[Home] [ICTV Taxonomy - Index of Viruses] [Virus Descriptions] [Character List] [Picture Gallery] [Tutorial] [Online Data Retrieval & Identification] [Virus Isolate Registration & Submission] [Search]

Structural Features of ICTVdB

The core infrastructure of ICTVdB is its "table of contents", the Index of Viruses, a list of approved virus names sanctioned by ICTV. Because virus names are changed frequently, contain diverse linguistic and geographical elements, and are usually coupled to a disease or its symptoms, virus nomenclature presents challenging semantic problems for a database. Thus ICTVdB now has several distinctive features not usually associated with taxonomy, but introduced of necessity. Chief among these is its decimal code. Originally introduced because the peculiar nomenclature used in virology defies direct and systematic interrogation in a database, and because virus taxonomy was changing rapidly, a decimal code (analogous to the code of enzyme nomenclature) seemed to offer a simple resolution of diverse problems.

Decimal Code

The decimal code is constructed in the Index of Viruses, and serves as a filename for database outputs as well as an accession number for external linkage to ICTVdB. The code was inspired by the recommendations on enzyme nomenclature prepared by the International Union on Biochemistry in 1978. In modern terms, it is analogous to the IP number of a PC. The decimal code at one and the same time affords unequivocal identification of a virus to the level of strain or isolate, and importantly, indicates its taxonomic context. For example, the close relationship between two semantically challenging members of the Family Reoviridae, Mal del Rio Cuarto virus (name includes geographical information) and Nilaparvata lugens reovirus (name includes vector/host and taxonomic family information), is immediately evident from inspection of their Decimal Codes (00.060.0.07.004 and 00.060.0.07.008 respectively). Moreover, the recent, controversial relegation of such widely used species names as Poliovirus 1, 2 and 3 to serotypes on the basis of pair-wise comparison of genomic data was conveniently accommodated by the code (Table 1).

The prevalence of zeros in the examples of the Code shown in Table 1 is designed to accommodate the rapid evolution of virus taxonomy in the direction of a more hierarchical and conventional Linnean systematic. The ICTV has yet to rule on higher-level taxonomy (Families, Orders and above) or on controversial concepts such as subspecies. Increasingly, the most pertinent new data are generated at the level of serotypes, strains and isolates. As taxonomy is revised in the light of new data, the history of the decisions will be tracked from the old to the new code, both of which are valid for search purposes. Now expanded to 19 digits to accommodate lower level taxonomic information, the code should cope with even the most ambitious "splitters" in the taxonomic community, indefinitely!

As the database developed, it became clear that the decimal code served as more than an unequivocal identifier for taxonomically correct internal linkages in the database. It is used as a filename for transposing ICTVdB to the web, and also serves as a surrogate accession number to link to ICTVdB used by sequence databases such as GenBank and Uniprot that link to ICTVdB. Taxonomic databases such as Species2000 and GBIF uses also these numbers to link to ICTVdB. The decimal code unequivocally identifies a virus, and simultaneously indicates its taxonomic status from order to isolate, and should be routinely cited in publications.

If a database is to accept the latest data from all branches of virology, and place these into contemporary taxonomic context, it will most commonly deal with information at the level of isolates. Descriptions at the low end of the taxonomic hierarchy include data needed for an unambiguous identification of and differentiation between strains and isolates, and are of great importance in medicine and agriculture. These data give insight into evolutionary trends, and precision of identification becomes especially important for new, re-emerging or uncommon viruses.

Thus, ICTVdB is designed to serve virus taxonomy "from the bottom up", facilitating the submission of primary data from researchers who use discipline specific semantics that often reflect diverse geographic and linguistic features, as well as internationally accepted terminology at the level of sequence data. At the same time, the database must also accept revisions and consolidations "from the top down" as the consensus in virus taxonomy reflects this new information. These decisions are taken by ICTV and increasingly rely on sequence data. Unfortunately the taxonomic decission making process is rather slow and thus the genomic databases are often several years ahead of the final approval of a new virus acceptance by ICTV which can lead to discrepencies in the taxonomic presentation between ICTV and ICTVdB and the sequence databanks.

Comments to ICTVdBManagement
by CorneliaBüchen-Osmond
Copyright © 2002    International Committee on Taxonomy of Viruses.    All rights reserved.