Friday, September 15, 2000

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Individual.Com Gene Expression Markup Language (GEML(TM)) - a Data format to Facilitate the Interchange of Gene Expression Data from Multiple Technologies - NOW AVAILABLE
"Rosetta Inpharmatics, Inc. (Nasdaq: RSTA) announced today the availability of a new file format, called Gene Expression Markup Language (GEML), to facilitate the interchange of data from DNA chip and other gene expression technologies into a consistent format for more efficient and extensive data analysis."

"GEML is an extensible markup language (XML-based) data file format that operates independently of any specific database schema. GEML supports data from various gene expression platforms including Affymetrix, Agilent, Incyte, Molecular Dynamics, 1-color or 2-color fluorescent labeling and scanning, nylon filters, and other data formats. GEML also tracks which data format was used, and with this knowledge enables normalization, integration, and comparison of data across technologies."

"As part of Rosetta's efforts to encourage this potential industry standard for gene expression data, Rosetta intends to offer users of GEML additional tools for viewing and analysis of genomic data in GEML format."

Rosetta Inpharmatics The Gene Expression Markup Language (GEML)
"This data standard is designed to separate data reporting and collection from methodology used. The profile_type attribute enables keeping track, in the data file, of which methodology was used, enabling normalization across methodologies and thus comparison of data which was collected by a variety of methodologies.

Expression analysis data is generated by a variety of sources and is usually stored in the form of disk files. Industry-wide standards for the formats of such files do not exist, so there are now many different formats, with different representations of data and different types of information stored. For example, some data file formats for chip scans reference a specific pattern, while others do not. Similarly, some data file formats for chip scans can contain the raw image data or can reference one or more image files, while others cannot.

"GEML is a free, public-domain, open-standard XML DTD. GEML was created and is licensed in order to define a single, distinct GEML format and avoid proliferation of incompatible variations.

You may freely use, publish, and redistribute the GEML DTDs, subject to the restrictions in these Terms of Use; write and sell applications which create, load, or write GEML-compliant files; or distribute or sell your own GEML-compliant files. You may transmit verbatim copies of the GEML DTD to any person if the entire original DTD file is transmitted and the recipient accepts the terms and conditions of this GEML Terms of Use.

You may not modify, lease, loan, sell, distribute, charge for, or create derivative works of the GEML DTDs, without written permission from Rosetta Inpharmatics."

The Rand Corporation : Scaffolding the New Web: Standards and Standards Policy for the Digital Economy The Emerging Challenge of Common Semantics
"With XML has come a proliferation of consortia from every industry imagineable to populate structured material with standard terms (see Appendix B). By one estimate, a new industry consortium is founded every week, perhaps one in four of which can collect serious membership dues. Rising in concert are intermediary groups to provide a consistent dictionary in cyberspace, in which each consortium's words are registered and catalogued.

Having come so far with a syntactic standard, XML, will E-commerce and knowledge organization stall out in semantic confusion?"

"How are semantic standards to come about?"

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."