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features
This page describes some of the varied features of OWLTools. Some of these may eventually be split off into separate projects.
For a complete and current list of sub-projects, see the API docs
OWLTools leverages the full features of the OWL API and OWL Reasoner API, but provides convenience methods for common tasks.
Although OWLTools wraps the OWLAPI, many of the ontologies currently being used are maintained as obo-format files. OWLTools provides simple access for OBO-style annotation properties such as synonyms, as well as direct access of OWLObjects via OBO-style IDs or unique labels.
See for example:
All obo files are parsed using the OWL-API
- Graph Reachability Queries
OWLtools provides a fast way to perform graph operations that respect the semantics of the underlying OWL. For example, what classes are reachable from "heart valve", and what is the relationship?
- [owltools.graph] (http://owlcollab.github.io/owltools/api/owltools/graph/package-summary.html)
Examples:
Code kindly provided by Tony Sawford of QuickGO
- owltools.gfx
OWL ontologies and Gene Association files can be loaded into a customizable solr index using the OWL-Solr package. For more details see:
See http://wiki.geneontology.org/index.php/GOlr
- loading and saving of GAFs
- utilities such as map2slim and basic term enrichment
See WebServices
The Obo Ontology Release Tool is built on top of OWLTools
It is possible to do advanced operations via chaining owltools operations on the command line
owltools comes with a javascript library called PachyOwl
The OwlSim package provides the ability to do a number of standard semantic similarity methods and includes novel methods for combining these with dynamic selection of anonymous grouping classes.
- OwlSim
- owltools.sim2 Java API Docs
An implementation of the McGary et al approach, on top of the OWL API and using graph reasoning