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Discussion of. Pathway Databases: A Case Study in Computational Symbolic Theories By Peter D. Karp. Types of Information. Biological entities Data (observations/measurements of experimental results) Theories
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Discussion of Pathway Databases: A Case Study in Computational Symbolic Theories By Peter D. Karp
Types of Information • Biological entities • Data (observations/measurements of experimental results) • Theories • “relationships inferred from interpretation and synthesis of many experimental results”
Pathway Database • Pathway defined: “linked set of biochemical reactions” • PGDB – pathway/genome db • Combines genome information with pathway
EcoCyc • EcoCyc PGDB begun in 1992 • Extended and expanded to include more cell functions, such as transporters, etc. • Pathway tools • Allow querying of database • Allow visualization of paths, etc.
EcoCyc and Inference • Strict ontology • 1000 classes encoding key concepts • 200 slots defining properties and relationships among classes • Biological objects/relationships stored in “frames” • Reasoning across the database • By computation, nonnumerical • Using symbolic computing (?)
Current Cyc-like Databases • EcoCyc • MetaCuc • BsubCyc • CtraCyc • CauloCyc • HinCyc • Etc. http://biocyc.org/
Questions • How does this symbolic computing work? • Do the cyc databases have a common structure? Can the visualization and query tools be used on any of them? • Is UltraStructure a type of pathway database? • What kind of problems can be and have been solved using pathway databases?