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{bio,medical} informatics

Wednesday, May 10, 2000

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Online Journal of Bioinformatics Bioinformatics and Extended Markup Language (XML)
"Bioinformatics is the systematic development and application of computing systems and solutions to enhance biological research but mostly to analyze gene and genomic data through experimentation, modeling, database searches, and instrumentation. Gene identification has become a priority as the human genome is decoded. Users are presently restricted by having to analyze multiple sequence databases, compare results from different algorithms, and compute and analyze alignments or linkage results at database level. The present study evaluates current genetic terms, Extended Markup language (XML), Document Type Declaration (DTD) genomic files, and genetic databases for the purpose of developing a wider electronic access platform. XML files were generated with Python and parsed against their DTD's. Many of the current genomic DTDs consisted of general access, formatting, reference and genetic elements in one XML file. Genetic databases had different terms for the same item. The authors propose the use of informative terms and the separation of elements. A unified platform to access the domain is proposed. "
bioperl XML Project
"The purpose of this web site is to coordinate information dissemination and discussion on the use of XML in bioinformatics, and to serve as a repository for metadata describing the relationships between biological XML data resources."

"Biology is a complex discipline and a wide variety of data resources and repositories have been developed to support biological research. Many of these are interrelated, but it is currently difficult to identify or use these in relationships computationally because the different data sources use incompatible formats and semantics. XML offers a way to serve and describe data in a uniform and automatically parseable format."

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."

[ 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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