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Links tagged with 'data mining'

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Found 21 links

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BAGEL2Tool Content

http://bagel2.molgenrug.nl

DNA > Gene Prediction
Model Organisms > Microbes

BAGEL2 (BActeriocin GEnome mining tooL) identifies putative bacteriocins on the basis of conserved domains, physical properties and genomic context. Improved genome mining capacity from BAGEL.

NAR Web Server Issue 2010
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tagsamino acid motifs anti-bacterial agents bacterial genome bacteriocins data mining genomics open reading frames

BioExtractTool Content

http://www.bioextract.org

Computer Related > Web Services
Computer Related > Workflows
DNA > DNA and Genomic Analysis

The BioExtract Server is a platform for the creation of bioinformatic workflows to aid the analysis of genomic data. A series of recorded tasks can be saved and shared. Integrated resources include NCBI databases, EMBL-Bank, UniProt and UniRef, as well as a large number of computational tools such as EMBOSS and KEGG.

NAR Web Server Issue 2011
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tagsbiopolymers computational biology data mining database management systems factual databases genetic databases genomics information dissemination systems integration workflow

BSQATool Content

http://www.beespace.uiuc.edu/QuestionAnswer

Literature > Text Mining and Semantics
Model Organisms > Fly

BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.

NAR Web Server Issue 2010
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tagsanimal behavior animals data mining drosophila melanogaster gene expression regulation homeodomain proteins insect genes insects systems integration trans-activators

CancerResourceDatabase Content

http://bioinformatics.charite.de/cancerresource/

Other Molecules > Databases

CancerResource, a database that integrates cancer-relevant relationships of compounds and targets from (i) literature mining and (ii) external resources complemented with (iii) essential experimental and supporting information on genes and cellular effects. CancerResource addresses the spectrum of research on compound-target interactions in natural sciences as well as in individualized medicine.

This content is being maintained by robertpreissner.

NAR Database Issue 2011
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tagsantineoplastic agents data mining gene expression humans neoplasm proteins protein databases systems integration tumor cell line

CCancerDatabase Content

http://mips.helmholtz-muenchen.de/proj/ccancer

Expression > Gene Set Analysis
Literature > Open Access Resources

CCancer is an automatically collected database of gene lists reported in various studies. The current coverage is 3369 gene lists from 2644 papers. Enrichment analysis reports intersecting gene lists with an inputted gene list.

NAR Web Server Issue 2010
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tagsaniline compounds cell aging data mining genetic databases humans monte carlo method neoplasm genes neoplasm proteins neoplasms neoplastic gene expression regulation nitriles protein kinase inhibitors quinolines

ChemMine ToolsTool Content

http://chemmine.ucr.edu

Other Molecules > Small Molecules

ChemMine Tools is an online service for analyzing and clustering small molecules. A suite of cheminformatics and data mining tools for data visualization, structure comparison, similarity searching, compound clustering and prediction of chemical properties are available.

NAR Web Server Issue 2011
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tagsalgorithms cluster analysis data mining drug discovery genomics pharmaceutical preparations small molecule libraries structure-activity relationship

COSMICDatabase Content

http://www.sanger.ac.uk/genetics/CGP/cosmic/

DNA > Databases
Human Genome > Databases

COSMIC curates comprehensive information on somatic mutations in human cancer. Release v48 (July 2010) describes over 136,000 coding mutations in almost 542,000 tumour samples; of the 18,490 genes documented, 4803 (26%) have one or more mutations. Full scientific literature curations are available on 83 major cancer genes and 49 fusion gene pairs. Biomart allows more automated data mining and integration with other biological databases. Annotation of genomic features has become a significant focus. COSMIC integrates many diverse types of mutation information and is making much closer links with Ensembl and other data resources.

NAR Database Issue 2010NAR Database Issue 2011
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tagscomputational biology data mining genetic databases human genome humans mutation neoplasms nucleic acid databases protein databases search engine tumor cell line

CytoscapeTool Content

http://www.cytoscape.org/

Protein > Interactions, Pathways, Enzymes

Cytoscape is a visualization platform for use with molecular interaction networks. Interaction data can be integrated with other state data such as gene expression profiles. The input to Cytoscape includes lists of interaction pairs, and tab/space delimited files containing mRNA expression profiles. The nodes of the interaction networks can be filtered by such variables as GO annotations and number of interactions.

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tagsalgorithms archaeal proteins bacteriophage lambda biological models computational biology data mining gene expression profiling gene regulatory networks genomics halobacterium messenger rna neural networks (computer) phenotype protein interaction mapping proteins proteomics software design stochastic processes

DDPCDatabase Content

http://apps.sanbi.ac.za/ddpc/

DNA > Databases

Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC.

NAR Database Issue 2011
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tagsdata mining genetic databases humans knowledge bases male neoplasm genes prostatic neoplasms

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

EDULISSDatabase Content

http://eduliss.bch.ed.ac.uk/

Other Molecules > Databases

EDULISS (EDinburgh University Ligand Selection System) database stores structural, physicochemical and pharmacophoric properties of small molecules. For each compound a single 3D conformer is stored along with over 1600 calculated descriptor values (molecular properties). A very efficient method for unique compound recognition is demonstrated by making use of small subgroups of the descriptors.

NAR Database Issue 2011
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tagscyclin-dependent kinases data mining enzyme inhibitors factual databases pharmaceutical preparations protein kinase inhibitors pyruvate kinase small molecule libraries

GénieTool Content

http://cbdm.mdc-berlin.de/tools/genie/

Literature > Text Mining and Semantics

Genie evaluates the literature attached to all genes in a genome and to their orthologs for a selected topic. Hundreds of species and millions of genes are supported. Running times range from a few seconds to a minute in most of the cases.

This content is being maintained by fontaine.

NAR Web Server Issue 2011
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tagsalgorithms animal models animals data mining gene expression profiling gene prioritization genes genomics heart humans medline mice orthology relationships text mining zebrafish

HITDatabase Content

http://lifecenter.sgst.cn/hit/

Other Molecules > Databases

A comprehensive and fully curated database for Herb Ingredients' Targets (HIT). Those herbal ingredients with protein target information were carefully curated. The molecular target information involves those proteins being directly/indirectly activated/inhibited, protein binders and enzymes whose substrates or products are those compounds. Those up/down regulated genes are also included under the treatment of individual ingredients. In addition, the experimental condition, observed bioactivity and various references are provided as well for user's reference. The database can be queried via keyword search or similarity search. Crosslinks have been made to TTD, DrugBank, KEGG, PDB, Uniprot, Pfam, NCBI, TCM-ID and other databases.

NAR Database Issue 2011
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tagschinese herbal drugs data mining drug discovery factual databases plant preparations proteins

LocDBDatabase Content

http://www.rostlab.org/services/locDB

Protein > Databases

LocDB is a manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Each database entry contains the experimentally derived localization in Gene Ontology (GO) terminology, the experimental annotation of localization, localization predictions by state-of-the-art methods and, where available, the type of experimental information. LocDB is searchable by keyword, protein name and subcellular compartment, as well as by identifiers from UniProt, Ensembl and TAIR resources.

NAR Database Issue 2011
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tagsarabidopsis proteins data mining humans intracellular space protein databases proteins

MIPSDatabase Content

http://mips.helmholtz-muenchen.de

Protein > Databases

The Munich Information Center for Protein Sequences (MIPS) provides annotated collections of biological data. High-quality reference resources include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis.

NAR Database Issue 2011
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tagsdata mining genetic databases genomics metabolomics micrornas neoplasm genes phenotype plant genome protein databases protein sequence analysis proteomics systems integration