Links tagged with 'data mining'

Found 19 links

Displaying 15 links

BioExtractTool Content

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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.

BSQATool Content

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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.

CancerResourceDatabase Content

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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.

ChemMine ToolsTool Content

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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.

COSMICDatabase Content

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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.

DDPCDatabase Content

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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.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
DDPC: Dragon Database of Genes associated with Prostate Cancer20114

DECATool Content

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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.

EDULISSDatabase Content

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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.

GénieTool Content

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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.

HITDatabase Content

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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.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
HIT: linking herbal active ingredients to targets20113

LocDBDatabase Content

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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.

MIPSDatabase Content

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Munich Information Centre for Protein Sequences projects include: fungal genome analysis, plant genome bioinformatics, structural genomics, proteomics and genome annotation. Projects and databases include: CYGD, MNCDB, NGFN, MPPI, SIMAP, QUIPOS, MATDB, MOsDB, SPUTNIK, and PEDANT.

MIPSDatabase Content

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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.

MitoGenesisDBDatabase Content

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MitoGenesisDB focuses on the dynamic of mitochondrial protein formation through global mRNA analyses. Three main parameters confer a global view of mitochondrial biogenesis: (i) time-course of mRNA production in highly synchronized yeast cell cultures, (ii) microarray analyses of mRNA localization that define translation sites and (iii) mRNA transcription rate and stability which characterize genes that are more dependent on post-transcriptional regulation processes. MitoGenesisDB integrates and establishes cross-comparisons between these data. Several model organisms can be analyzed via orthologous relationships between interspecies genes.

MutalyzerTool Content

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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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