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{bio,medical} informatics

Saturday, November 08, 2003

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find related articles. powered by google. Bio-IT World Sun Microsystems Bolts I3C

"Loralyn Mears, Sun's market development group manager, life sciences, said, "Looking back the vision was grand: 'Let's create the solutions where everybody can plug everything in.' Well, you know it's hard to define what that everything is, especially when every couple of months there's a new everything to add."

"Over time, especially the last year, it became apparent that the I3C wanted to pursue a direction of formal specifications and standards, which was never really the original intent," said Mears."

redux [08.13.02]
find related articles. powered by google. Bio-IT World Necessary Liasons:Making Standards Work

"For researchers it's really about using the absolute best applications. Our universities are turning out a tremendous number of the most important applications that people are using -- there's huge innovation that happens in government and university labs. We need to be able to integrate the applications that come from both public and private sectors.

So the idea of I3C is to make this layer open, and agree on a set of standards. There will have to be a lot of domain specifics to this middleware architecture, probably done as XML vocabulary around particular areas of chemistry and biology and expression data analysis. And the applications will have to become compliant, so it is a little bit of work for the [informatics suppliers], but ultimately there's a value proposition for everybody."

redux [06.27.01]
find related articles. powered by google. GenomeWeb Informatics Infrastructure Consortium Unveils Demo Protocol

"The Interoperable Informatics Infrastructure Consortium (I3C) unveiled its first demonstration of a working protocol Tuesday at the BIO 2001 Conference."

The XML-driven format allowed the exchange and analysis of sequence data across 10 different organizations? products. I3C views the demonstration as a bridge to the next step to defining components needed for a more general open architecture."

redux [05.23.01]
find related articles. powered by google. The Washington Post Biotech Industry Developing Worldwide Standard for Data

"The new coalition, led by the Biotechnology Industry Organization (BIO), a Washington trade group, plans to spend the next year or so creating a detailed specification for biological data. This specification would be available without fee to any company or scientist that wanted to use it to help organize and mine information."

The project has been dubbed the Interoperable Informatics Infrastructure Consortium, or I3C."

redux [02.21.01]
find related articles. powered by google. Genomeweb Sun Forms Industry-Wide Collaboration to Develop Open Platform for Life Sciences

"Sun Microsystems said Wednesday it would partner with the Biotechnology Industry Organization, the National Cancer Institute, and several commercial bioinformatics vendors to support a collaborative effort to develop an open platform for the life sciences based on Java and XML.

The proposed initiative, temporarily referred to as Life Force or LI4 (Lifescience Informatics Interoperability Infrastructure Initiative) aims to develop an open platform to support data integration and interoperability and to focus the growing number of standards efforts."

redux [03.15.01]
find related articles. powered by google. MIT Technology Review Gene Babel

"Small DNA-laden wafers have transformed biology. Using these DNA chips, geneticists can see which genes are turned on, or expressed, in a cell at a particular time. Such gene expression experiments allow bioscientists to diagnose different diseases, quickly screen thousands of drug candidates for efficacy and safety and even learn the functions of newly discovered genes.

Sharing this information over the Web could lead to an explosion in biological knowledge. But each experiment generates gigabytes of data written in one of several formats, depending on the type of chip used. And with dozens of chips on the market and hundreds of ways to analyze the data, the Web is in danger of becoming a genetic Tower of Babel."

"Companies and academics have begun creating uniform formats for representing gene expression data, designed to work on any computer."

redux [05.10.00]
find related articles. powered by google. The XML Cover Pages XML and Semantic Transparency

"We may rehearse this fundamental axiom of descriptive markup in terms of a classical SGML polemic: the doubly-delimited information objects in an SGML/XML document are described by markup in a meaningful, self-documenting way through the use of names which are carefully selected by domain experts for element type names, attribute names, and attribute values. This is true of XML in 1998, was true of SGML in 1986, and was true of Brian Reid's Scribe system in 1976. However, of itself, descriptive markup proves to be of limited relevance as a mechanism to enable information interchange at the level of the machine.

As enchanting as it is to contemplate the apparent 'semantic' clarity, flexibility, and extensibility of XML vis--vis HTML (e.g., how wonderfully perspicuous XML <bookTitle> seems when compared to HTML <i>), we must reckon with the cold fact that XML does not of itself enable blind interchange or information reuse. XML may help humans predict what information might lie "between the tags" in the case of <trunk> </trunk>, but XML can only help. For an XML processor, <trunk> and <i> and <booktitle> are all equally (and totally) meaningless. Yes, meaningless .

Just like its parent metalanguage (SGML), XML has no formal mechanism to support the declaration of semantic integrity constraints, and XML processors have no means of validating object semantics even if these are declared informally in an XML DTD. XML processors will have no inherent understanding of document object semantics because XML (meta-)markup languages have no predefined application-level processing semantics. XML thus formally governs syntax only - not semantics."

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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