Name Hyperlink Management System
Aliases biodb.jp
Description

"Hyperlink Management System is an original tool for setting hyperlinks to major databases related to human genes and proteins worldwide. For details, please refer to the document here (http://staff.aist.go.jp/t.imanishi/about_hms.html)."

Type Tool
Main Institutes of management "Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST)"
Country of the Institute Japan
URL of the site http://biodb.jp/
Interface GUI | CGI
Input

ID(Text)

Output

Results(Text)

Input example

A hyperlink to H-InvDB (Transcript view) using Accession Number "BC053657": http://biodb.jp/hfs.cgi?id=BC053657&type=ACC_ID&db=TRANSCRIPTVIEW

Keyword
ID | Link | Convert | Human | Mouse | Rattus | Ciona intestinalis | Chemical compounds
Amount of the all data for download(Mbyte) | Method to obtain the all data. unknown|in preparation
External resources (databases) in building the product. H-InvDB | NCBI | GeMDBJ | HUGO | MutationView | H-GOLD | PDBj | UniProt | GGDB | fRNAdb | Ensembl Transcript | Ensembl Gene | Ensembl Protein | NBRC | HGPD | KEGG Gene | KEGG Pathway | HPRD | LEGENDA | Evola | H-DBAS | G-Compass | CIPRO | H-ANGEL | FLJ Human cDNA | VarySysDB | PDBeChem | DrugBank | Wikipedia Human proteins | JSNP | NCBI RefSeq protein | DGV | COXPRESdb | Human Protein ATLAS | Peptide Atlas
Data type Data identifiers (IDs)
Biological species in the main concern
HumanMus musculus | Rattus norvegicus | Cinoa intestinails
Conditions of use Attribution&Share Alike
Frequency of updates (in last two years) 730
Last date of updates (date of confirmation) 2013/10/18 (2013/11/01)
Main IDs used in the products Accession Number | CIPRO ID | Clone ID (NBRC) | DGV ID | DrugBank ID | Ensembl Gene ID | Ensembl Protein ID | Ensembl Transcript ID | FLJ ID (NBRC) | GeneID | H-GOLD Marker ID | H-Inv cluster ID (HIX) | H-Inv protein ID (HIP) | H-Inv transcript ID (HIT) | HPRD ID | HUGO gene symbol | KEGG Gene ID | KEGG Pathway ID | OMIM ID | PDB ID | PdbeChem ID | Peptide Accession | PubMed ID | RefSeq ID | RefSeq Protein ID | UniProt Accession Number | dbSNP rs# (GemDBJ) | fRNAdb ID | ALLELE ID | BRC ID | Clone ID(FANTOM) | MGI Marker Accession ID | Mouse Gene Symbol RGD ID | CAS ID | ChEBI ID | DrugBank ID | HMDB Accession Number | KEGG Compound ID | KEGG Drug ID | KNApSAcK ID | NIKKAJI ID | PDBeChem ID | PharmGKB ID | PubChem Compound ID | PubChem Substance ID
How to make a link to get access to each IDs. http://biodb.jp/hfs.cgi?id=[ID]&type=[ID Type]&db=[Database name]
external databases to which this database/tool have links

H-InvDB (Transcript view) (http://www.h-invitational.jp/hinv/spsoup/transcript_view) | H-InvDB (Locus view) (http://www.h-invitational.jp/hinv/spsoup/locus_view) | H-InvDB (G-integra) (http://www.h-invitational.jp/hinv/g-integra/cgi-bin/f_genemap.cgi) | H-InvDB (PPI view) (http://www.h-invitational.jp/hinv/ppi/ppi_view.cgi) | NCBI RefSeq nucleotide (http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi) | NCBI GenBank (http://www.ncbi.nlm.nih.gov/nuccore) | NCBI Entrez Gene (http://www.ncbi.nlm.nih.gov/sites/entrez) | NCBI OMIM (http://omim.org/entry) | NCBI PubMed (http://www.ncbi.nlm.nih.gov/pubmed) | GeMDBJ (https://gemdbj.nibio.go.jp/gv/gv/GVIndex) | HUGO (http://www.genenames.org/data/hgnc_data.php) | MutationView (http://mutview.dmb.med.keio.ac.jp/cgi-bin/mutcgi/mut_login/genewin.exe/mutview3/mutview_a/java/) | H-GOLD (http://www.h-invitational.jp/gdbs/viewer/Viewer) | PDBj (http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/DetailServlet) | UniProt (http://www.uniprot.org/uniprot/) | GGDB (http://riodb.ibase.aist.go.jp/rcmg/ggdb/Homolog) | fRNAdb (http://togodb.biosciencedbc.jp/togodb/view/frnadb_summary) | Ensembl Transcript (http://www.ensembl.org/Homo_sapiens/Transcript/Transcript?t) | Ensembl Gene (http://www.ensembl.org/Homo_sapiens/geneview) | Ensembl Protein (http://www.ensembl.org/id/) | NBRC (http://www.nbrc.nite.go.jp/cgi-bin/hflcdna/e/Sequence_ID_Search.cgi) | HGPD (http://riodb.ibase.aist.go.jp/hgpd/cgi-bin/pg_locus_list.cgi) | KEGG Gene (http://www.genome.jp/dbget-bin/www_bget) | KEGG Pathway (http://www.genome.jp/kegg-bin/show_pathway) | HPRD (http://www.hprd.org/summary) | LEGENDA (http://www.h-invitational.jp/legenda/relations-view.htm) | Evola (http://www.h-invitational.jp/evola_main/annotation.cgi) | H-DBAS (http://h-invitational.jp/h-dbas/locusOverview.do) | G-Compass (http://h-invitational.jp/g-compass/cgi-bin/gc_main.cgi) | H-InvDB (Protein View) (http://h-invitational.jp/hinv/protein/protein_view.cgi) | CIPRO (http://cipro.ibio.jp/2.5) | H-ANGEL (http://h-invitational.jp/hinv/h-angel/wge_server.cgi) | FLJ Human cDNA (http://flj.lifesciencedb.jp/v03/cgi/sv_cdna_locus_info.cgi) | VarySysDB (http://www.h-invitational.jp/varygene/gene.htm) | PDBeChem (http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/) | DrugBank (http://www.drugbank.ca/drugs) | Wikipedia Human proteins (http://en.wikipedia.org/wiki) | JSNP (http://snp.ims.u-tokyo.ac.jp/cgi-bin/SnpInfo.cgi) | NCBI RefSeq protein (http://www.ncbi.nlm.nih.gov/protein/) | DGV (http://projects.tcag.ca/cgi-bin/variation/xview?source=hg19&view=variation&id) | COXPRESdb (http://coxpresdb.jp/data/gene/) | Human Protein ATLAS (http://www.proteinatlas.org/) | Peptide Atlas (https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptide?searchWithinThis=Peptide+Name&searchForThis)

Published papers (PubMed IDs)

pmid:19454601