BNS Provides Faster Symbol Mapping

Biological databases typically tag their records with unique identifiers called accession numbers. These locators simplify record retrieval, but they are also database-specific, presenting a headache for bioinformaticians who want to map records in one database with their equivalents in another. Typically this is done manually, a tedious, error-prone task, especially when applied genome-wide.A few years ago, Robert Kincaid, a senior research scientist at Agilent Laboratories, Palo Alto, Calif.,

Jeffrey Perkel
Jun 6, 2004
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Biological databases typically tag their records with unique identifiers called accession numbers. These locators simplify record retrieval, but they are also database-specific, presenting a headache for bioinformaticians who want to map records in one database with their equivalents in another. Typically this is done manually, a tedious, error-prone task, especially when applied genome-wide.

A few years ago, Robert Kincaid, a senior research scientist at Agilent Laboratories, Palo Alto, Calif., came up with another approach. Inspired by Internet domain naming services that map, for instance, http://www.the-scientist.com to its actual address, 216.120.98.132, Kincaid developed the Biomolecule Naming Service (BNS, http://openbns.sourceforge.net).

Kincaid's prototype derives its lookup information from NCBI's LocusLink database. So, for example, it can resolve gene aliases into their preferred names or GenBank accession numbers to a UniGene cluster. But BNS is more generic than that and can map other types of data, Kincaid says in an E-mail.

Kincaid says...

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