What ontologies that cover both biology and chemistry world are you aware of?
This was selected as Best Answer Sepp, I think taking a look at what the National Library of Medicine is doing in that area is a good starting point. The link below is to the “Health Information Technology and Health Data Standards at NLM” web-page. There are several ontologies with different focus (clinical findings, clinical labs, Rx), but you might find much of what your looking for in SNOMED-CT, quoting from their site: The January 2007 release of SNOMED-CT contained over 308,000 active concepts portrayed by more than 777,000 active descriptions and associated to each other by in excess of 924,000 defining relationships. These concepts with their inherent unique meanings and formal logic-based definitions are arranged into 19 hierarchies covering the following areas: Clinical findings Procedures/interventions Observable entities Body structure Organism Substance Pharmaceutical/biologic product Specimen Qualifier value Physical object Physical force Environments/geographic locations
