Tuesday, May 28, 2002

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Wired News A Map That Maps Gene Functions

"The genetics revolution is generating such a gigantic glut of information that artificial intelligence may be the only way scientists will ever put it to practical use.

Inspired by an AI effort to record all of the common-sense knowledge shared among humans called Cyc, scientists have come up with a technology that can gather all of the information scientists know about an organism."

redux [09.19.01]
GenomeWeb Paper Calls for Broader Use of AI-Based Methods in Bioinformatics

"Future understanding of genomic data may be severely limited unless bioinformaticists gain a better understanding of knowledge representation, according to Peter Karp, director of SRI International's Bioinformatics Research Group."

"As biological research grows more and more dependent on information technology to make sense of increasing amounts of genomic data, Karp wrote, it will be crucial for bioinformaticists to keep up with new developments in symbolic computing. "The genome revolution is increasing the need for pathway databases in the biological sciences, and similar developments will occur in other sciences. However, effective implementation of this paradigm is hampered because most biologists (and most other scientists) receive essentially no education in databases or knowledge representation."

redux [08.19.01]
Stanford Medical Informatics Preprint Archive Management of Data, Knowledge, and Metadata on the Semantic Web: Experience with a Pharmacogenetics Knowledge Base

"Biomedical researchers are decoding the human genome with astonishing speed, but the clinical significance of the massive volumes of data collected remains largely undiscovered. Progress requires communication and data sharing among scientists. These data may be in the form of (1) raw data, derived data, and inferences that result from computational analyses, or (2) text documents published by experts who present their conclusions in natural language. The World Wide Web provides a valuable infrastructure for enabling researchers to share the rapidly growing knowledge about biology and medicine, and a fully functional Semantic Web is necessary to support data submission and retrieval, the sharing of knowledge, and interoperation of related resources."

redux [05.10.00]
SemanticWeb.Org Tutorial on Knowledge Markup Techniques

"There is an increasing demand for formalized knowledge on the Web. Several communities (e.g. in bioinformatics and educational media) are getting ready to offer semiformal or formal Web content. XML-based markup languages provide a 'universal' storage and interchange format for such Web-distributed knowledge representation. This tutorial introduces techniques for knowledge markup: we show how to map AI representations (e.g., logics and frames) to XML (incl. RDF and RDF Schema), discuss how to specify XML DTDs and RDF (Schema) descriptions for various representations, survey existing XML extensions for knowledge bases/ontologies, deal with the acquisition and processing of such representations, and detail selected applications. After the tutorial, participants will have absorbed the theoretical foundation and practical use of knowledge markup and will be able to assess XML applications and extensions for AI. Besides bringing to bear existing AI techniques for a Web-based knowledge markup scenario, the tutorial will identify new AI research directions for further developing this scenario."