1. About Hyperlink Management System
2. How to create hyperlinks using the system
3. All database search
4. ID converter system
5. Downloading ID tables
6. ID Resolver
7. Web Service
8. Collected databases/IDs
9. Release history

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/)

(1) A simple method

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]

The parameters given to the CGI-program are as follows.

1. [ID]
   Source ID (original ID).
   
   
2. [ID Type]
   The type of source ID. Choose from below.
   ID list
   
   
3. [Database name]
   The name of target database. Choose from below.
   Database list

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

In HTML, you can write as follows.

<a href='http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW'>BC053657</a> Sample：BC053657

ID list for human

No.	Format	Outline
1	ACC_ID	Accession Number
2	HIT_ID	H-Inv transcript ID (HIT)
3	HIX_ID	H-Inv cluster ID (HIX)
4	HIP_ID	H-Inv protein ID (HIP)
5	UNIPROT_ID	UniProt Accession Number
6	GENE_SYMBOL	HUGO gene symbol
7	REF_SEQ	RefSeq
8	OMIM_ID	OMIM ID
9	GENE_ID	GeneID
10	PUBMED_ID	PubMed ID
11	JSNP_ID	dbSNP rs#
12	MS_ID	Marker Name
13	PDB_ID	PDB ID
14	FR_ID	fRNAdb ID
15	ENST_ID	Ensembl Transcript ID
16	ENSG_ID	Ensembl Gene ID
17	CLONE_ID	Clone ID (by NBRC)
18	FLJ_ID	FLJ ID (by NBRC)
19	HPRD_ID	HPRD ID
20	CIPRO_ID	CIPRO ID

ID list for mouse

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
6	MMU_GENE_ID	GeneID
7	MMU_PUBMED_ID	PubMed ID
8	MMU_ENST_ID	Ensembl Transcript ID
9	MMU_ENSG_ID	Ensembl Gene ID
10	MMU_CLONE_ID	Clone ID(FANTOM)
11	MMU_GENE_SYMBOL	Mouse Gene Symbol(MGI)
12	MMU_PDB_ID	PDB ID
13	MMU_BRC_MS_ID	BRC ID
14	MMU_ALLELE_ID	ALLELE ID

ID list for Chemical compounds

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

*1 CAS Registry Number is a Registered Trademark of the American Chemical Society.

ID list for Ciona intestinalis

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
6	CIN_GENE_ID	GeneID
7	CIN_PUBMED_ID	PubMed ID
8	CIN_ENST_ID	Ensembl Transcript ID
9	CIN_ENSG_ID	Ensembl Gene ID
10	CIN_CIPRO_ID	Cipro ID
11	CIN_GHOST_ID	Ghost ID
12	CIN_ANISEED_ID	Aniseed Gene ID

Database list for human

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	Nucleotide (NCBI)
6	GENBANK	GenBank (NCBI)
7	ENTREZGENE	Entrez Gene (NCBI)
8	OMIM	OMIM (NCBI)
9	PUBMED	PubMed (NCBI)
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

Database list for mouse

No.	Format	Outline
1	NUCLEOTIDE	Nucleotide (NCBI)
2	GENBANK	GenBank (NCBI)
3	ENTREZGENE	Entrez Gene (NCBI)
4	PUBMED	PubMed (NCBI)
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

Database list for Chemical compounds

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	PubMed (NCBI)
13	PDBJ	PDBj
13	UNIPROT	UniProt

Database list for Ciona intestinalis

No.	Format	Outline
1	NUCLEOTIDE	Nucleotide (NCBI)
2	GENBANK	GenBank (NCBI)
3	ENTREZGENE	Entrez Gene (NCBI)
4	PUBMED	PubMed (NCBI)
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

(2) Using Real-Time Link Generator

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.

Usage

Search page

(1)The form of converted ID is selected.
ID/Type list

(2)Input converted ID.

(3)The data base of the forwarding destination is selected.
Database list

(4)Please click "Search".
The search result will be displayed.


Result page

- ID converter system

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.

Usage

(1)Input IDs (Figure 1)
Input IDs of unknown origins. You can input multiple IDs separated by commas, spaces, or new lines.


Figure 1. Input

(2)Push the "Search" button
Results (Figure 2) are shown in a table. From left to right, category of IDs, IDs (input), types of IDs, kinds of database (with links, Fig 2A), and links to "All Database Search" (icons) are shown. You can download the results by pushing the "Download" button above (Fig 2B). A tab-delimited file will be downloaded.


Figure 2. Results

Distinguishable IDs Please refer to the tables here.

- Web service

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.

database for for human

H-InvDB   http://www.h-invitational.jp/hinv/ahg-db/index.jsp -Accession Number -H-Inv transcript ID(HIT) -H-Inv cluster ID (HIX) -H-Inv protein ID (HIP)

NCBI   http://www.ncbi.nlm.nih.gov/ -Accession Number -HUGO gene symbol -RefSeq -OMIM ID -GeneID -PubMed ID

HUGO   http://www.genenames.org/ -HUGO gene symbol -RefSeq

H-GOLD   http://www.h-invitational.jp/gdbs/ -Accession Number -H-GOLD Marker ID

GeMDBJ   https://gemdbj.nibio.go.jp/ -HUGO gene symbol -dbSNP rs#

PDBj   http://www.pdbj.org/ -UniProt Accession Number -PDB ID

MutationView   http://mutview.dmb.med.keio.ac.jp/MutationView/jsp/mutview/index.jsp -HUGO gene symbol -OMIM ID

Ensembl   http://www.ensembl.org/index.html -HUGO gene symbol -Ensembl Transcript ID (ENST) -Ensembl Gene ID (ENSG)

UniProt   http://www.uniprot.org/ -UniProt Accession Number -Accession Number

fRNAdb   http://www.ncrna.org/frnadb -Accession Number -fRNAdb ID

GGDB   http://riodb.ibase.aist.go.jp/rcmg/ggdb/ -HUGO Gene Symbol -RefSeq

HGPD   http://www.HGPD.jp/ -Accession Number -Clone ID -FLJ ID

KEGG   http://www.genome.jp/kegg/ -GeneID -KEGG Gene ID -KEGG Pathway ID

HPRD   http://www.hprd.org/ -GeneID -HPRD ID

NBRC   http://www.nbrc.nite.go.jp/e/index.html -Accession Number -Clone ID -FLJ ID

LEGENA   http://h-invitational.jp/legenda/top.htm -GeneID

Evola   http://www.h-invitational.jp/evola/search.html -Mouse Accession Number -H-Inv transcript ID(HIT)

H-DBAS   http://h-invitational.jp/h-dbas/ -Accession Number -H-Inv cluster ID (HIX)

G-Compass   http://h-invitational.jp/g-compass/ -Accession Number -H-Inv transcript ID(HIT)

Protein View   http://h-invitational.jp/hinv/help/help_index.html -Accession Number -H-Inv protein ID (HIP)

CIPRO   http://cipro.ibio.jp/ -Accession Number -CIPRO ID

H-ANGEL   http://h-invitational.jp/hinv/h-angel/ -Accession Number -H-Inv protein ID (HIP)

FLJ Human cDNA   http://flj.hinv.jp/ -Accession Number -Clone ID -FLJ ID

VarySysDB   http://h-invitational.jp/varygene/home.htm -Accession Number -H-Inv transcript ID(HIT)

Figure. ID network for human molecular data

database for mouse

NCBI   http://www.ncbi.nlm.nih.gov/ -Accession Number -RefSeq -GeneID -PubMed ID

Ensembl   http://www.ensembl.org/index.html -Accession Number -Ensembl Transcript ID (ENST) -Ensembl Gene ID (ENSG)

UniProt   http://www.uniprot.org/ -UniProt Accession Number -Accession Number

KEGG   http://www.genome.jp/kegg/ -GeneID -KEGG Gene ID -KEGG Pathway ID

Evola   http://www.h-invitational.jp/evola/search.html -H-Inv transcript ID(HIT) -Accession Number

MGI   http://www.informatics.jax.org/ -MGI Marker Accession ID -Accession Number -Mouse Gene Symbol

IKMC   http://www.knockoutmouse.org -MGI Marker Accession ID

FANTOM   http://fantom3.gsc.riken.jp/ -Accession Number -Clone ID(FANTOM)

PDB   http://www.pdbj.org/ -PDB ID -UniProt Accession Number

BRC Mouse Strain   https://database.riken.jp/sw/en/BRC_Mouse_Strain/cria315s1i/    -BRC ID -Allele ID -MGI Marker Accession ID

MGI Allele   http://www.informatics.jax.org/ -Allele ID -MGI Marker Accession ID

Figure. ID network for mouse molecular data

database for Chemical compounds

PubChem   http://pubchem.ncbi.nlm.nih.gov/ -PubChem Compound ID -PubChem Substance ID -ChEBI ID

DrugBank   http://www.drugbank.ca/ -DrugBank ID -PubChem Compound ID -Uniprot Accession Number

KeggDrug   http://www.kegg.jp/kegg/drug/ -KEGG Drug ID -PubChem Substance ID

KeggCompound   http://www.genome.jp/kegg/compound/ -KEGG Compound ID -PubChem Substance ID -NIKKAJI ID

ChEBI   http://www.ebi.ac.uk/chebi/ -ChEBI ID -PDBeChem ID -PubMed ID -CAS ID

PharmGKB   http://www.pharmgkb.org/ -PharmGKB IDr -DrugBank ID

PDBeChem   http://www.ebi.ac.uk/msd-srv/msdchem/cgi-bin/cgi.pl?APPLICATION=1 -PDBeChem ID -PDB 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 -Accession Number

Figure．ID network for chemical compounds and drugs.
For chemical compounds and drugs, we linked between IDs of the same molecules.
For UniProt protein sequences, we linked to "target proteins" that are known to bind with the chemicals and drugs in question.
For PDB structure data, we linked to structure data of protein complexes that contain the chemicals or drugs.

database for Ciona intestinalis

NCBI   http://www.ncbi.nlm.nih.gov/ -Accession Number -RefSeq -GeneID -PubMed ID

UniProt   http://www.uniprot.org/ -UniProt Accession Number -UniRef100 Accession Number -Accession Number

Ensembl   http://www.ensembl.org/index.html -Ensembl Transcript ID (ENST) -Ensembl Gene ID (ENSG)

Cipro   http://cipro.ibio.jp/ -Cipro ID -RefSeq -H-Inv transcript ID(HIT)

Ghost   http://hoya.zool.kyoto-u.ac.jp/ -Ghost ID -Cipro ID

Aniseed   http://aniseed-ibdm.univ-mrs.fr/index.php -Aniseed Gene ID -Cipro ID

Figure. ID network for Ciona intestinalis data

December 26, 2007 Official public release of Hyperlink Management System.

June 19, 2008 PDBj, MutationView were included. Official public release of ID Converter System.

January 06, 2009 Ensembl, GGDB and HPRD were included.

January 12, 2009 This system was licensed under a Creative Commons License.

August 20, 2009 "All Databases" was added as a target database of Hyperlink Management System.

September 29, 2009 KEGG were included.

October 21, 2009 HPRD were included.

December 28, 2009 "previous symbols" of HUGO Gene Symbol were added.

January 28, 2010 PubMed, GenBank, OMIM and NBRC were included.

February 25, 2010 Downloading data ID tables was enabled. LEGENDA and Evola were included.

April 08, 2010 For mouse,NCBI,Ensembl,Uniprot,KEGG,Evola,MGI and IKMC were added.

April 20, 2010 FANTOM were included.

May 26, 2010 H-DBAS, G-Compass, Protein View were included.

Jun 30, 2010 CIPRO, H-ANGEL, FLJ Human cDNA, VarySysDB were included.

September 10, 2010 We started a Pre-release of "Chemical comounds and Drugs". PubChem,DrugBank,KeggDrug,KeggCompound,ChEBI,PharmGKB and NIKKAJI were included.

December 14, 2010 "secondary accession number" of Uniprot were added.

January 27, 2011 "secondary accession number" of GenBank were added.

February 16, 2011 ID Resolver was enabled.

March 07, 2011 We started a Pre-release of "Ciona intestinalis". NCBI,Ensembl,Uniprot and Cipro were included.

April 13, 2011 We started an Official public release of "Ciona intestinalis". Ghost and aniseed were included.

May 10, 2011 Mouse Gene Symbol were included.

August 01, 2011 Wikipedia Human proteins were included.

September 14, 2011 JSNP DATABASE were included.

October 26, 2011 Mouse PDB, BRC Mouse Strain and MGI Alleles were included.

December 12, 2011 Newly linked data are highlighted in All Database Search.