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The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data.

Cytoscape is an open source software platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.

SWAT4LS aims at providing an open and stimulating environment that brings together researchers, both developers and users, from the various fields of Biology, Bioinformatics and Computer Science, to discuss goals, current limits and real experiences in the use of Semantic Web technologies in Life Sciences.

As with any Web Services framework, SADI can expose any source of dynamically-generated information. In most cases this means Web-based analytical algorithms, but any source of data would be applicable - including robots, or even distributed human curators. Because SADI Services are stateless and atomic, Web Services that expose a set of stateful object methods cannot easily be exposed as SADI Services (though in many cases these services could be re-written to follow SADI conventions, and take advantage of the added semantic behaviours). Our observations suggest, however, that almost all services currently available in the bioinformatics space have a SADI-like behaviour that easily maps onto the SADI conventions.

OBO-Edit is optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. OBO-Edit is developed by the Berkeley Bioinformatics and Ontologies Project, and is funded by the Gene Ontology Consortium. Contributions to the OBO-Edit codebase are always welcome.

The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The groups developing ontologies who have expressed an interest in this goal are listed below, followed by other relevant efforts in this domain.