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{bio,medical} informatics

Saturday, February 24, 2001

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find related articles. powered by google. Stanford Medical Informatics Preprint Archive One Size Does Fit All: Acquiring Semantic Web Contents with Protege-2000
"One of the most recent trends in the evolution of the World Wide Web is the growing awareness of the need for a Semantic Web, a Web of information that machines can understand and process. The requirement to encode machine-interpretable information on the Web led to the development of a number of languages for representing this information. These languages are coming from different communities that have different sets of requirements and goals in mind. The languages that are emerging have many similar features, but each of them is different from the others. Currently, there is no consensus on which language or set of languages should become the standard and researchers and developers continue to experiment with the existing languages and to develop new ones. Protege-2000 is an ontology-development and knowledge-acquisition environment developed in our laboratory. It has a graphical user interface which enables ontology developers to concentrate on conceptual modeling without knowing or thinking about syntax of an output language. Protege-2000 has a flexible knowledge model and an extensible plugin architecture. These two features allow developers to adapt Protege-2000 quickly and easily to work as an ontology-editing environment for new Semantic Web languages; there is no need to create new tools for these languages from scratch. As a result, developers obtain a graphical and easy-to-use editor for conceptual models in the new language. They can experiment with the features of the language, decide if the language itself is sufficiently expressive, or sufficiently flexible to meet their requirements. In this paper, we describe how Protege-2000 can be adapted for editing models in different Semantic Web languages. We describe as examples Protege-based editors for RDFS and OIL."
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-à-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."

redux [10.13.00]
find related articles. powered by google. Scientific American Hooking up Biologists: Consortia are forming to sort out a common cyberlanguage for life science
"Imagine that your co-worker in the next cubicle has some information you need for a report that's due soon. She e-mails it to you, but the data are from a spreadsheet program, and all you have is a word processor, so there's no possibility of your cutting and pasting it into your document. Instead you have to print it out and type it in all over again. That's roughly the situation facing biologists these days. Although databases of biological information abound--especially in this post-genome-sequencing era--many researchers are like sailors thirsting to death surrounded by an ocean: what they need is all around them, but it's not in a form they can readily use.

To solve the problem, various groups made up of academic scientists and researchers from biotechnology and pharmaceutical companies are coming together to try to devise computer standards for bioinformatics so that biologists can more easily share data and make the most of the glut of information resulting from the Human Genome Project. Their goal is to enable an investigator not only to float seamlessly between the enormous databases of DNA sequences and those of the three-dimensional protein structures encoded by that DNA. They also want a scientist to be able to search the databases more efficiently so that, to use an automobile metaphor, if someone typed in "Camaro," the results would include other cars as well because the system would be smart enough to know that a Camaro is another kind of car."

"Eric Neumann, a member of both the Bio-Ontologies and BioPathways consortia, is a neuroscientist who is now vice president for life science informatics at the consulting firm 3rd Millennium in Cambridge, Mass. (no relation to Millennium Pharmaceuticals). He says Extensible Markup Language (XML) is shaping up to be the standard computer language for bioinformatics."

redux [09.15.00]
find related articles. powered by google. 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?"

find related articles. powered by google. 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."

[ 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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