Published online 19 May 2009 Nucleic Acids Research, 2009, Vol. 37, Web Server issue W17–W22 doi:10.1093/nar/gkp355 Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases Tadashi Imanishi1,* and Hajime Nakaoka1,2,3 1Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, 2Japan Biological Informatics Consortium, Time 24 Bldg. 10F, 2-45 Aomi, Koto-ku, Tokyo 135-8073 and 3C’s Lab Co., Ltd., Kinyo-Kanda Bldg. 7F, 1-3 Kanda-Tomiyama-cho, Chiyoda-ku, Tokyo 101-0043, Japan Received February 1, 2009; Revised April 16, 2009; Accepted April 23, 2009 ABSTRACT Hyperlink Management System (HMS) is a system for automatically updating and maintaining hyper- links among major public databases in the field of life science. We daily create corresponding tables of data IDs of major databases for human genes and proteins, and provide a CGI-program that returns correct and up-to-date URLs for showing data of various databases that correspond to user- specified IDs. The HMS can deal with various IDs: accession numbers of International Nucleotide Sequence Databases, HUGO Gene Symbols and IDs of UniProt, PDB, H-InvDB and others, and it can return URLs of various databases: H-InvDB, HUGO Gene Nomenclature Committee Database, NCBI Entrez Gene, UniProt, PDB and others. For example, 23 297 pages of Locus view of H-InvDB are reachable by using HUGO Gene Symbols through the HMS. Not only the CGI-program, the HMS provides a Web page for finding and opening URLs of these databases. Although hyperlinking is an effective way of relating biological data among different databases, updating hyperlinks has been a laborious work. The HMS fully automates the job, enabling maintenance-free hyperlinks. We also developed the ID Converter System (ICS) for simply converting data IDs by using corresponding tables in the HMS. The HMS and ICS are freely avail- able at http://biodb.jp/. INTRODUCTION There are currently 1170 biological databases in the world (1) that are being utilized for various researches and developments. It is now possible for biologists to try to make discoveries by combining and linking data of diﬀerent types obtained from multiple databases. For example, by combining protein sequences and protein structure data that are stored separately in major data- bases, biologists can study the basic rules of protein 3D structure such as how amino-acid sequences organize themselves into speciﬁc and stable 3D structures. In this way, linking speciﬁc data stored in multiple databases will lead to the organization of biological knowledge and will provide useful resources for novel researches. Finding corresponding data in diﬀerent databases and setting hyperlinks among them is an eﬀective way of integrating information that are stored in independently operated databases in diﬀerent organizations. The main- tenance of the hyperlinks among many databases, how- ever, requires a huge cost, because the number of pairs of databases is generally very large. For example, possible ways of hyperlinks among N related databases will be (N 1)N, if we consider the directions of hyperlinks. Suppose if one of the N databases is updated, 2(N 1) ways of hyperlinks need to be updated. If each of N data- bases is periodically updated in every 3 months, at most 8(N 1)N ways of hyperlinks need to be updated in a year, which will be a laborious work. We thus need a novel system to automate the maintenance of hyperlinks. Here, we developed a Web server for automatically managing and updating hyperlinks that can connect *To whom correspondence should be addressed. Tel: +81 3 3599 8800; Fax: +81 3 3599 8801; Email: t.imanishi@aist.go.jp This website is free and open to all users and there is no login requirement. The website address is ‘http://biodb.jp/’. The website was officially made public on April 2007, and has been running since then. The Hyperlink Management System has been used by the HUGO Gene Nomenclature Committee (HGNC) Database, GeneCards, H-InvDB and other public databases to maintain hyperlinks among these databases. The ID Converter System has been used by hundreds of users since we opened it in March 2008. 2009 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.