PATO2YAMATO

Aiming the facilitation of the advanced integration of measurement data across various biological experiments, we have investigated the fundamental methodology to expand the Phenotypic Quality Ontology (PATO) commonly used for descriptions of biological phenotypes with the framework of the Yet Another More Advanced Top-level Ontology (YAMATO). The mapping of ontology terms of PATO to YAMATO’s framework represents several advanced aspects such as the introduction of the classification of quality values to represent scales of measurements, the distinction of the different contexts of the comparison of ordinal values, and the establishment of the interoperability of quality description formalisms between different top-level ontologies. In this study, we propose a logical base to integrate cross-species and cross-experimental annotations of biological measurements.

Download

PATO2YAMATO

(version 1.0)
*Hozo file
*OWL file (in preparation)

View ontology

*Hozo Web viewer
(See quality value, property, and generic quality (screen shot) )
*RIKEN SciNeS viewer (in preparation)

EQ2EAV tool
A perl script to generate from EQ-double with PATO ontology to quality representation with EAV-triple.
* EQ2EAV

EQ2EAV_DB
A visualization tool of EAV styled biological measurement data in the database-like interface.
Caution: This tool is in development.
* EQ2EAV_DB.zip

Reference

Masuya H, Mizoguchi R. Toward fully integration of mouse phenotype information, Interdisciplinary Ontology, 2009 2: 35-44. PDF
Mizoguchi R. Yet Another Top-level Ontology : YATO, Proceedings of the 2nd Interdisciplinary Ontology Meeting, 2009: in press