of terms form ISA-world to MetWare-world.
Once we have that, the core of the import utility can be rewritten
to use the ISA-SKOS for Building the corresponding MetWare Objects,
so that the converter can remain fixed, even if the Ontologies evolve.
Egonw, your opiniion ? Suggestions ?
IPB Halle AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann http://www.IPB-Halle.DE
Weinberg 3 http://msbi.bic-gh.de
06120 Halle Tel. +49 (0) 345 5582 - 1470
+49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409