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Uber-Database Strives to be the Hub of Human Biology

COLD SPRING HARBOR, NY, May 9 - An international team of researchers has created a novel Internet-based data hub that seeks to link two disparate scientific mainstays--fully automated genomic-annotation databases and hypothesis-driven research that fuels conventional scientific publishing.


This info-conduit, the Human Genome Knowledgebase, hopes to close the knowledge gap between these two ideas through a web site that integrates every bit and byte of data that describes human biological processes and pathways. Right now, though, the Knowledgebase, in its pilot stage, only carries data about DNA replication.


According to Elizabeth Nickerson, a researcher at Cold Spring Harbor Lab's genome and bioinformatics department, the Knowledgebase web site will be an intricate web of peer-reviewed "mini-reviews" of every aspect of human biology. Once completed, it will be a medium that links researchers around the world to the rich cache of data ranging from genomic and proteomic databases, literature reviews, and the Gene Ontology.


"Ultimately we want to be a comprehensive resource for people that want information about biological processes in the human organism," Nickerson told GenomeWeb beside her group's poster here at Cold Spring Harbor's 2002 Genome Sequencing & Biology meeting. "We'd like this to be a reliable place to go where you can say, 'I don't understand this topic,' and 'What's known about this topic and how do I link out to everything else that is known about it?'"


For example, complete pathways are described as text with assertion statements nearby. These are written in short-form, bulleted style that is meant to help readers better comprehend the key parts of a particular biological process. It will likely play an important role in scientific research; currently there are resources, like online textbooks, but they don't link scientists to original papers or to the genome databases, Nickerson said.


"We approached a lot of people in different fields to be authors because the information should come from people in the fields and is peer-reviewed by people in the field," Nickerson said in the early-evening chill outside Vannevar Bush Hall overlooking Cold Spring Harbor's sprawling, manicured campus. "When I approached the authors, more often than not they say, 'This is great,' and 'Something like this is really needed.' So many are enthusiastic about this that they're ready to get on board and write for us."


The research, which is funded by a grant from the US National Institutes of Health, included work by researchers at Lawrence Berkeley Lab and the Wellcome Trust.

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