Difference between revisions of "FMAInOwl"
| (11 intermediate revisions by 2 users not shown) | |||
| Line 7: | Line 7: | ||
The '''description''' of the transformation is available as an SMI Technical report [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1234 SMI-2007-1234] | The '''description''' of the transformation is available as an SMI Technical report [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1234 SMI-2007-1234] | ||
| − | The '''OWL representation''' of the FMA is available at [http://bioontology.org/projects/ontologies/ | + | The '''OWL representation''' of the FMA is available at [http://bioontology.org/projects/ontologies/fma 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 | 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/ | + | [http://bioontology.org/projects/ontologies/fma/fmaOwlFullComponent_2_0.owl 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/ | + | 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 http://bioontology.org/projects/ontologies/fma/fmaOwlDlComponent_2_0.owl]). |
| − | The '''conversion script''' is also available: download the [[Media: | + | The '''conversion script''' is also available: download the [[Media:fmaToOWL_v2.zip|FMA-TO-OWL Converter]] |
The conversion script takes the following arguments: | The conversion script takes the following arguments: | ||
| Line 26: | Line 26: | ||
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 | 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 | ||
| + | |||
| + | * [http://obo.svn.sourceforge.net/viewvc/obo/fma-conversion/trunk/fma2_obo.obo?view=log fma2_obo.obo] on OBO sourceforge | ||
| + | |||
| + | 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 | ||
| + | |||
| + | * Pre-release available on [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fma_lite FMA Page at OBO] | ||
| + | * [http://www.berkeleybop.org/ontologies/obo-all/fma_lite_prerelease/fma_lite_prerelease.owl fma_lite_prerelease.owl] | ||
| + | |||
| + | Please contact the obo-admin list concerning the obo translation | ||
Latest revision as of 19:14, 12 October 2008
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
- fma2_obo.obo on OBO sourceforge
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
- Pre-release available on FMA Page at OBO
- fma_lite_prerelease.owl
Please contact the obo-admin list concerning the obo translation