Software Tools

 

Ontology Repositories / Browsers

(For links to individual ontologies and projects, see this page.)

Ontology Editors

APIs / Libraries

  • Bio::Chado::Schema (Perl interface for Chado, incl. CV module) (cpan)
  • OWL API – Most widely used API for OWL. Provides support for a whole range of OWL reasoner. Under active development (http://owlapi.sourceforge.net/) with a good, active mailing list. Built-in OBO to OWL conversion is incomplete but usable.
  • GO::perl: http://search.cpan.org/~cmungall/go-perl-0.13/go-perl.pod – Various OBO tools in perl. Among other things, useful for graph navigation. Not under active development (?)
  • Ontoperl: http://search.cpan.org/~easr/ONTO-PERL/ – Set of OBO tools in perl. Under active development. Note, at time of writing, OBO to OWL conversion in onto perl uses a deprecated spec. The resulting OWL ontologies are very slow to reason with.
  • Pellet: http://clarkparsia.com/pellet/ – Open source owl reasoner and associated API (the same company has proprietary RDB-based reasoners as well).
  • obo_parser: https://github.com/mjy/obo_parser – A Ruby gem reads obo files into a simple class object (memory).

Ontology Based Interfaces

  • Phenoscape Knowledgebase: http://kb.phenoscape.org, http://www.phenoscape.org – Combines ontologically annotated phenotypic character data for a large and diverse group of fishes with phenotypic annotations from the ZFIN model organism database. The web application provides query and browsing interfaces which allow users to exploit the the logical framework provide by the ontologies which underpin the data.
  • eagle-i: http://www.eagle-i.net/ – Search and data curation interfaces driven off of an ontology. External ontologies imported via OWL.
  • LepTREE: http://www.leptree.net/ – Community collaboration dedicated to advancing progress toward a phylogenetic tree for all Lepidoptera.
  • Hymglossary: http://glossary.hymao.org

Converters and Import Tools

  • obolib: http://oboformat.googlecode.com – Coverts OBO to OWL using the new (draft) OBO 1.4 standard conversion. This is the most complete mapping of OBO to OWL available. For the first time, it converts domain, range and property chains and completely parses annotation properties (definitions, references, synonyms).
  • OntoFoxhttp://ontofox.hegroup.org/ – Supports MIREOT imports in OWL.

Curation and Workflow Tools

EQ Data Stores

Reasoners

Visualization Tools

Alignment Tools

Concept Mapping Tools

Educational Resources / Outreach