GFO-Bio

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  1. 1. Development
  2. 2. Ontology
  3. 3. Tools
  4. 4. Acknowledgements

We create a biomedical core ontology based on the top-level ontology GFO (General Formal Ontology?).

There are versions in OWL which can be tried, and any input is very much appreciated. You will need a DL reasoner to classify the ontology. We recommend the use of SWOOP, which comes with the Pellet reasoner.

1.  Development

The CVS repository for GFO-Bio can be found on Savannah.

2.  Ontology

The URI of the ontology is http://onto.eva.mpg.de/gfo-bio/gfo-bio.owl and http://onto.eva.mpg.de/gfo-bio/gfo-bio-meta.owl If you use an ontology editor such as SWOOP, just enter the URI in the appropriate field.

gfo-bio.owl is an ontology of individuals, and it is similar in this sense to the Simple Bio Upper Ontology or the BioTop ontology. gfo-bio-meta.owl is an ontology of categories. Instances of classes in gfo-bio-meta.owl are some of the categories of gfo-bio.owl. It can be used to structure categories and ontologies according to the facet taken on the principle categories, Cell and Organsism.

Using http://onto.eva.mpg.de/gfo-bio/gfo-bio.owl and http://onto.eva.mpg.de/gfo-bio/gfo-bio-meta.owl together will yield OWL-Full, for which a reasoner such as Euler could be used.

3.  Tools

In order to convert ontologies available in the OBO file format to the OWL format, we provide a java package. The java package can be used to convert OBO ontologies to either the OWL format required for gfo-bio.owl or for gfo-bio-meta.owl.

4.  Acknowledgements

Many inspirations come from the Simple Bio Upper Ontology by Alan Rector, Robert Stevens, Jeremy Rogers and the CO-ODE and BioHealth Informatics Teams. Although most of the work is based on the General Formal Ontology, it has also been inspired by the DOLCE Ontology and the Ontology of Functions. Further sources for this work are the Open Biomedical Ontologies and the discussions on the OBO Relationship Ontology Mailinglist. Contact

If you try out our work, we would be very happy about feedback (even if you hate it). You are very much invited to join the development of this ontology. If you are interested, please contact Robert (hoehndorf (at) eva.mpg.de) or our public mailinglist (gfo-users (at) nongnu.org).