The NCBI Taxonomy database (http://www.ncbi .nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC's nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community. The NCBI Taxonomy project began in 1991, when we designed the first version of the Entrez information retrieval system. At that time, each of the partners of what was to become the International Nucleotide Sequence Database Collaboration (INSDC)-GenBank, EMBL and the DDBJ-maintained the taxonomic nomenclature and classification in their own sequence entries independently. The classifications used by the three partners were clearly derived from a common source, but had drifted apart over the years. Sequence entries were regularly exchanged within the collaboration, but the source organism nomenclature and taxonomic classifications were inconsistent and were updated irregularly. Protein sequences were maintained separately from the nucleotide sequences, in two different databases-Swiss-Prot (1) and PIR (2). Each of these databases maintained their own taxonomies, each very different from the other and from the more closely related taxonomies in use by the INSDC partners. Entrez (3) was the first system to link nucleotide sequences and protein sequences (from all of these sources) together with relevant abstracts from the scientific literature in a single unified resource. It was obviously important to provide a single taxonomic classification to index the entire set of entries in Entrez. The first step was to shuffle together the taxonomies from each of the contributing databases, each of which covered a somewhat different set of species with often very different internal classifications. The end result of this process was a hideous abomination, but it did provide a single classification that spanned all of the entries in Entrez, which we set out to improve. At this point we hosted series of taxonomy workshops to provide advice and direction for the project. David Hillis, John Taylor and Gary Olsen, in particular, put in a significant amount of time and effort in the initial cleanup of our merged classification. The next step forward was the 1997 agreement by the INSDC members to resolve taxonomic issues of nomenclature and classification prior to the release of new sequence data. Sequences submitted to GenBank are screened for organism names that are new to the taxonomy database, and result in a taxonomy consult sent to the taxonomy group. Prior to this agreement, we would not see the organism names in entries from the collaborating databases until they had been released to the public-issues involving synonymies, misspellings and alternate classifications had to be resolved and corrected after the fact. To improve this situation, the INSDC partners agreed to send taxonomy consults to the NCBI when they first processed their entries, just as the GenBank indexing group does. As a consequence, the NCBI agreed that our public taxonomy pages would only show taxa that are linked to public sequence entries. The NCBI Taxonomy database was developed to fill a practical and very specific need-to provide nomenclature
The corpus was used for the development and evaluation of their NER tool based on the dictionary provided by the NCBI taxonomy database REF for detecting species names.
The NCBI Taxonomy database
Nucleic Acids Research
Nucleic Acids Research
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