W18 Nucleic Acids Research, 2009, Vol. 37, Web Server issue molecular information in multiple databases about human genes and proteins. Furthermore, we developed a Web server for converting data IDs from one type to another. These Web servers will be useful for both database devel- opers and biologists. The reason for it is that, for database developers, these systems can realize automated, work- saving and eﬃcient management of databases, and can reduce the large cost of maintaining biological databases. Also, for biologists, especially those who are unfamiliar with the data IDs of major biological databases, our newly developed Web servers will be of help in carrying out eﬃ- cient analyses of ‘big data’ that are being produced mas- sively in laboratories (2). We hope that many database managers and researchers will ﬁnd our Web servers useful. WEB SERVER FEATURES Usage of the Hyperlink Management System (HMS) CGI-program HMS is a tool for automatically updating and maintaining hyperlinks between databases in the ﬁeld of life science. The HMS automatically downloads the lists of data IDs for human genes and proteins and their relations from major biological databases everyday, and produces large corresponding tables of all data IDs of these databases (Tables 1 and 2). Then, using the corresponding tables of data IDs, the HMS shows the most up-to-date 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. Currently, the HMS collects 17 types of data IDs for human genes and proteins (Table 2). Among the 17 types of data IDs, we deﬁned accession numbers of International Nucleotide Sequence Database (INSD; DDBJ/EMBL/GenBank), HUGO Gene Symbols and UniProt IDs as ‘common IDs’ that are used as key IDs in creating corresponding tables. We collect corresponding tables between a common ID and an other ID from each of source databases (Figure 1). We also obtain a corresponding table between accession numbers and HUGO Gene Symbols from NCBI and a corresponding table between accession numbers and UniProt IDs from UniProt. Using these tables, we create a large correspond- ing table that shows the relationships among 17 types of data IDs. The common IDs deﬁne the route of ID conversion (as shown in Figure 1). For example, when converting HIX of H-InvDB into PDB IDs, we Table 1. Databases and viewers handled by the HMS Database name Viewer name Formata H-InvDB (3,4) Transcript view TRANSCRIPTVIEW Locus view LOCUSVIEW G-integra GINTEGRA PPI view PPI INSD (DDBJ/EMBL/ NCBI Nucleotide NUCLEOTIDE GenBank) (5–7) NCBI Entrez Gene (8) Entrez Gene ENTREZGENE Genome Medicine Database GeMDBJ GEMDBJ of Japan (GeMDBJ) (9) HUGO Gene Nomenclature HGNC Committee (HGNC) Database (10) MutationView (11) MutationView MUTATIONVIEW H-GOLD (12) H-GOLD HGOLD PDB (13) PDB PDB UniProt (14) UniProtKB UNIPROT Ensembl (15) Gene Summary ENSG Transcript ENST Summary GlycoGene DataBase GGDB GGDB (GGDB) (16) fRNAdb (17) fRNAdb FRNADB Human Gene and Protein HGPD HGPD Database (HGPD) (18) HUGO aParameters of database names used in the HMS CGI-program, ICS and Web service. Table 2. Data IDs used in the HMS Source database H-InvDB INSD NCBI GeMDBJ HUGO H-GOLD PDB UniProt Ensembl fRNAdb HGPD Data ID H-Inv transcript ID (HIT) H-Inv cluster ID (HIX) H-Inv protein ID (HIP) Accession Number OMIM ID RefSeq ID Entrez Gene ID dbSNP rs# HUGO Gene Symbol H-GOLD Marker Name PDB ID UniProt ID Ensembl Transcript ID Ensembl Gene ID fRNAdb ID cDNA clone ID FLJ cDNA clones Formata HIT_ID HIX_ID HIP_ID ACC_ID OMIM_ID REF_SEQ GENE_ID JSNP_ID GENE_SYMBOL MS_ID PDB_ID UNIPROT_ID ENST ENSG FR_ID PDB_ID FLJ_ID Countb 219 765 43 159 133 629 222 136 16 253 48 671 40 235 76 024 26 421 494 50 958 84 422 63 280 37 435 41 501 21 340 21 340 aParameters of ID types used in the HMS CGI-program, ICS and Web service. bNumber of data as of 23 January 2009. ﬁrst convert HIX into UniProt IDs and then convert it into PDB IDs. The HMS directly opens a Web page of the target data- base if there is only one data ID corresponding to the source ID. However, in converting data IDs, an ID does not always correspond to one ID of another type. If there