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Hyperlink Management System
| 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 (2019/06/03) |
| 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 |
| Operational Status | Available |
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