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43 Rdfized database topics matching:
Filter this Collection| x name | x image | x Bio2RDF rdfizer | x article |
|---|---|---|---|
| x MGI : Mouse genome database (MGD) from Mouse Genome Informatics (MGI) |
|
mgi:all |
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...
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| mgi:$1 | |||
| x OMIM : Online Mendelian Inheritance in Man |
|
xml/omim:$1 |
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...
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| search:$1@omim | |||
| omim:all | |||
| omim:$1 | |||
| x PDB : The RCSB Protein Data Bank; a repository for 3D biological macromolecular |
|
xml/pdb:$1 |
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...
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| pdb:all | |||
| image/pdb:$1 | |||
| pdb:$1 | |||
| x Pfam : Protein families |
|
pfam:all |
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Less... Proteins are generally composed of one or more...
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| pfam:PB$1 | |||
| pfam:PF$1 | |||
| x WikiPathways : Pathways for the people |
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wikipathways:$1:$2 |
WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents...
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| wikipathways:all | |||
| x Affymetrix : Alliance for Cellular Signaling |
|
affymetrix:$1 |
Affymetrix' GeneChip® technology was invented in the late 1980's by a
team of scientists led by Stephen P.A. Fodor, Ph.D. The theory behind
their work was revolutionary - a notion that semiconductor
manufacturing techniques could be united with...
|
| x BioCarta : Charting pathways of life |
|
biocarta:category-$1 |
Observe how genes interact in dynamic graphical models. Our online
maps depict molecular relationships from areas of active research. In
an "open source" approach, this community-fed forum constantly
integrates emerging proteomic information from...
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| biocarta:category-all | |||
| biocarta:all | |||
| biocarta:$1Pathway | |||
| x CrystalEye |
The aim of the CrystalEye project is to aggregate
crystallography from web resources, and to provide methods to easily
browse, search, and to keep up to date with the latest published
information. At present we are
aggregating the crystallography...
|
||
| x GeneID : Database of genes from NCBI RefSeq genomes |
|
geneid:$1-all |
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...
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| geneid:$1 | |||
| x PubMed: NCBI bibliographic database |
|
pubmed:$1 |
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 ...
|
| search:$1@pubmed | |||
| x MeSH : Medical Subject Headings |
|
search:$1@mesh |
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...
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| search:$1@entrez-mesh | |||
| mesh:$1_$2 | |||
| mesh:[A-Z]$1 | |||
| mesh:[0-9]$1 | |||
| more ▼ | |||
| x UniProt : The Universal Protein Resource |
|
uniprot:$1-all |
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...
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| uniprot:$1 | |||
| x EC : The Enzyme Commission |
|
ec:all |
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...
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| ec:$1 | |||
| x Ensembl : Eukaryotic genome annotation project |
|
ensembl:MMU$1 | |
| x GDB : Human Genome Database |
|
gdb:$1 | |
| x GenBank : Nucleotide sequence database |
|
genbank:$1 |
The Entrez Nucleotide database is a collection of sequences from
several sources, including GenBank, RefSeq, and PDB. The number of bases
in these databases continues to grow at an exponential rate.
As of April 2006,...
|
| x GI : GenInfo identifier, used as a unique sequence identifier for nucleotide and protein | gi:$1 |
The GI number has been used for many years by NCBI to track sequence
histories in GenBank and the other sequence databases it maintains. The
VERSION system of identifiers was adopted in February 1999 by the
International Nucleotide Sequence Database...
|
|
| x GO : Gene Ontology |
|
go:$1 |
Biologists currently waste a lot of time and effort in searching
for all of the available information about each small area of research.
This is hampered further by the wide variations in terminology that may
be common usage at any given time,...
|
| go:all | |||
| x GOBASE : The organelle genome database |
|
GOBASE is a taxonomically broad organelle genome database that
organizes and integrates diverse data related to mitochondria and
chloroplasts. GOBASE is currently expanding to include information on
representative bacteria that are thought to be...
|
|
| x GoPubMed : Search PubMed and get results sorted by GO and MeSH |
|
gopubmed:$1 |
The search engines GoPubMed and MeSHPubMed reduce search time and
increase the relevance of search results significantly. The engines use
a generic technology which can be adopted to other domains like the
finance or food industry.
|
| search:$1@gopubmed | |||
| x HGNC : Human Gene Nomenclature Database |
|
hgnc:[A-Z]$1 |
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...
|
| hgnc:$1 | |||
| x InterPro : Integrated resource of protein families, domains and functional sites |
|
Interpro:all |
The InterPro database was established in 1999 when the InterPro Consortium was formed between the SWISS-PROT group at EBI and SIB, and the founding member databases Prints, PROSITE, Pfam and ProDom. The first release was later that year. ...
|
| interpro:$1 | |||
| x Keywords : UniProtKB entries are tagged with keywords | keywords:$1 |
UniProtKB entries are tagged with keywords (KW) that can be used to retrieve
particular subsets of protein sequence entries.
There are 10 categories of keywords:
› Biological process
› Cellular component
...
|
|
| keywords:all | |||
| x CPD : KEGG Ligand Database for Chemical Compound |
|
cpd:$1 |
KEGG COMPOUND is a chemical structure database for metabolic compounds and other chemical substances that are relevant to biological systems.
Each entry is identified by the C number, such as C00047 for L-lysine, and contains various links to other...
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| cpd:all | |||
| image/cpd:$1 | |||
| x MapView : NCBI Map Viewer |
|
mapview:$1-$2-$3-$4 | |
| x LSID : Life Science IDentifier syntax for URN | urn:lsid:bio2rdf.org:$1:$2 |
A proposed URN syntax for URI in bioinformatics is proposed by the LSID project. It is possible to obtain LSIDized document from Bio2RDF service by asking for it
|
|
| x Path : KEGG PATHWAY Database |
|
path:$1-all |
KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks for: 1. Metabolism Carbohydrate Energy ...
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| path:$1 | |||
| Image/path:$1 | |||
| x RN : KEGG Ligand Database for Chemical Reaction |
|
rn:$1 |
KEGG REACTION contains all reactions taken from KEGG ENZYME and additional reactions taken from the KEGG metabolic pathways.
Each reaction is identified by the R number, such as R00259
for the acetylation of L-glutamate.
Reactions are linked to...
|
| rn:all | |||
| image/rn:$1 | |||
| x DR : KEGG Ligand Database for Drug |
|
dr:$1 |
KEGG DRUG is a chemical structure based information resource for
all approved drugs in Japan and the U.S.A. Each chemical structure is
identified by the D number, and is associated with generic names, trade
names, efficacy, target information, etc....
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| dr:all | |||
| image/dr:$1 | |||
| x GL : KEGG Ligand Database for Carbohydrate Structure |
|
gl:$1 |
Functional information of genes and proteins is organized in KEGG as ortholog groups, called KEGG Orthology (KO) groups, to cover all organisms. The KO groups for glycosyltransferases are finely classified ortholog groups distinguishing known...
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| gl:all | |||
| image/gl:$1 | |||
| x ProDom : A protein domain database |
|
Prodom:all |
ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely...
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| Prodom:$1 | |||
| x PROSITE : A protein domain and family database |
|
Prosite:$1 |
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them [More details / References / Disclaimer / Commercial users]. PROSITE is complemented...
|
| x PubChem : Information on biological activities of small molecule |
|
Pubchem:$1 |
PubChem provides information on the biological activities of small
molecules. It is a component of NIH's Molecular Libraries Roadmap
Initiative. If you would like to learn more about how to use the
PubChem resources, please go to our help page. ...
|
| x Reactome : A knowledgebase of biological pathways and processes |
|
reactome:$1 |
Reactome is a database of cellular level processes from simple events, such as biochemical reactions, to complex events, such as the cell cycle. It provides process-level annotation of the structure and function of the Human Genome, with dynamic...
|
| reactome:all | |||
| x Taxon : NCBI Taxonomy | rdf+xml/taxon:$1 |
Organisms are classified in a hierarchical tree structure.
Our taxonomy database contains every node (taxon) of the tree.
UniProtKB taxonomy data is manually curated: next to manually
verified organism names,
we...
|
|
| taxon:$1 | |||
| x UniRef : UniProt Non-redundant Reference Databases |
|
Rdf+xml/uniref:$1 |
The UniProt NREF (UniProt Reference Clusters) database.
The two major objectives of UniRef are:
(i) to facilitate sequence merging in UniProt, and
(ii) to allow faster and...
|
| uniref:$1 | |||
| x UniParc : UniProt Archive a non-redundant archive of protein sequences extracted from Swi |
|
rdf+xml/uniparc:$1 |
UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences extracted from public databases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, PIR-PSD, EMBL, EMBL WGS, Ensembl, IPI, PDB, PIR-PSD, RefSeq, FlyBase, ...
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| uniparc:$1 | |||
| x Swoogle : Semantic Web Search Engine |
|
search:$1@swoogle | |
| x Sindice : A lookup index for Semantic Web documents |
|
Sindice is a lookup index for Semantic Web documents built on data intensive cluster computing techniques.
Sindice indexes the Semantic Web and can tell you which sources mention a resource URI, IFP, or keyword.
Sindice does not...
|
|
| x ChEBI : Chemical Entities of Biological Interest database of small molecules |
|
image/chebi:$1 |
Chemical Entities of Biological Interest (ChEBI) is a freely
available dictionary of molecular entities focused on ‘small’ chemical
compounds. The term ‘molecular entity’ refers to any constitutionally
or isotopically distinct atom, molecule, ion,...
|
| chebi:$1 | |||
| chebi:all | |||
| x CellMap : The Cancer Cell Map |
|
The Cancer Cell Map is a selected set of human cancer focused pathways. Biologists can browse and search the Cancer Cell Map pathways. View gene expression data on any pathway. Computational biologists can download all pathways in BioPAX format for...
|
|
| x DBpedia |
|
dbpedia:Hexokinase |
Wikipedia
is the by far largest publicly available encyclopedia on the Web.
Wikipedia editions are available in over 250 languages with the English
one accounting for more than 1.95 million articles. Wikipedia...
|
| x OBO : Open Biomedical Ontologies |
|
obo:all |
In addition to a listing of OBO ontologies, this site also provides
a statement of the OBO Foundry principles, discussion fora, technical
infrastructure, and other services to facilitate ontology development.
We welcome feedback and encourage...
|
