Obol
From GO Public
Obol is the name of a piece of software for automatically generating cross-product definitions (aka genus-differentia definitions) from the names of terms/classes in OBO ontologies. It relies on (a) a consistent grammatical style employed in naming terms or exact synonyms (b) Consistent naming across ontologies
Obol generates results in .obo format, which can also be converted to owl. The results are in the form of genus-differentia definitions, which can then be fed into a reasoner to check for consistency between and within ontologies, or can be used for cross-ontology queries
Obol will also generate synonyms for terms, based on the synonyms of the cross-product component terms. It will also (to a lesser extent) generate textual definitions, based on the xp definition, and the standard definition forms used in GO
Contents |
[edit] Reference
Christopher J. Mungall Obol: integrating language and meaning in bio-ontologies Comparative and Functional Genomics; Volume 5, Issue 6-7, 2004. Pages 509-520
[edit] Results
- http://www.berkeleybop.org/obol (This page is not kept up to date)
See also
- http://berkeleybop.org/ontologies#logical_definitions -- many of the XPs here were seeded using obol
Most of the current results are directly integrated into Category:Cross Products .obo files
[edit] Grammars
[edit] Availability
The current version of obol is a sub-package in the blipkit svn repository
The version of obol used in the 2004 CFG paper is still available in the obol directory in geneontology cvs on sourceforge. See geneontology sf page. The atomic vocabulary is available in cvs
