The Bio-Ontologies SIG provides a forum for discussion of the latest and most innovative research in the appplication of ontologies and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. Bio-Ontologies has existed as a SIG at ISMB for 13 years, making it one of the longest running.
The Bio-Ontologies kblog site is a kblog which operates as repository for papers accepted for presentation at the SIG. All articles have permanent URLs (as well as DOIs) and can be cited through these. The site is archived by the UK Web Archive. This kblog is the first of its kind, and now hosts 3 years of Bio-Ontologies papers
You may also be interested in Ontogenesis which also publishes papers about ontologies, but designed as a tutorial rather than primary research content.