{bio,medical} informatics
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GenomeWeb
Nature Clarifies Role in GEML Community; Denies it 'Endorses' Standard "While the Nature Publishing Group has joined Rosetta Inpharmatics's Gene Expression Markup Language Community, the journal " is not taking sides or picking any standard over another," a Nature spokesman said Friday."
"This clarification of Nature's role in the GEML community came in response to Rosetta's recent public relations campaign, which claimed the journal " officially endorses" the GEML standard.
The announcement prompted the Microarray Gene Expression Database Group to send a letter to the journal stating that the Microarray Markup Language, which the MGED supports, has wider support in academia and industry."
redux [10.13.00]
"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]
"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?"
[ 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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