About Hyperlink Management System

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Hyperlink Management System (HMS) is a system for automatically updating and maintaining hyperlinks among major public databases in the field of life science. We 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 of corresponding data in many databases.


Background

Finding corresponding data in different databases and setting hyperlinks among them is an effective way of integrating information that is stored in independently operated databases in various organizations. The maintenance of the hyperlinks among many databases, however, requires a huge cost, because the number of pairs of databases is generally very large (Figure 1). For example, if one of the N hyperlinked databases is updated, 2(N-1) ways of hyperlinks need to be changed. If each database is periodically updated in every three months, at most 8N(N-1) ways of hyperlinks need to be changed in a year, which will be a laborious work. We thus designed and created the "Hyperlink Management System" in order to fully automate the updating and maintenance of hyperlinks.

Figure 1. The cost of maintaining hyperlinks among databases. There are 30 possible ways of hyperlinking among 6 databases, the maintenance of which will be laborious.

How the HMS works

The HMS automatically downloads the lists of data IDs from major biological databases everyday, and produces corresponding tables of data IDs of these databases (Figure 2). Then, using the corresponding tables of data IDs, the HMS shows the URLs for data in a database that are corresponding to a user-specified ID of another database. The URL is easily obtained by running a CGI-program of the HMS.

Suppose that the manager of database A wishes to create hyperlinks from database A to database B. Usually in this case, the manager uses data IDs of database B in the URLs of hyperlinks. However, if the manager uses the HMS, he can use data IDs of database A to create hyperlinks to database B. This is very useful because we can easily create hyperlinks without knowing data IDs of target databases. We can therefore drastically reduce the cost of creating and maintaining hyperlinks among databases.


Figure 2. How the HMS works.

How to create hyperlinks using the HMS

In order to create hyperlinks using the HMS, use the following URL as a target URL.
    http://biodb.jp/hfs.cgi?id=[ID]&type=[ID Type]&db=[Database name]
Here, [ID] is a data ID of the database from which hyperlink is set, [ID Type] is a kind of the ID, and [Database name] is the name of database to which hyperlink is set. For details about parameter settings, please refer to the HELP page of the HMS. For example, using BC053657, an accession number of DDBJ/EMBL/GenBank, you can create a hyperlink toward the corresponding Transcript View of H-InvDB in the following way.
    <a href="http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW">BC053657</a>
To see how the CGI-program works, please click the accession number in the following line.
BC053657



About the HMS

The Hyperlink Forwarding System was developed at the Biological Information Research Center of the National Institute of Advanced Industrial Science and Technology with the financial support from the JST (2006-2008). Since 2008, the HMS is supported by the Integrated Database Project of the Ministry of Economy, Trade and Industry of Japan (METI).
For more details, please contact below.

Tadashi Imanishi
Integrated Database and Systems Biology Team, Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Japan
Email: t.imanishi [at] aist.go.jp

Last updated on April 13, 2009