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Links tagged with 'controlled vocabulary'

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Found 28 links

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AliasServerDatabase Content

http://cbi.labri.fr/outils/alias/

DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval

A tool for converting identifiers in which multiple aliases are used to refer to sequences. Also available as a stand-alone tool.

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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

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

CARMAwebTool Content

https://carmaweb.genome.tugraz.at/carma/

Expression > Transcript Expression Analysis

Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.

This content is being maintained by johannes.rainer.

NAR Web Server Issue 2006
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tagscluster analysis controlled vocabulary gene expression profiling oligonucleotide array sequence analysis

ChEBIDatabase Content

http://www.ebi.ac.uk/chebi/

Other Molecules > Databases

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities.

NAR Database Issue 2010
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tagsagrochemicals animals biological products chemical dictionaries computational biology controlled vocabulary factual databases humans pharmaceutical preparations
setsEuropean Bioinformatics Institute (EBI)

eTBLASTDatabase Content

http://etest.vbi.vt.edu/etblast3/

Literature > Search Tools

eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.

NAR Web Server Issue 2007
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tagsalgorithms artificial intelligence authorship automated pattern recognition bibliographic databases controlled vocabulary database management systems humans informatics medline natural language processing peer review periodicals as topic publications publishing pubmed software design

FunSimMatDatabase Content

http://www.funsimmat.de

Protein > Databases

FunSimMat is a functional similarity database and web service for ranking genes/proteins by function. It provides different semantic similarity measures for Gene Ontology terms and offers functional similarity values for proteins contained in UniProtKB and for protein families/domains in Pfam and SMART. Users can perform semantic similarity searches with GO terms and functional similarity searches with proteins or protein families. FunSimMat also supports prioritizing disease gene candidates.

This content is being maintained by albrecht.

NAR Database Issue 2010
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tagsbioinformatics computational biology controlled vocabulary disease functional similarity gene gene database gene ontology gene prioritization protein protein database protein prioritization

G-SESAMETool Content

http://bioinformatics.clemson.edu/G-SESAME

Expression > Gene Set Analysis
Literature > Text Mining and Semantics
Sequence Comparison > Comparative Genomics

G-SESAME is a suite of online tools for measuring the semantic similarities of Gene Ontology (GO) terms and the functional similarities of gene products, as well as data mining the GO database.

NAR Web Server Issue 2009
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tagscluster analysis controlled vocabulary genes genetic databases

GFINDerTool Content

http://www.medinfopoli.polimi.it/GFINDer/

Expression > Transcript Expression Analysis

Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.

NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagscomputational biology controlled vocabulary gene expression profiling genetic databases genomics humans inborn genetic diseases oligonucleotide array sequence analysis phenotype proteins statistical data interpretation systems integration

GODatabase Content

http://www.geneontology.org/

Model Organisms > Databases

The Gene Ontology (GO) Consortium (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

NAR Database Issue 2010
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tagsanimals computational biology controlled vocabulary genetic databases genomics humans nucleic acid databases protein databases

GOEASTTool Content

http://omicslab.genetics.ac.cn/GOEAST/

Expression > Protein Expression
Expression > Transcript Expression Analysis

Gene Ontology Enrichment Analysis (GOEAST) is a toolkit for the identification of over-represented GO terms in a given gene set. Distinguishing features include: capacity to analyze data from various sources and from multiple species, and the capacity to cross compare GO enriched terms across experiments to identify correlations.

This content is being maintained by e00011027.

NAR Web Server Issue 2008
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tagscontrolled vocabulary gene expression profiling genes oligonucleotide array sequence analysis

GoGeneTool Content

http://gopubmed.biotec.tu-dresden.de/gogene

DNA > Annotations
Literature > Text Mining and Semantics

GoGene performs high-throughput text mining to complement annotation of genes. GoGene supports search for genes in PubMed, EntrezGene and BLAST.

NAR Web Server Issue 2009
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tagsanimals bone resorption controlled vocabulary gene expression profiling genes hepatoerythropoietic porphyria humans mice mutation oligonucleotide array sequence analysis osteoporosis pancreatic neoplasms pubmed rats

GoPubMedTool Content

http://www.gopubmed.org/

Literature > Search Tools

GoPubMed is a tool that allows users to explore the results of PubMed queries in the context of Gene Ontology (GO) terms.

NAR Web Server Issue 2005
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tagscontrolled vocabulary enzyme inhibitors genetic databases levamisole pubmed subject headings

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

Human Protein Reference DatabaseDatabase Content

http://www.hprd.org/

Protein > Interactions, Pathways, Enzymes
Protein > Proteomics

The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature.

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tagsbrca1 protein computational biology controlled vocabulary disease genomics humans macromolecular substances medical genetics post-translational protein processing protein binding protein databases protein interaction mapping proteins proteome proteomics quaternary protein structure substrate specificity tertiary protein structure

IntActDatabase Content

http://www.ebi.ac.uk/intact/

Protein > Databases

IntAct is molecular interaction database and toolkit. Data is abstracted from the literature or from direct data depositions by expert curators following a deep annotation model providing a high level of detail. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view.

NAR Database Issue 2010
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tagsanimals computational biology controlled vocabulary false positive reactions genetic databases humans programming languages protein databases protein interaction mapping proteins tertiary protein structure