> Tag > Links tagged with 'controlled vocabulary'

Links tagged with 'controlled vocabulary'

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Found 24 links

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AliasServerDatabase Content

http://cbi.labri.fr/outils/alias/ [open in a new window]

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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.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
AliasServer: a web server to handle multiple aliases used to refer to proteins200426
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tagsalgorithms controlled vocabulary database management systems documentation natural language processing protein databases protein sequence analysis proteins sequence alignment

BINDTranslationDatabase Content

http://download.baderlab.org/BINDTranslation/ [open in a new window]

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Expression > Networks
Other Molecules > Databases
Protein > Databases

Biomolecular Interaction Network Database (BIND): a database of curated biomolecular interactions.

This content is being maintained by baderg.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
The Biomolecular Interaction Network Database in PSI-MI 2.520115
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tagsanimals controlled vocabulary humans protein binding protein databases proteomics rats reproducibility of results
setsUniversity of Toronto

CARMAwebTool Content

https://carmaweb.genome.tugraz.at/carma/ [open in a new window]

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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.

links directory index: 103
TitlePublication YearGoogle Scholar Citation Count
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis2006103
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/ [open in a new window]

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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.

links directory index: 97
TitlePublication YearGoogle Scholar Citation Count
Chemical Entities of Biological Interest: an update201097
NAR Database Issue 2010
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external linksLink on Wikipedia
tagsagrochemicals animals biological products chemical dictionaries computational biology controlled vocabulary factual databases humans pharmaceutical preparations
setsEuropean Bioinformatics Institute (EBI)

FunSimMatDatabase Content

http://www.funsimmat.de [open in a new window]

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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.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
FunSimMat update: new features for exploring functional similarity20103
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

GFINDerTool Content

http://www.medinfopoli.polimi.it/GFINDer/ [open in a new window]

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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.

links directory index: 115
TitlePublication YearGoogle Scholar Citation Count
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists200552
GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining200463
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/ [open in a new window]

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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.

links directory index: 139
TitlePublication YearGoogle Scholar Citation Count
The Gene Ontology: enhancements for 201120124
The Gene Ontology in 2010: extensions and refinements2010135
NAR Database Issue 2010
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external linksLink on Twitter Link on Wikipedia
tagsanimals computational biology controlled vocabulary genetic databases genomics humans nucleic acid databases protein databases

GoGeneTool Content

http://gopubmed.biotec.tu-dresden.de/gogene [open in a new window]

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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.

links directory index: 14
TitlePublication YearGoogle Scholar Citation Count
GoGene: gene annotation in the fast lane200914
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/ [open in a new window]

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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.

links directory index: 267
TitlePublication YearGoogle Scholar Citation Count
GoPubMed: exploring PubMed with the Gene Ontology2005267
NAR Web Server Issue 2005
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external linksLink on Wikipedia
tagscontrolled vocabulary enzyme inhibitors genetic databases levamisole pubmed subject headings

GPSDBDatabase Content

http://biomint.pharmadm.com/ [open in a new window]

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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.

links directory index: 12
TitlePublication YearGoogle Scholar Citation Count
GPSDB: a new database for synonyms expansion of gene and protein names200512
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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/ [open in a new window]

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Protein > Networks & Interactions, Pathways and 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.

links directory index: 953
TitlePublication YearGoogle Scholar Citation Count
Human protein reference database as a discovery resource for proteomics2004264
Development of human protein reference database as an initial platform for approaching systems biology in humans2003689
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external linksLink on Wikipedia
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/ [open in a new window]

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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.

links directory index: 271
TitlePublication YearGoogle Scholar Citation Count
The IntAct molecular interaction database in 2012201214
The IntAct molecular interaction database in 20102010257
NAR Database Issue 2010
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external linksLink on Twitter
tagsanimals computational biology controlled vocabulary false positive reactions genetic databases humans programming languages protein databases protein interaction mapping proteins tertiary protein structure

JProGOTool Content

http://www.jprogo.de/index.jsp [open in a new window]

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Expression > Transcript Expression Analysis
Model Organisms > Microbes

JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

links directory index: 26
TitlePublication YearGoogle Scholar Citation Count
JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information200626
NAR Web Server Issue 2006
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tagsarchaea archaeal genes bacteria bacterial genes controlled vocabulary gene expression profiling oligonucleotide array sequence analysis statistical data interpretation

KAASTool Content

http://www.genome.jp/kegg/kaas/ [open in a new window]

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DNA > Annotations
Protein > Networks & Interactions, Pathways and Enzymes
Sequence Comparison > Comparative Genomics

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

links directory index: 168
TitlePublication YearGoogle Scholar Citation Count
KAAS: an automatic genome annotation and pathway reconstruction server2007168
NAR Web Server Issue 2007
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tagsanimals artificial intelligence automation chromosome mapping computational biology controlled vocabulary database management systems documentation genome humans proteome sequence analysis signal transduction

KOBASTool Content

http://kobas.cbi.pku.edu.cn [open in a new window]

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DNA > Annotations
Human Genome > Databases
Protein > Networks & Interactions, Pathways and Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

links directory index: 215
TitlePublication YearGoogle Scholar Citation Count
KOBAS server: a web-based platform for automated annotation and pathway identification200675
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary2005140
NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

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