More information XML output
| Name | H-InvDB |
|---|---|
| Aliases | H-Invitational database |
| Description | H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, protein functions, etc. |
| Type | DB |
| Main Institutes of management | Biomedicinal Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST) |
| Country of the Institute | Japan |
| URL of the site | http://www.jbirc.jbic.or.jp/hinv/ahg-db/index.jsp |
| Interface | GUI|FTP|SOAP web service|REST web service |
| Input example | Enter the keyword “protein” in the text box on the upper right of the top page and click “GO” button. |
| Keyword |
cDNA | annotation | integration
|
| Amount of the all data for download（Mbyte） | Method to obtain the all data. | 3160.848 | Download from the following sites FTP:ftp://ftp.ddbj.nig.ac.jp/mirror_database/hinv/ or HTTP:http://www.h-invitational.jp/hinv/dataset/download_jp.cgi |
| External resources (databases) in building the product. | CHGC | DKFZ/MIPS | IMSUT | KDRI | MGC/NCI | BIND | BodyMap | CCDS | dbSNP | DDBJ/EMBL/GenBank | DIP | Ensembl | EntrezGene | fRNAdb | GenAtlas | Gene ontology (GO) | GeneCards | GGDB | GTOP | HGNC | H-GOLD (GDBS) | HPRD | IntAct | InterPro | KEGG | LIFEdb | LSBM | MGI | MINT | Mutation view | NC-IUBMB (EC) | OMIM | PubMed | RefSeq | UCSC | UniGene | UniProt |
| Data type | RNA human full-length cDNA, mRNA |
| Biological species in the main concern |
Human
|
| Conditions of use | Attribution&Share Alike User account is not required. |
| Frequency of updates (in last two years) | 6 |
| Last date of updates (date of confirmation) | 2010/09/10 (2010/09/10) |
| Main IDs used in the products | HIX (gene cluster) | HIT (transcript) | HIP (protein) | HIF (gene family/group) |
| How to make a link to get access to each IDs. | http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=[HIXID] |
| external databases to which this database/tool have links | CHGC (http://www.chgc.sh.cn/en/) | DKFZ/MIPS (http://www.dkfz.de/) | IMSUT (http://www.ims.u-tokyo.ac.jp/imsut/en/) | KDRI (http://www.kazusa.or.jp/e/) | MGC/NCI (http://mgc.nci.nih.gov/) | BIND (http://bond.unleashedinformatics.com/) | BodyMap (http://bodymap.ims.u-tokyo.ac.jp/) | CCDS (http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi?REQUEST=CCDS&DATA=CCDS4091) | dbSNP (http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs35752268) | DDBJ (http://getentry.ddbj.nig.ac.jp/search/get_entry?accnumber=BC053657) | DIP (http://dip.doe-mbi.ucla.edu) | Ensembl (http://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000113532;r=5:100145357-100238970;t=ENST00000231461) | EntrezGene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=7903) | fRNAdb (http://www.ncrna.org/frnadb/detail.html?i_name=FR075942) | GenAtlas | Gene ontology (GO) (http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008373) | GeneCards (http://www.genecards.org/cgi-bin/carddisp.pl?gene=ST8SIA4) | GGDB (http://riodb.ibase.aist.go.jp/rcmg/ggdb/Homolog?cat=symbol&symbol=ST8SIA4) | GTOP (http://sybock.genes.nig.ac.jp/~hinv7/cgi-bin/mas.pl.cgi?org=hinv7&id=HIT000044689) | HGNC (http://www.genenames.org/data/hgnc_data.php?match=ST8SIA4) | H-GOLD (GDBS) (http://hinv.jp/gdbs/viewer/Viewer?ch=5&fr=100145359&to=100238970&gv=new&md=1) | HGPD (http://riodb.ibase.aist.go.jp/hgpd/cgi-bin/pg_locus_list.cgi?txt_srch_cdna_name=FLJ82330) | HPRD (http://www.hprd.org/) | IntAct (http://www.ebi.ac.uk/intact/main.xhtml) | InterPro (http://www.ebi.ac.uk/interpro/IEntry?ac=IPR012163) | KEGG (http://www.genome.jp/dbget-bin/www_bget?hsa+7903) | LIFEdb (http://www.lifedb.de/lifedb/) | MGI (http://www.informatics.jax.org/searchtool/Search.do?query=mgi:106018) | MINT (http://mint.bio.uniroma2.it/mint/Welcome.do) | Mutation view (http://mutview.dmb.med.keio.ac.jp/MutationView/jsp/mutview/java/geneWin.jsp?omimId=?602859) | NC-IUBMB (EC) | OMIM (http://omim.org/entry/601888) | PubMed (http://www.ncbi.nlm.nih.gov/pubmed/7624364?dopt=Abstract) | RefSeq (http://www.ncbi.nlm.nih.gov/nucleotide/NM_175052) | UCSC (http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&position=chr5:100142639-100238987&db=) | UniGene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene) | UniProt (http://www.uniprot.org/uniprot/Q92187) |
| Published papers (PubMed IDs) | 19933760 Yamasaki C, et al. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res. 2010 Jan;38(Database issue):D626-32 | 18089548 Yamasaki C, et al. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research 36, Database issue D793-D799, 2008 | 15103394 T. Imanishi et al. Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones.PLoS Biology 2 (6), 856-875 2004 |
| Project name | Genome Information Integration Project (GIIP) |
|---|---|
| Area | Genome Informatics |
| Purpose | # construction of "all human gene catalogue" # development of annotation technique based on H-InvDB # data integration of disease, gene expression and PPI information |
| Introduction | GIIP project was a model project of METI, which executed for 3 years since 2005 to 2007. The representative institute of the commission was Japan Biological Informatics Consortium (JBIC) and also the other six research institutes took their parts. The aim of the project is to construct an annotated human gene database of the world highest quality, based on H-Invitational Database (H-InvDB). |
| Keyword | genome | gene | annotation | integrated | database |
| Patent (Japan, overseas) | JP2006323830(A) | JP2008097189(A) |
| Archives | |
| Product (Database, Tool) | Nothing |
| Project name | Life science database integration project |
|---|---|
| Area | Genome Informatics |
| Purpose | This project aims to facilitate the research and development in both industry and academia. |
| Introduction | The project develops a portal site that provides various information on databases and analysis tools for life science which were developed by the projects directly sponsored by METI, or developed by the Institutes sponsored by METI. The second aim is to develop an integrated system to utilize the various outcomes related to METI, based on H-Invitationl DB (all human gene database) that was developed in "Genome Information Integration Project (GIIP)". |
| Keyword | database | analysis tool | product | portal | integration |
| Patent (Japan, overseas) | - |
| Archives | |
| Product (Database, Tool) | Nothing |