A case study in pathway knowledgebase verification

Background: Biological databases and pathway knowledgebases are proliferating rapidly. We are developing software tools for computer-aided hypothesis design and evaluation, and we would like our tools to take advantage of the information stored in these repositories. But before we can reliably use a pathway knowledgebase as a data source, we need to proofread it to ensure that it can fully support computer-aided information integration and inference. Results: We design a series of logical tests to detect potential problems we might encounter using a particular knowledgebase, the Reactome database, with a particular computer-aided hypothesis evaluation tool, HyBrow. We develop an explicit formal language from the language implicit in the Reactome data format and specify a logic to evaluate models expressed using this language. We use the formalism of finite model theory in this work. We then use this logic to formulate tests for desirable properties (such as completeness, consistency, ...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Stephen A. Racunas, Nigam Shah, Nina V. Fedoroff
• Keywords: BMCBI 2006, Computer-aided Hypothesis, Hypothesis Evaluation Tools, Pathway Knowledgebase