FMAInOwl

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We have created a transformation for the FMA into OWL that pursues the following two goals:

1. representing only the information that is explicitly present in the frames representation of the FMA or that can be directly inferred from the semantics of Protege frames;

2. representing al l the information that is present in the frames representation of the FMA, thus producing an OWL representation for the complete FMA.

The description of the transformation is available as an SMI Technical report SMI-2007-1234

The OWL representation of the FMA is available at http://bioontology.org/projects/ontologies/fma

If you want to access the OWL file directly, point your OWL tool (e.g. the Protege OWL ontology editor) to

http://bioontology.org/projects/ontologies/fma/fmaOwlFullComponent_2_0.owl

Note that it will use owl:imports to import another OWL ontology in the same directory (http://bioontology.org/projects/ontologies/fma/fmaOwlDlComponent_2_0.owl).

The conversion script is also available: download the FMA-TO-OWL Converter

The conversion script takes the following arguments:

- the path to the Protege project with the frames version of the FMA

- the namespace to use for the OWL DL component

- the namespace to use for the OWL Full component

Note: the following files (available in the Protege installation directory must also be on the classpath): icu4j_3_4.jar:iri.jar:xercesImpl.jar:protege.jar:commons-logging.jar:jena.jar:driver.jar:protege-owl.jar

Obo Translation

There is an alpha version of the translation of the FMA2 to obo

This is based on a translation of the OWL above by cjm. It is independent of yet dependent on the OWL translation above.

The translation captures a subset of the relations used in the FMA (specifically spatial relations) and of the metadata (synonyms). The goal is to conform to OBO and RO guidelines.

UPDATE: 2008/10/12

Please contact the obo-admin list concerning the obo translation

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