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Discussion of

This case study delves into pathway databases, linking biochemical reactions, and utilizing symbolic computing for querying and visualizing biological relationships. Learn about EcoCyc, unique ontology, and reasoning in current Cyc-like databases.

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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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