Event

February 7-10, 2010 Crystal City, Virginia

Genomic Science 2010

Awardee Workshop VIII and USDA-DOE Knowledgebase Workshop
The adoption of DNA sequencing as the preferred method of rapidly characterizing Bacteria and Archaea has tremendously accelerated during the past five years, with the expected consequences. At present, the rate at which “named” sequences are added to the GenBank taxonomy exceeds the rate at which validly published names appear in the taxonomic record by a factor of approximately 35. This confounds the retrieval of related information from various databases and the scientific, technical and medical literature as many of these invalidly named species can not be readily tracked over time, nor can relationships be inferred to those species for which at least one genome sequence is available. This disconnect between the knowledge contained in the literature and the accumulated genomic data is likely to grow as faster and cheaper sequencing methods come into the market place.
The adoption of DNA sequencing as the preferred method of rapidly characterizing Bacteria and Archaea has tremendously accelerated during the past five years, with the expected consequences. At present, the rate at which “named” sequences are added to the GenBank taxonomy exceeds the rate at which validly published names appear in the taxonomic record by a factor of approximately 35. This confounds the retrieval of related information from various databases and the scientific, technical and medical literature as many of these invalidly named species can not be readily tracked over time, nor can relationships be inferred to those species for which at least one genome sequence is available. This disconnect between the knowledge contained in the literature and the accumulated genomic data is likely to grow as faster and cheaper sequencing methods come into the market place.

Charles Parker will be presenting poster number 231 (“NamesforLife Semantic Resolution Services for the Life Sciences”, Abstract Book, page 179) in the Tuesday afternoon reception and scientific mixer of the Genomes-to-Life Awardee Workshop.

Please also visit poster 230 (“Standards in Genomic Sciences: Launch of a Standards Compliant Open-Access Journal for the ‘Omics Community”, Abstract Book, page 178) on Monday evening for an update on the recently launched Open Access journal Standards in Genomic Sciences.

Now that the Bacterial Nomenclature database is complete and updated in synchrony with the valid publication of nomenclatural changes, NamesforLife is in the process of linking together Bacterial Nomenclature, technical literature, and the various projects of the Genomes-to-Life program. In N4L, each individual organism is represented by a metadata object (an N4L Exemplar), which is identified by a DOI.

An N4L Exemplar aggregates what is known about an individual organism. The Genomes OnLine Database (GOLD), Standards in Genomic Sciences (SIGS), Genomic Encyclopedia for Bacteria and Archaea (GEBA) and Genomes and Metagenomes Catalogue (GEM) all use unique identifiers that link to each other in some way; via the GCat identifier, GOLD stamp, and GEBA Taxon Identifier. However, there is no single common link to the literature. NamesforLife is closing this gap by tying these disparate sources of information together via N4L Exemplars, which are integrated with the N4L Nomenclature Database and N4L Contextual Index.

The Beta release of the N4L Browser Add-on is officially scheduled to coincide with the Society for General Microbiology conference at the end of March 2010, but it is already available for early testing. Instructions on installation and use can be found at the NamesforLife website. This Firefox Add-on detects and links bacterial names to the N4LDB, providing up-to-date nomenclature, strain and genome information, and a full bibliography.

Parker et al., “NamesforLife Semantic Resolution Services for the Life Sciences”

Download Poster (2.3MB PDF) Download Abstract Book (10.5MB PDF)

[permalink] Posted February 1, 2010.

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