Leland Stanford Junior University

Mark Musen

Leonore A Herzenberg

David R Parks

Wayne A Moore

Stephen W Meehan

Russ B Altman

Nigam H Shah

Yael Garten

James Tung

Adrien Coulet

Methods for developing an ontology of pharmacogenomics (PGx) relationships starting from a lexicon of key pharmacogenomic entities and a syntactic parse is described. The syntactic structure of PGx statements is used to systematically extract commonly occurring relationships and to map them to a common schema. In an embodiment, extracted relationships have a 70-87.7% precision and involve not only key PGx entities such as genes, drugs, and phenotypes (e.g., VKORC1, warfarin, clotting disorder), but also critical entities that are frequently modified by these key entities (e.g., VKORC1 polymorphism, warfarin response, clotting disorder treatment).

Method and system for extraction and normalization of relationships via ontology induction

The present invention is related to databases and the exchange of scientific information. Specifically the invention discloses a laboratory data management system including a knowledge base that stores characteristics of laboratory reagents, experiment subjects, tissues and cells. The invention also includes an experiment input module that accepts input of parameters of an experiment and data from a knowledge base module. Further, the invention includes a protocol creator connected to the knowledge base module and the experiment input module that creates a laboratory protocol for an experiment based on data supplied from the knowledge base module and the experiment input module. The invention also includes methods to use the described system.

System and method for internet-accessible tools and knowledge base for protocol design, metadata capture and laboratory experiment management

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Palo Alto, CA, United States of America

Mark Musen