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Showing 1 to 5 of 5 items tagged as ontologies


UniProt

database

Provider: UniProt Consortium
Contents: ,
Access Level: ,
Descriptions: "The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information."  Available material consists of: UniProtKB, a two-section protein knowledge-base consisting of SwissProt and TrEMBL; UniRef (sequence clusters;) UniParc (a sequence archive for tracking sequences and identifiers) and the supporting data (literature citations, taxonomy, keywords, nomenclature, guidelines and indexes.) A user manual and primer on annotation are provided as well. UniProt is distributed free under a Creative Commons attribution license. Updates are frequent and updated releases must be downloaded from the website. Much of UniProt's funding is provided by the NIH.
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NextBio Basic

database

Provider: NextBio
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Access Level: ,
Descriptions: NextBio Basic is a free web application for searching biomedical and genetic information. It provides access to a 'curated, correlated database' of public data into which NextBio integrates Medline literature, clinical trial information, and news. Its semantic framework is based on gene, tissue, disease and compound ontologies. Registered users (registration for this basic version is free) can personalize their experience, communicate, collaborate and share data with the rest of the NextBio community. For the registered user, a single search for a gene yields quick results arranged by category: an overview of the gene; a list of tissues in which the gene is expressed; diseases and compounds relating to the gene; a list of the top associated researchers and authors; literature, associated clinical trials, and more.
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MeSH (Medical Subject Headings)

database

Provider: National Library of Medicine
Contents:
Access Level: ,
Descriptions: MeSH is the National Library of Medicine's controlled vocabulary thesaurus, consisting of sets of descriptors in a hierarchical structure to permit searching with increasing levels of specificity. This thesaurus is used by NLM for indexing articles from the world's leading biomedical journals for the MEDLINE/PubMed® database. It is also used for LocatorPlus, the NLM-produced catalog of books, documents, and audiovisuals acquired by the National Library of Medicine. Each bibliographic record is associated with a set of MeSH terms describing the item's content. MeSH vocabulary can be used in search queries to find items on a desired topic in any NLM database.
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GoPubMed

database

Provider: Transinsight
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Access Level: ,
Descriptions: GoPubMed is an innovative, powerful search tool that combines the MeSH (Medical Subject Headings) and GO (Gene Ontology) terminologies to optimize the effectiveness of queries to PubMed- for everyone, but for molecular biologists in particular. Searching elicits results presented very quickly (maximum display: the most recent 1,000 citations), along with a sidebar presenting the full results in categorized, hierarchical groups of terms that help the user to focus in further- the producers of this search engine refer to it as a "knowledge-based semantic search." There are many more features to this search tool than can be described here.
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Gene Ontology

database

Provider: Gene Ontology Project
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Access Level: ,
Descriptions: "The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data."  The Ontologies describe three aspects of molecular biology- biological processes, cellular components, and molecular functions. Gene Ontology's collected tools list includes hundreds from all over the world: specialized browsers, search engines, statistical analysis and visualization tools, and many other kinds. This project began as a collaboration between three model organism databases, FlyBase (Drosophila), the Saccharomyces Genome Database  and the Mouse Genome Database  in 1998. Since then, the GO Consortium has grown to include many other databases, including several of the world's major repositories for plant, animal and microbial genomes. See the GO Consortium page for a full list of member organizations.
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