Hyperlink Management System is a system for automatically updating and maintaining hyperlinks among major public databases in the field of life science. Everyday, we create corresponding tables of data IDs that are used in major databases for genes and proteins, and provide a cgi-program that returns correct and up-to-date URLs of corresponding data in many databases.
By using the CGI program on this server, users can easily create hyperlinks to major databases in their own databases and homepages. Furthermore, on this web site, we provide useful tools such as "All Database Search", "ID converter system", and "Downloading ID tables".
This System was developed at the Biological Information Research Center of the National Institute of Advanced Industrial Science and Technology (AIST) with the financial support from the JST (2006-2008). Since 2008, the system is developed at the Biomedicinal Information Research Center of AIST with a support from the Integrated Database Project of the Ministry of Economy, Trade and Industry of Japan (a portal for the project: MEDALS).
This work is licensed under a Creative Commons Attribution 2.1 Japan License.
Please cite the paper below if you utilize the systems provided on
this web site.
Imanishi T and Nakaoka H (2009) Hyperlink Management System and ID
Converter System: enabling maintenance-free hyperlinks among major
biological databases. Nucleic Acids Research 37(Web Server Issue)
doi:10.1093/nar/gkp355. (http://biodb.jp/)
In order to create hyperlinks using the CGI-program of the Hyperlink Management System, use the following URL as a target URL..
http://biodb.jp/hfs.cgi?id=[ID]&type=[ID Type]&db=[Database Name] |
Sample
The hyperlink to the "Transcript view" of H-InvDB using the INSD accession number "BC053657" will be the following URL.
http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW |
<a href='http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW'>BC053657</a> Sample:BC053657 |
No. | Format | Outline |
---|---|---|
1 | HIX_ID | H-Inv cluster ID (HIX) |
2 | HIT_ID | H-Inv transcript ID (HIT) |
3 | HIP_ID | H-Inv protein ID (HIP) |
4 | GENE_ID | GeneID |
5 | ACC_ID | Accession Number |
6 | PROTEIN_ID | RefSeq Protein ID |
7 | OMIM_ID | OMIM ID |
8 | REF_SEQ | RefSeq ID |
9 | PUBMED_ID | PubMed ID |
10 | UNIPROT_ID | UniProt Accession Number |
11 | GENE_SYMBOL | HUGO gene symbol |
12 | JSNP_ID | dbSNP rs# |
13 | MS_ID | Marker Name |
14 | PDB_ID | PDB ID |
15 | FR_ID | fRNAdb ID |
16 | ENSG_ID | Ensembl Gene ID |
17 | ENST_ID | Ensembl Transcript ID |
18 | ENSP_ID | Ensembl Protein ID |
19 | CLONE_ID | Clone ID (by NBRC) |
20 | FLJ_ID | FLJ ID (by NBRC) |
21 | HPRD_ID | HPRD ID |
22 | CIPRO_ID | CIPRO ID |
23 | KEGG_ID | KEGG Gene ID |
24 | PATHWAY_ID | KEGG Pathway ID |
25 | DGV_ID | DGV ID |
26 | PEPTIDE_ID | Peptide Accession |
27 | CCO_PDBECHEM_ID | PdbeChem ID |
28 | CCO_DRUGBANK_ID | DrugBank ID |
No. | Format | Outline |
---|---|---|
1 | RS_NO | Reference cluster ID(rs#) |
2 | SNP_GENE_ID | GeneID |
No. | Format | Outline |
---|---|---|
1 | MMU_MGI_ID | MGI Marker Accession ID |
2 | MMU_ACC_ID | Accession Number |
3 | HIT_ID | H-Inv transcript ID (HIT) |
4 | MMU_UNIPROT_ID | UniProt Accession Number |
5 | MMU_REF_SEQ | RefSeq ID |
6 | MMU_GENE_ID | GeneID |
7 | MMU_PROTEIN_ID | RefSeq Protein ID |
8 | MMU_PUBMED_ID | PubMed ID |
9 | MMU_ENST_ID | Ensembl Transcript ID |
10 | MMU_ENSG_ID | Ensembl Gene ID |
11 | MMU_CLONE_ID | Clone ID(FANTOM) |
12 | MMU_GENE_SYMBOL | Mouse Gene Symbol(MGI) |
13 | MMU_PDB_ID | PDB ID |
14 | MMU_BRC_MS_ID | BRC ID |
15 | MMU_ALLELE_ID | ALLELE ID |
16 | MMU_KEGG_ID | KEGG Gene ID |
17 | MMU_PATHWAY_ID | KEGG Pathway ID |
No. | Format | Outline |
---|---|---|
1 | RNO_ACC_ID | Accession Number |
2 | HIT_ID | H-Inv transcript ID (HIT) |
3 | RNO_REF_SEQ | RefSeq ID |
4 | RNO_GENE_ID | GeneID |
5 | RNO_PROTEIN_ID | RefSeq Protein ID |
6 | RNO_PUBMED_ID | PubMed ID |
7 | RNO_UNIPROT_ID | UniProt Accession Number |
8 | RNO_ENST_ID | Ensembl Transcript ID |
9 | RNO_ENSG_ID | Ensembl Gene ID |
10 | RNO_RGD_ID | RGD ID |
11 | RNO_KEGG_ID | KEGG Gene ID |
12 | RNO_PATHWAY_ID | KEGG Pathway ID |
No. | Format | Outline |
---|---|---|
1 | CIN_ACC_ID | Accession Number |
2 | HIT_ID | H-Inv transcript ID (HIT) |
3 | CIN_UNIPROT_ID | UniProt Accession Number |
4 | CIN_UNIREF_ID | UniRef100 Accession Number |
5 | CIN_REF_SEQ | RefSeq ID |
6 | CIN_GENE_ID | GeneID |
7 | CIN_PROTEIN_ID | RefSeq Protein ID |
8 | CIN_PUBMED_ID | PubMed ID |
9 | CIN_ENST_ID | Ensembl Transcript ID |
10 | CIN_ENSG_ID | Ensembl Gene ID |
11 | CIN_CIPRO_ID | Cipro ID |
12 | CIN_GHOST_ID | Ghost ID |
13 | CIN_ANISEED_ID | Aniseed Gene ID |
No. | Format | Outline |
---|---|---|
1 | CCO_CHEBI_ID | ChEBI ID |
2 | CCO_DRUGBANK_ID | DrugBank ID |
3 | CCO_KEGGCOMPOUND_ID | KEGG Compound ID |
4 | CCO_KEGGDRUG_ID | KEGG Drug ID |
5 | CCO_NIKKAJI_ID | NIKKAJI ID |
6 | CCO_PDBECHEM_ID | PDBeChem ID |
7 | CCO_PHARMGKB_ID | PharmGKB ID |
8 | CCO_C_ID | PubChem Compound ID |
9 | CCO_S_ID | PubChem Substance ID |
10 | PDB_ID | PDB ID |
11 | CCO_PUBMED_ID | PubMed ID |
12 | UNIPROT_ID | Uniprot Accession Number |
13 | CCO_CAS_ID | CAS ID *1 |
14 | CCO_KNAPSACK_ID | KNApSAcK ID |
15 | CCO_HMDB_ID | HMDB Accession Number |
No. | Format | Outline |
---|---|---|
1 | TRANSCRIPTVIEW | H-InvDB (Transcript view) |
2 | LOCUSVIEW | H-InvDB (Locus view) |
3 | GINTEGRA | H-InvDB (G-integra) |
4 | PPI | H-InvDB (PPI view) |
5 | NUCLEOTIDE | NCBI RefSeq nucleotide |
6 | GENBANK | NCBI GenBank |
7 | ENTREZGENE | NCBI Entrez Gene |
8 | OMIM | NCBI OMIM |
9 | PUBMED | NCBI PubMed |
10 | GEMDBJ | GeMDBJ |
11 | HUGO | HUGO |
12 | MUTATIONVIEW | MutationView |
13 | HGOLD | H-GOLD |
14 | PDB | PDB |
15 | UNIPROT | UniProt |
16 | ENST | Ensembl Transcriptview |
17 | ENSG | Ensembl Geneview |
18 | GGDB | GGDB |
19 | FRNADB | fRNAdb |
20 | NBRC | NBRC |
21 | HGPD | HGPD |
22 | KEGG | KEGG Gene |
23 | PATHWAY | KEGG Pathway |
24 | HPRD | HPRD |
25 | LEGENDA | LEGENDA |
26 | EVOLA | EVOLA |
27 | HDBAS | H-DBAS |
28 | GCOMPASS | G-Compass |
29 | PROTEINVIEW | Protein View |
30 | CIPRO | CIPRO |
31 | HANGEL | H-ANGEL |
32 | FLJH | FLJ Human cDNA |
33 | VARYSYSDB | VarySysDB |
34 | PDBECHEM | PDBeChem |
35 | DRUGBANK_H | DrugBank |
36 | WIKIPEDIA_HP | Wikipedia Human proteins |
37 | PROTEIN | NCBI RefSeq protein |
38 | DGV | DGV |
49 | COXPRES | COXPRESdb |
40 | ATLAS | Human Protein ATLAS |
41 | PEPTIDE | Peptide Atlas |
42 | ENSP | Ensembl Protein |
43 | NEXTPROT | neXt Prot |
44 | DISGENET | DisGeNet |
No. | Format | Outline |
---|---|---|
1 | DBSNP | dbSNP |
2 | VADE | VaDE |
3 | IJGVD | iJGVD |
4 | HGVD | HGVD |
5 | GWAS | GWAS Catalog |
6 | CLINVAR | ClinVar |
7 | ENTREZGENE | NCBI Entrez Gene |
No. | Format | Outline |
---|---|---|
1 | NUCLEOTIDE | NCBI RefSeq nucleotide |
2 | GENBANK | NCBI GenBank |
3 | ENTREZGENE | NCBI Entrez Gene |
4 | PUBMED | NCBI PubMed |
5 | UNIPROT | UniProt |
6 | ENST | Ensembl Transcriptview |
7 | ENSG | Ensembl Geneview |
8 | KEGG | KEGG Gene |
9 | PATHWAY | KEGG Pathway |
10 | EVOLA | EVOLA |
11 | MGI | MGI Gene |
12 | IKMC | IKMC |
13 | FANTOM | FANTOM |
14 | PDB | PDB |
15 | BRC_MS | BRC Mouse Strain |
16 | ALLELE | MGI Allele |
17 | SYMBOL | Mouse Gene Symbol |
18 | PROTEIN | NCBI RefSeq protein |
19 | COXPRES | COXPRESdb |
No. | Format | Outline |
---|---|---|
1 | NUCLEOTIDE | NCBI RefSeq nucleotide |
2 | GENBANK | NCBI GenBank |
3 | ENTREZGENE | NCBI Entrez Gene |
4 | PUBMED | NCBI PubMed |
5 | UNIPROT | UniProt |
6 | ENST | Ensembl Transcriptview |
7 | ENSG | Ensembl Geneview |
8 | KEGG | KEGG Gene |
9 | PATHWAY | KEGG Pathway |
10 | EVOLA | EVOLA |
11 | RGD | Rat Genome Database |
12 | PROTEIN | NCBI RefSeq protein |
13 | COXPRES | COXPRESdb |
No. | Format | Outline |
---|---|---|
1 | NUCLEOTIDE | NCBI RefSeq nucleotide |
2 | GENBANK | NCBI GenBank |
3 | ENTREZGENE | NCBI Entrez Gene |
4 | PUBMED | NCBI PubMed |
5 | UNIPROT | UniProt |
6 | UNIREF | UniRef100 |
7 | ENST | Ensembl Transcriptview |
8 | ENSG | Ensembl Geneview |
9 | CIPRO | Cipro |
10 | TRANSCRIPTVIEW | H-InvDB (Transcript view) |
11 | GHOST | Ghost |
12 | ANISEED | Aniseed |
13 | PROTEIN | NCBI RefSeq protein |
No. | Format | Outline |
---|---|---|
1 | PUBCHEM_C | PubChem Compound |
2 | PUBCHEM_S | PubChem Substance |
3 | DRUGBANK | DrugBank |
4 | KEGGDRUG | Kegg Drug |
5 | KEGGCOMPOUND | Kegg Compound |
6 | CHEBI | ChEBI |
7 | PHARMGKB | PharmGKB |
8 | PDBECHEM | PDBeCem |
9 | NIKKAJI | NIKKAJI |
10 | CAS | CAS |
11 | CITEXPLORE | CiteXplore |
12 | PUBMED | NCBI PubMed |
13 | PDBJ | PDBj |
14 | UNIPROT | UniProt |
15 | KNAPSACK | KNApSAcK |
16 | HMDB | HMDB |
17 | JECDB | JECDB |
By a web-service connection to the Real-Time Link Generator of Hyperlink Forwarding System, you can show hyperlinks only when data exists at the destination. This is useful because users can know whether the link is active or not. If there is no data at the destination, "No Link" will be shown.
Please see the HTML sources of the following two examples, and copy and paste them as you like (you need to change only IDs).
Sample 1
Sample 2
The sample 1 shows hyperlinks to Locus view of H-InvDB based on a OMIM ID. The sample 2 shows hyperlinks to 24 kinds of databases. By simply inserting several lines of JavaScript in your HTML, you can use this function.
By specifying IDs of any kind, this system searches for IDs in other databases that correspond to the specified IDs. By default, [All Databases] is selected as a database to open.
Highlighting newly linked data: Newly linked data since Monday in the previous week are highlighted with blinking "New" marks. So, if you open the All Database Search at least once in every week, you will not miss newly linked data.
You can download corresponding tables of two IDs. Select two IDs, push the search button, and start downloading the file of corresponding tables. The files are in tab-delimited text format.
"ID Resolver" is a tool for discriminating various types of data IDs. If you have any data IDs of unknown origin, please try it. Multiple IDs can be discriminated at a time.
This system acquires data from the following data bases.
We analyze correspondence of data IDs based on the following ID networks. By tracing the paths connected by solid lines, we make corresponding tables for all possible pairs of IDs.
H-InvDB http://www.h-invitational.jp/hinv/ahg-db/index.jsp
-H-Inv cluster ID (HIX) |
NCBI http://www.ncbi.nlm.nih.gov/
-GeneID |
HUGO http://www.genenames.org/
-HUGO gene symbol |
H-GOLD http://www.h-invitational.jp/gdbs/
-H-GOLD Marker ID |
GeMDBJ https://gemdbj.nibio.go.jp/
-dbSNP rs# |
PDBj http://www.pdbj.org/
-PDB ID |
MutationView http://mutview.dmb.med.keio.ac.jp/MutationView/jsp/mutview/index.jsp
-OMIM ID |
Ensembl http://www.ensembl.org/index.html
-Ensembl Gene ID (ENSG) |
UniProt http://www.uniprot.org/
-UniProt Accession Number |
fRNAdb http://www.ncrna.org/frnadb
-fRNAdb ID |
GGDB http://riodb.ibase.aist.go.jp/rcmg/ggdb/
-HUGO Gene Symbol |
HGPD http://www.HGPD.jp/
-FLJ ID |
KEGG http://www.genome.jp/kegg/
-KEGG Gene ID |
HPRD http://www.hprd.org/
-HPRD ID |
NBRC http://www.nbrc.nite.go.jp/e/index.html
-FLJ ID |
LEGENA http://h-invitational.jp/legenda/top.htm
-GeneID |
Evola http://www.h-invitational.jp/evola/search.html
-H-Inv transcript ID(HIT) |
H-DBAS http://h-invitational.jp/h-dbas/
-H-Inv cluster ID (HIX) |
G-Compass http://h-invitational.jp/g-compass/
-H-Inv transcript ID(HIT) |
Protein View http://h-invitational.jp/hinv/help/help_index.html
-H-Inv protein ID (HIP) |
CIPRO http://cipro.ibio.jp/
-CIPRO ID |
H-ANGEL http://h-invitational.jp/hinv/h-angel/
-H-Inv protein ID (HIP) |
FLJ Human cDNA http://flj.hinv.jp/
-FLJ ID |
VarySysDB http://h-invitational.jp/varygene/home.htm
-H-Inv transcript ID(HIT) |
PDBeChem http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?APPLICATION=1
-PDBeChem ID |
DrugBank http://www.drugbank.ca/
-DrugBank ID |
Wikipedia Human proteins http://en.wikipedia.org/wiki/Category:Human_proteins
-HUGO gene symbol |
DGV http://projects.tcag.ca/variation/announcements.php
-DGV ID |
COXPRESdb http://coxpresdb.jp/
-GeneID |
Human Protein ATLAS http://www.proteinatlas.org/
-Ensembl Gene ID (ENSG) |
Peptide Atlas http://www.peptideatlas.org/
-Peptide Accession |
neXt Prot http://www.nextprot.org/db/
-UniProt Accession Number |
DisGeNet http://www.disgenet.org/web/DisGeNET/menu/home
-GeneID |
dbSNP http://www.ncbi.nlm.nih.gov/projects/SNP/index.html
-Reference cluster ID(rs#) |
VaDE http://bmi-tokai.jp/VaDE/
-Reference cluster ID(rs#) |
iJGVD http://ijgvd.megabank.tohoku.ac.jp/
-Reference cluster ID(rs#) |
HGVD http://www.genome.med.kyoto-u.ac.jp/SnpDB/
-Reference cluster ID(rs#) |
GWAS Catalog https://www.ebi.ac.uk/gwas/home
-Reference cluster ID(rs#) |
ClinVar http://www.ncbi.nlm.nih.gov/clinvar/
-Reference cluster ID(rs#) |
NCBI http://www.ncbi.nlm.nih.gov/
-GeneID |
NCBI http://www.ncbi.nlm.nih.gov/
-GeneID |
Ensembl http://www.ensembl.org/index.html
-Ensembl Transcript ID (ENST) |
UniProt http://www.uniprot.org/
-UniProt Accession Number |
KEGG http://www.genome.jp/kegg/
-KEGG Gene ID |
Evola http://www.h-invitational.jp/evola/search.html
-H-Inv transcript ID(HIT) |
MGI http://www.informatics.jax.org/
-MGI Marker Accession ID |
IKMC http://www.knockoutmouse.org
-MGI Marker Accession ID |
FANTOM http://fantom3.gsc.riken.jp/
-Clone ID(FANTOM) |
PDB http://www.pdbj.org/
-PDB ID |
BRC Mouse Strain https://database.riken.jp/sw/en/BRC_Mouse_Strain/cria315s1i/
-BRC ID |
MGI Allele http://www.informatics.jax.org/
-Allele ID |
COXPRESdb http://coxpresdb.jp/
-GeneID |
PubChem http://pubchem.ncbi.nlm.nih.gov/
-PubChem Compound ID |
DrugBank http://www.drugbank.ca/
-DrugBank ID |
KeggDrug http://www.kegg.jp/kegg/drug/
-KEGG Drug ID |
KeggCompound http://www.genome.jp/kegg/compound/
-KEGG Compound ID |
ChEBI http://www.ebi.ac.uk/chebi/
-ChEBI ID |
PharmGKB http://www.pharmgkb.org/
-PharmGKB IDr |
PDBeChem http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?APPLICATION=1
-PDBeChem ID |
NIKKAJI http://nikkajiweb.jst.go.jp/nikkaji_web/pages/top_e.jsp
-NIKKAJI ID |
PDBj http://www.pdbj.org/
-PDB ID |
UniProt http://www.pir.uniprot.org/
-Uniprot Accession Number |
NCBI http://www.ncbi.nlm.nih.gov/
-GeneID |
UniProt http://www.uniprot.org/
-UniProt Accession Number |
Ensembl http://www.ensembl.org/index.html
-Ensembl Transcript ID (ENST) |
Cipro http://cipro.ibio.jp/
-Cipro ID |
Ghost http://ghost.zool.kyoto-u.ac.jp/indexr1.html
-Ghost ID |
Aniseed http://aniseed-ibdm.univ-mrs.fr/index.php
-Aniseed Gene ID |