February 8-11, 2009 Bethesda, Maryland
GTL Awardee Workshop VII and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop
Charles Parker will be presenting poster number 135 (“NamesforLife Semantic Resolution Services for the Life Sciences”, Abstract Book, page 182) in the Tuesday afternoon poster session of the Genomes-to-Life Awardee Workshop.
While you’re here please also visit poster 134 (“Release of Taxomatic and Refinement of the SOSCC Algorithm”, Abstract Book, page 180) for updates on the SOSCC algorithm and poster 136 (“Standards in Genomic Sciences: an Open-Access, Standards-Supportive Publication that Rapidly Disseminates Concise Genome and Metagenome Reports in Compliance with MIGS/MIMS Standards”, Abstract Book, page 183) for information on the launch of a new Open Access journal, Standards in Genomic Sciences.
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 target audience of N4L services is the broad scientific community and others who may need to know the precise meaning of biological names or other terms, in correct temporal context as they are encountered in other digital content (scientific or technical literature, regulatory literature, databases, etc). The dynamic, yet asynchronous nature of biological nomenclature and similar terminology poses a significant burden on information providers, as they must either invest in constantly maintaining their offerings to keep current or shift that burden to their end-users. If the former, the costs can be significant, and, in the absence of a means to synchronize updates across an entire domain of knowledge, end users are still confronted with apparent discrepancies across data sources and content providers. If the burden is shifted to end-users, they must then locate alternative information sources, typically hosted through a web portal, that must be queried separately. This makes utilization of content cumbersome and can lead to considerable ambiguity.
The NamesforLife approach is to semantically enable content in a manner that is transparent to end-users at two points in the value chain: at the source (the data provider or publisher) and at the client side (the end-user). In either case, the end-user experience is the same. At each occurrence of a validly published bacterial or archaeal name, they can have access to precise authoritative information by simply clicking on the name. Tools to enable publishers’ content at the pre-publishing stage that embed persistent N4L identifiers in inline text ensures that their readers will always have access to the correct meaning of the name (as well as additional information), even if the name has changed since publication. Our web-based client supports semantic enablement of other digital content, on-the-fly, providing similar seamless access to NamesforLife content at each point where a validly published name occurs. This provides the reader with direct access to a wealth of information to aid in the interpretation of each enabled article.
[permalink] Posted February 8, 2009.