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16 Bioinformatics database from Banff Manifesto topics matching:
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PDB : The RCSB Protein Data Bank; a repository for 3D biological macromolecular
Welcome. The PDB is the single worldwide repository for the processing and distribution of 3-D structure data of large molecules of proteins and nucleic acids. New structures are released each Wednesday by 1:00am Pacific time. Details about the...
Bioinformatics tag:
View entire collection »Identifier example:
- PDB:1A4U ,
- 1A4U
Download:
Provider homepage:
- http://www.rcsb.org/pdb/
Replaces:
Available format:
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- GO : Gene Ontology ,
- [bm:linkdb] ,
- [bm:lsrn]
Freebase Topic:
Link From:
Reserved namespace:
- pdb
URL pattern:
- http://www.rcsb.org/pdb/cgi/explore.cgi?pid=223051005992697&pdbId=%s ,
- http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e
MGI : Mouse genome database (MGD) from Mouse Genome Informatics (MGI)
Gene Expression Database (GXD) Project
GXD integrates different types of gene expression information from the
mouse and provides a searchable index of published experiments on
endogenous gene expression during development.(See About GXD.)
Mouse...
Database schema:
Identifier example:
- MGI:80863 ,
- 98834
Provider homepage:
- http://www.informatics.jax.org/
Replaces:
Available format:
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- EMBL nucleotide sequence database ,
- GO : Gene Ontology ,
- International Protein Index
Freebase Topic:
Citation:
Reserved namespace:
- mgi
URL pattern:
- http://www.informatics.jax.org/searches/accession_report.cgi?id=mgi:%s ,
- http://www.informatics.jax.org/searches/accession_report.cgi?id=%s
Search URL:
Ensembl : Eukaryotic genome annotation project
Bioinformatics tag:
View entire collection »Identifier example:
- ENSEMBL:ENSP00000265949
Provider homepage:
- http://www.ensembl.org/
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- GO : Gene Ontology ,
- International Protein Index ,
- [bm:nar]
Reserved namespace:
- ensembl
URL pattern:
- http://www.ensembl.org/perl/protview?peptide=%s ,
- http://www.ensembl.org/perl/textview?idx=All&species=All&q=%s
Description:
- Ensembl is a joint project between EMBL - EBI (a href=http:www.ebi.ac.ukhttp:www.ebi.ac.uka) and the Sanger Institute (a href=http:www.sanger.ac.ukhttp:www.sanger.ac.uka) to develop a software system which produces and maintains automatic annotation on metazoan genomes. Ensembl is primarily funded by the Wellcome Trust (a href=http:www.wellcome.ac.ukhttp:www.wellcome.ac.uka). This site provides free access to all the data and software from the Ensembl project.
PubMed: NCBI bibliographic database
PubMed, available via the NCBI Entrez retrieval
system, was developed by the National
Center for Biotechnology Information (NCBI) at the
National Library of Medicine (NLM), located at the
U.S. National Institutes of Health ...
Bioinformatics tag:
Identifier example:
- 16446403
Provider homepage:
- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
Replaces:
See also:
Available format:
Referenced by:
View entire collection »Freebase Topic:
Link To:
- GI : GenInfo identifier, used as a unique sequence identifier for nucleotide and protein ,
- MeSH : Medical Subject Headings
Link From:
View entire collection »Reserved namespace:
- pubmed
URL pattern:
- http://www.ncbi.nlm.nih.gov/pubmed/%s
Description:
- The PubMed database is available on the Entrez retrieval system, and was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM). PubMed provides free access to MEDLINE, NLM's database of more than 13 million bibliographic citations and abstracts in the fields of biomedicine, nursing, dentistry, veterinary medicine, health care systems, and preclinical sciences. PubMed also includes access to additional selected life sciences journals not in MEDLINE. PubMed's LinkOut feature a href=http:www.ncbi.nlm.nih.goventrezlinkouthttp:www.ncbi.nlm.nih.goventrezlinkouta provides access to a wide variety of relevant web-accessible online resources, including full-text publications, biological databases, consumer health information, and research tools. Links are also available to the molecular biology databases maintained by NCBI. New citations are typically added to PubMed Tuesday through Saturday.
HomoloGene : Discover Homologs
HomoloGene is a system for automated detection of homologs among
the annotated genes of several completely sequenced eukaryotic genomes.
Bioinformatics tag:
Download:
Provider homepage:
- http://www.ncbi.nlm.nih.gov/sites/entrez?db=homologene
Referenced by:
View entire collection »Link From:
Reserved namespace:
- homologene
MeSH : Medical Subject Headings
MeSH is the National Library of Medicine's controlled vocabulary
thesaurus. It consists of sets of terms naming descriptors in a
hierarchical structure that permits searching at various levels of
specificity. MeSH descriptors are arranged in both an...
Database schema:
Bioinformatics tag:
Identifier example:
- MeSH:mitosis ,
- mitosis
Download:
Provider homepage:
- http://www.nlm.nih.gov/mesh/2005/MBrowser.html
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- GO : Gene Ontology ,
- [bm:lsrn]
Freebase Topic:
Citation:
Reserved namespace:
- mesh
URL pattern:
- http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=%s
Search URL:
IUPAC : International Union of Pure and Applied Chemistry
Bioinformatics tag:
Provider homepage:
- http://www.iupac.org/
Referenced by:
Link From:
View entire collection »Reserved namespace:
- iupac
Description:
- The IUPAC Nomenclature database is mainly concerned with biochemical and organic chemical nomenclature. It includes most nomenclature recommendations prepared by the IUPAC-IUBMB Joint Commission on Biochemical Nomenclature and the IUPAC Commission on Nomenclature of Organic Chemistry. Documents included are the nomenclature of steroids, carbohydrates, amino acids and peptides and glossaries of organic class names, physical organic chemistry and stereochemistry. For additional biochemical recommendations prepared by the Nomenclature Committee of IUBMB see a href=http:www.chem.qmul.ac.ukiubmbhttp:www.chem.qmul.ac.ukiubmba. Selected other IUPAC documents such as the latest table of atomic weights and glossaries of medicinal chemistry and bioinorganic chemistry are included; as well as an extensive bibliography of IUPAC nomenclature publications together with, where known, translations into other languages. The database may be accessed at a href=http:www.chem.qmul.ac.ukiupachttp:www.chem.qmul.ac.ukiupaca.
InChi : The IUPAC International Chemical Identifier
Bioinformatics tag:
Identifier example:
- 1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
Provider homepage:
- http://www.iupac.org/inchi/
Referenced by:
Link From:
View entire collection »Reserved namespace:
- inchi
SMILES : The simplified molecular input line entry specification
Freebase Topic:
Link From:
View entire collection »Reserved namespace:
- smiles
CAS Registry
Bioinformatics tag:
Identifier example:
- 58-08-2
Provider homepage:
- http://www.cas.org/
Referenced by:
Link From:
View entire collection »Reserved namespace:
- cas
HGNC : Human Gene Nomenclature Database
We have already approved over 24,000 symbols;
the vast majority of these are for protein-coding genes, but also
include symbols for pseudogenes, non-coding RNAs,
phenotypes and genomic features (see HGNC Search).
Our current priority is...
Bioinformatics tag:
View entire collection »Identifier example:
- 11998
Provider homepage:
- http://www.genenames.org/
Replaces:
See also:
Available format:
Referenced by:
View entire collection »Link From:
Reserved namespace:
- hgnc
URL pattern:
- http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC:%s ,
- http://www.genenames.org/data/hgnc_data.php?hgnc_id=%s
Description:
- pThe HUGO Gene Nomenclature Committee (HGNC) designates approved symbols for all human genes, in accordance with the Guidelines for Human Gene Nomenclature (a href=http:www.genenames.orgguidelines.htmlhttp:www.genenames.orgguidelines.htmla). It is necessary to provide a unique symbol for each gene, preferably one which maintains parallel construction in different members of a gene family and can also be used in other species, especially the mouse.ppThe HGNC is responsible for the assignment of these symbols as well as alonger and more descriptive gene name. Considerable efforts are made to use a symbol acceptable to workers in the field, but sometimes it is not possible to use exactly what has previously appeared in the literature. However, wherever the HGNC is aware of such symbols, they are listed as aliases and information on the gene in question can be retrieved by searching with the aliases and the approved symbol in the HGNC Database(a href=http:www.genenames.orgcgi-binhgnc_search.plhttp:www.genenames.orgcgi-binhgnc_search.pla). Approved gene symbols are marked as such and given priority in databases including Entrez Gene, Ensembl, GeneCards, OMIM and GenAtlas. The HGNC also works closely with a number of journals to promote standardization of gene nomenclature. These include Nature Genetics, Nature, Genomics, Human Mutation and Cytogenetic and Genome Research.p ,
- Genew, the Human Gene Nomenclature Database, is the only resource that provides data for all human genes which have approved symbols. It is managed by the HUGO Gene Nomenclature Committee (HGNC) as a confidential database, containing over 16,000 records, 80% of which are represented on the Web by searchable text files. The data in Genew are highly curated by HGNC editors and gene records can be searched on the Web by symbol or name to directly retrieve information on gene symbol, gene name, cytogenetic location, OMIM number and PubMed ID. Data are integrated with other human gene databases e.g. GDB, LocusLink and SWISS-PROT and approved gene symbols are carefully co-ordinated with the Mouse Genome Database (MGD). Approved gene symbols are available for querying and browsing at: a href=http:www.gene.ucl.ac.ukcgi-binnomenclaturesearchgenes.plhttp:www.gene.ucl.ac.ukcgi-binnomenclaturesearchgenes.pla.
UniProt : The Universal Protein Resource
The Swiss-Prot, TrEMBL, and PIR protein database activities have united to form the Universal Protein Resource (UniProt), which provides a central resource on protein sequences and functional annotation with three database components, each...
Bioinformatics tag:
View entire collection »Identifier example:
- UniProt:P51587
Provider homepage:
- http://www.uniprot.org/
Replaces:
- The Universal Protein Knowledgebase, a central repository of protein sequence an ,
- section of the UniProt Knowledgebase, containing computationally analysed record ,
- section of the UniProt Knowledgebase, containing annotated records, which includ ,
- Namespace for UniProt gene symbol status: depreciated alias.
References:
- UniGene gene-oriented nucleotide sequence clusters ,
- EchoBASE - an integrated post-genomic database for E. coli ,
- Escherichia coli strain K12 genome database ,
- EMBL nucleotide sequence database
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- [bm:lsrn] ,
- [bm:nar] ,
- [bm:srs]
Freebase Topic:
Link From:
- Affymetrix : Alliance for Cellular Signaling ,
- ChEBI : Chemical Entities of Biological Interest database of small molecules ,
- DBpedia
Reserved namespace:
- uniprot
URL pattern:
- http://www.uniprot.org/uniprot/%s
Description:
- The Swiss-Prot, TrEMBL, and PIR protein database activities have united to form the Universal Protein Resource (UniProt), which provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKBSwiss-Prot section and the automatically annotated UniProtKBTrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations, and literature-based evidence attribution enable scientists to analyze proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90), or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. The UniProt databases continue to grow in size and in availability of information. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division, and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon.
RefSeq : NCBI Reference Sequences
The Reference Sequence (RefSeq) database
is a non-redundant collection of richly annotated DNA, RNA, and protein
sequences from diverse taxa. The collection includes sequences from
plasmids, organelles, viruses, archaea, bacteria, and eukaryotes....
Bioinformatics tag:
- bm:General sequence databases ,
- bm:Sequence databases ,
- bm:Nucleotide Sequence Databases ,
- bm:Protein sequence databases
Provider homepage:
- http://www.genome.ad.jp/dbget-bin/www_bfind_info?refseq
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- [bm:linkdb] ,
- [bm:nar] ,
- [bm:srs]
Reserved namespace:
- refseq
URL pattern:
- http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=%s
Description:
- The NCBI Reference Sequence project (RefSeq) will provide reference sequencestandards for the naturally occurring molecules of the central dogma, fromchromosomes to mRNAs to proteins. RefSeq standards provide a foundation for thefunctional annotation of the human genome. They provide a stable referencepoint for mutation analysis, gene expression studies, and polymorphismdiscovery.pScope: Currently, RefSeq records are provided for the following molecule typesand genomes:PREMolecule Accession Format Genome Complete Genome NC_###### Organelle Complete Chromosome NC_###### Saccharomyces cerevisiae Genomic Contig NT_###### Homo sapiens Mus musculusmRNA NM_###### Limited Vertebrate Homo sapiens Mus musculus Rattus norvegicus Protein NP_###### All of the abovePRE ,
- The National Center for Biotechnology Information Reference Sequence (RefSeq) database provides curated non-redundant sequence standards for genomic regions, transcripts (including splice variants), and proteins. brRecords are compiled using a combined approach of collaboration, automated methods, prediction, and curation and are extensively integrated with other NCBI resources facilitating navigation and discovery. RefSeq records represent the current best view of genomes and their transcript andor protein products.
GeneID : Database of genes from NCBI RefSeq genomes
Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that...
Identifier example:
- 7157
Provider homepage:
- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
Available format:
Referenced by:
- [bm:lsrn] ,
- National Center for Biotechnology Information, Bethesda ,
- UniProt : The Universal Protein Resource
Link From:
View entire collection »Reserved namespace:
- geneid
URL pattern:
- http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids=%s ,
- http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=%s
EC : The Enzyme Commission
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each...
Bioinformatics tag:
Identifier example:
- 3.4.11.4
Provider homepage:
- http://www.chem.qmw.ac.uk/iubmb/enzyme/
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- GO : Gene Ontology ,
- [bm:lsrn]
Reserved namespace:
- ec
URL pattern:
- http://www.genome.ad.jp/dbget-bin/www_bget?ec:%s
OMIM : Online Mendelian Inheritance in Man
Welcome to OMIM, Online Mendelian Inheritance in Man. This database is a
catalog of human genes and genetic disorders authored and edited by Dr.
Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and
developed for the World Wide...
Bioinformatics tag:
View entire collection »Identifier example:
- OMIM:190198 ,
- 191170
Download:
Provider homepage:
- http://www.genome.ad.jp/dbget-bin/www_bfind_info?omim
See also:
Referenced by:
- BioMoby : System for interoperability between biological data hosts and analytical services ,
- GO : Gene Ontology ,
- [bm:linkdb] ,
- [bm:lsrn]
Statistics:
Reserved namespace:
- omim
URL pattern:
- http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=%s ,
- http://www3.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim?%s
Description:
- The OMIM(TM) (Online Mendelian Inheritance in Man) database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. ,
- Online Mendelian Inheritance in Man (OMIM) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support research and education in human genomics and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (a href=http:www.ncbi.nlm.nih.govomimhttp:www.ncbi.nlm.nih.govomima) is now distributed electronically by the National Center for Biotechnology Information (NCBI), where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype andor gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, approved gene nomenclature, and the highly detailed mapviewer, as well as patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics.
