EXACT (An ontology of EXperiment ACTions)

We propose the EXACT ontology as the basis of a method of representing biological laboratory protocols. EXACT provides a model for the description of experiment actions, and it can be used for the fully formalized representation of protocols, or it can be combined with other formalisms for the description of bio-medical investigations.

Examples of protocols formalised using EXACT

• Yeast competent cells v1 protocol.
• Compound library reformatting protocol.

Ontology

Files for use in Protege:

The ontology (EXACT/EXPO):

• EXACT-EXPO-May2008.owl
• EXACT-EXPO-May2008.pprj

The ontology (EXACT/OBI):

• EXACT-OBI-May2008.owl
• EXACT-OBI-May2008.pprj

An example using the ontology:

• EXACT-example.owl
• EXACT-example.pprj

Implementation in Haskell

Examples of how parts of the Competent Cells protocol could be implemented in a programming language for validation/simulation purposes.

• CompetentCells.hs
• Actions.hs