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Links tagged with 'terminology as topic'

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Found 24 links

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ACELATool Content

http://www.nactem.ac.uk/acela/

Literature > Text Mining and Semantics

The ACELA (ACcElerated Annotation) tool aims to reduce the human effort required to produce a gold standard corpus of named entity (NE) annotations.

This content is being maintained by pthompson.

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tagsaccelerated annotation algorithms annotation tool artificial intelligence automated pattern recognition bibliographic databases named entity annotation natural language processing terminology as topic text mining
setsUniversity of Manchester

BioPortalDatabase Content

http://bioportal.bioontology.org

DNA > Annotations
Expression > Transcript Expression Analysis
Human Genome > Annotations
Literature > Open Access Resources
Literature > Search Tools

BioPortal is a web accessible open repository of biomedical ontologies. Users may browse, search and visualize ontologies, as well as participate in the evaluation and evolution of ontology reviews by adding notes, corrections, reviews, etc. Data from other sources such as GEO, ClinicalTrials.gov and ArrayExpress may also be integrated with the ontologies.

This content is being maintained by whetzel.

NAR Web Server Issue 2009NAR Web Server Issue 2011
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tagsbiomedical research controlled vocabulary natural language processing systems integration terminology as topic

BRENDA - The Comprehensive Enzyme Information SystemDatabase Content

http://www.brenda-enzymes.org/

Protein > Interactions, Pathways, Enzymes

Information about reaction and specificity, post-translational modifications, structure, stability, and references to other databases; free for academics.

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tagsanimals enzymes factual databases genomics humans ligands membrane proteins organ specificity protein conformation protein databases protein transport rats substrate specificity systems integration terminology as topic

DBASS3 and DBASS5Database Content

http://www.dbass.org.uk/

DNA > Databases

DBASS3 and DBASS5 provide comprehensive repositories of new exon boundaries that were induced by pathogenic mutations in human disease genes. Aberrant 5'- and 3'-splice sites were activated either by mutations in the consensus sequences of natural exon-intron junctions (cryptic sites) or elsewhere ('de novo' sites). DBASS3 and DBASS5 data can be searched by disease phenotype, gene, mutation, location of aberrant splice sites in introns and exons and their distance from authentic counterparts, by bibliographic references and by the splice-site strength estimated with several prediction algorithms. The user can also retrieve reference sequences of both aberrant and authentic splice sites with the underlying mutation.

NAR Database Issue 2011
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tagsdisease humans mutation nucleic acid databases rna splice sites terminology as topic

DECATool Content

http://www.nactem.ac.uk/deca_details/start.cgi

Literature > Text Mining and Semantics

DECA is a species disambiguation system for biological named entities. The system will identify protein entities and disambiguate them according to species, by assigning NCBI Taxonomy organism IDs.

This content is being maintained by pthompson.

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tagsartificial intelligence data mining factual databases named entity recognition natural language processing species disambiguation species specificity terminology as topic text mining

ENZYME - Enzyme nomenclature databaseDatabase Content

http://us.expasy.org/enzyme/

Protein > Interactions, Pathways, Enzymes

Repository of enzyme nomenclature information; useful selection of cross references to other databases; free for research purposes only.

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tagsenzymes factual databases terminology as topic

genenames.orgDatabase Content

http://www.genenames.org

Literature > Databases

genenames.org displays all approved nomenclature within Symbol Reports that contain data curated by HUGO Gene Nomenclature Committee (HGNC) editors and links to related genomic, phenotypic and proteomic information. New features include a new Quick Gene Search, a new List Search, an integrated HGNC BioMart and a new Statistics and Downloads facility.

This content is being maintained by HGNC.

NAR Database Issue 2011
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tagsanimals gene symbols genes genetic databases genomics humans nomenclature phenotype proteomics terminology as topic

GObletTool Content

http://goblet.molgen.mpg.de/

Protein > Annotation and Function
Sequence Comparison > Analysis of Aligned Sequences

GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.

NAR Web Server Issue 2004NAR Web Server Issue 2003
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tagsanimals complementary dna dna sequence analysis genes humans invertebrates mice plants protein databases protein sequence analysis proteins reproducibility of results sequence homology terminology as topic

GPSDBDatabase Content

http://biomint.pharmadm.com/

Literature > Search Tools
Literature > Text Mining and Semantics

Gene and Protein Synonym DataBase (GPSDB) is a collection of gene and protein names, organized by species that can be used to search for a given gene/protein name, retrieve all synonyms for this entity, and query Medline with a set of user-selected terms.

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tagscontrolled vocabulary database management systems documentation information dissemination medline natural language processing protein databases proteins terminology as topic

HGNC: HUGO Gene Nomenclature CommitteeResource Content

http://www.genenames.org

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
Human Genome > Other Resources
Protein > Sequence Retrieval

The HGNC approves a unique gene name and symbol for each known human gene. The HGNC Database is searchable and contains all approved symbols. For each symbol, if known, the database associates gene location, aliases, previous symbols and links out to sequence data and other databases.

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tagsanimals computational biology genes genetic databases genetic variation genomics human genome humans mice systems integration terminology as topic

IMGT/HLA databaseDatabase Content

http://www.ebi.ac.uk/imgt/hla/

Human Genome > Databases

The IMGT/HLA database provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute, we are able to provide public access to this data.

NAR Database Issue 2011
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tagsalleles hla antigens humans protein databases terminology as topic

LIPID MAPSTool Content

http://www.lipidmaps.org/tools/index.html

Human Genome > Other Resources
Other Molecules > Metabolites

LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.

NAR Web Server Issue 2007
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tagsanimals chemical models computational biology database management systems factual databases glycosphingolipids humans isomerism lipid metabolism lipids mice molecular conformation molecular structure polysaccharides protein databases proteome proteomics terminology as topic

LitInspectorTool Content

http://www.litinspector.org/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

A literature search tool providing gene homonym mining within the PubMed database. Search terms are highlighted in the results. LitInspector also performs signal transduction pathway mining using a manually curated database of pathway names, pathway components and pathway keywords.

NAR Web Server Issue 2009
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tagsanimals humans mice pubmed rats signal transduction terminology as topic

Mouse Genome Database (MGD)Database Content

http://www.informatics.jax.org/

Model Organisms > Databases

The Mouse Genome Database (MGD) is the community model organism database for the laboratory mouse and the source for phenotype and functional annotations of mouse genes. MGD includes a complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information. MGD contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Major improvements to the Mouse Genome Database include comprehensive update of genetic maps, implementation of new classification terms for genome features, development of a recombinase (cre) portal and inclusion of all alleles generated by the International Knockout Mouse Consortium (IKMC).

NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms alleles animal models animals chromosome mapping computational biology genetic databases genetic models genome genomics genotype integrases knockout mice mice mutant strains mice nucleic acid databases phenotype terminology as topic

MutalyzerTool Content

https://mutalyzer.nl/

Human Genome > Annotations
Human Genome > Genomics
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms

Mutalyzer was primarily developed to check the description of sequence variants identified in a gene during genetic testing according to the rules of the standard human sequence variant nomenclature of the Human Genome Variation Society. The Mutalyzer 2 parser is based on a formalized description of the nomenclature in Extended Backus-Naur Form. Mutalyzer applies the nomenclature rules and corrects variant descriptions accordingly.

This content is being maintained by P.Taschner.

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tagsamino acid sequence base sequence computational biology data mining dna mutational analysis dna sequence analysis genetic variation human genome humans molecular sequence data mutation nucleic acid databases proteins single nucleotide polymorphism terminology as topic