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Discussion of

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

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  1. Discussion of Pathway Databases: A Case Study in Computational Symbolic Theories By Peter D. Karp

  2. Types of Information • Biological entities • Data (observations/measurements of experimental results) • Theories • “relationships inferred from interpretation and synthesis of many experimental results”

  3. Pathway Database • Pathway defined: “linked set of biochemical reactions” • PGDB – pathway/genome db • Combines genome information with pathway

  4. 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.

  5. 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 (?)

  6. Current Cyc-like Databases • EcoCyc • MetaCuc • BsubCyc • CtraCyc • CauloCyc • HinCyc • Etc. http://biocyc.org/

  7. 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?

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