ICTVdB: The Next Step

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The current system is based on the DELTA format (DEscription Language for TAxonomy). At its core, Delta is based on linear lists of information (flat files) which specify taxa and their defining characteristics. The Delta system has been engineered to uniquely suit the needs of the worldwide taxonomic community and is used for the classification of plants, animals, viruses, etc... Unfortunately, this taxonomic format and the associated software are no longer being developed. Updates to the Delta database require a highly trained curator with an in depth knowledge of the system. Publication of the database to the web is done using a mixture of specialized programs, scripts and hand editing. As a result the web-based ICTVdB is actually a set of static web pages which must be regenerated each time data is released. It has been a general complaint that the user interface for searching the ICTVdB is too complex. This, at least partially, stems from difficulties in manually maintaining accurate and consistent index pages when regenerating the website with each revision. Interactive virus identification is currently through the Windows application Intkey. Intkey is the interactive taxonomic keying system that is shipped with Delta. It allows a user to identify an organism by successive pruning of taxa. As details are entered about the organism, the number of taxa matching the specified information is listed. This is a valuable tool but the lack of cross-platform compatibility (Windows only) is a major complaint. Isolate data, describing viruses found around the world, are submitted through EntVir, a system of PHP-based forms which also must be regenerated each time the database is published. Isolate data ultimately ends up as an email which must be handled and imported into the Delta system manually. In the current system, all isolate review and database entry is handled through a single curator.

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The proposed replacement architecture utilizes a relational database (MySQL) where the flat files have been translated to their equivalents in a relational database schema. The relational database will capture the taxonomic hierarchy, descriptive data for taxa, and isolate descriptions. Users will interact with the MySQL database through a custom web application with the following functions:

• Browse - A taxonomic tree will be used to navigate through viral taxa. This will allow visual browsing of the taxonomic hierarchy. Viruses will also be indexed by name, host and genome organization.
• Query - A basic search will allow users to query the taxonomic hierarchy, virus names and other data. The stand-alone IntKey application will be replaced by an advanced search function with a flexible system of forms and search refinement.
• Data Entry - An improved data entry system will be used to keep the ICTVdB up to date and to make data entry as simple as possible. Until this system is fully functional, the current EntVir system will remain in place.

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• One time conversion of current Delta format flatfiles to the database
• Annual taxonomy and nomenclature updates from the ICTV executive committee
• Virus annotations made by Curators
• Contributors submission of virus isolates

An important feature of the revised system is the concept of decentralized data entry and review. Isolate submission will be reviewed by the Head Curator and/or other specialists with knowledge of particular viral families. These Curators will be given the ability to review Pending isolate submissions for correctness and approve them for transfer from a Pending status to Approved isolates for release in the next ICTVdB version. Curators will be volunteers and will have the ability to decline to review isolates, in a manner similar to the peer review system used by journals. Yearly updates to the taxonomy will be made using the Master Species List maintained by the ICTV. The Master Species List contains the current description of virus taxonomy down to the species level and is updated, as needed, by the ICTV executive committee (EC). Decentralization is expected to greatly improve the accuracy and speed of the ICTVdB update process.