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Links tagged with 'systems integration'

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Found 113 links

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The BRENDA Tissue Ontology (BTO)Database Content

http://www.BTO.brenda-enzymes.org [open in a new window]

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Other Molecules > Databases

BTO, the BRENDA Tissue Ontology is a structured encyclopedia of tissue terms. BTO contains different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). Most of the terms are endowed with comments on their derivation or definitions. Four different types of relationships between the terms are implemented. A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues.

This content is being maintained by Dietmar Schomburg.

links directory index: 5
TitlePublication YearGoogle Scholar Citation Count
The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources20115
NAR Database Issue 2011
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tagscell line cells controlled vocabulary dictionaries as topic enzymes factual databases systems integration

The GRID - General Repository for Interaction DatasetsDatabase Content

http://www.thebiogrid.org/ [open in a new window]

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Model Organisms > Fly
Model Organisms > Yeast
Protein > Networks & Interactions, Pathways and Enzymes

Database of genetic and physical interactions; contains interaction data from several genome/proteome wide-studies, the MIPS database, and BIND; provides a powerful visualization system for looking at interactions graphically.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
The GRID: the General Repository for Interaction Datasets20032
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tagsanimals caenorhabditis elegans computer graphics database management systems drosophila melanogaster fungal dna fungal genes genes genetic databases genetic models humans internet multiprotein complexes nucleic acid databases protein databases protein interaction mapping saccharomyces cerevisiae saccharomyces cerevisiae proteins software systems integration user-computer interface

TogoWSTool Content

http://togows.dbcls.jp/ [open in a new window]

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Computer Related > Databases
Computer Related > Web Services
Computer Related > Workflows

TogoWS service provides solutions to web service incompatibilities such as interface and data type incompatibilities. TogoWS REST API and TogoWS SOAP API resolve these issues.

links directory index: 9
TitlePublication YearGoogle Scholar Citation Count
TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services20109
NAR Web Server Issue 2010
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tagscomputational biology factual databases systems integration

Universal Protein Resource (UniProt)Database Content

http://www.uniprot.org [open in a new window]

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Protein > Databases

Universal Protein Resource (UniProt) maintains a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database.

links directory index: 1408
TitlePublication YearGoogle Scholar Citation Count
Reorganizing the protein space at the Universal Protein Resource (UniProt)201213
Ongoing and future developments at the Universal Protein Resource2011154
The Universal Protein Resource (UniProt) in 2010201053
The Universal Protein Resource (UniProt)20071170
Update on genome completion and annotations: Protein Information Resource200418
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms amino acid sequence animals computational biology europe fungal genome human genome humans nucleic acid databases protein databases protein isoforms protein sequence analysis proteins proteome proteomics systems integration viral genome

Virtual RibosomeTool Content

http://www.cbs.dtu.dk/services/VirtualRibosome/ [open in a new window]

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DNA > DNA and Genomic Analysis
DNA > Gene Prediction

The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The tool can also highlight the intron/exon structure of genes using information found in the feature table of GenBank flatfiles in the final translation results.

links directory index: 22
TitlePublication YearGoogle Scholar Citation Count
Virtual Ribosome--a comprehensive DNA translation tool with support for integration of sequence feature annotation200622
NAR Web Server Issue 2006
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tagsanimals dna sequence analysis exons initiator codon introns open reading frames protein biosynthesis ribosomes systems integration terminator codon

VisANTTool Content

http://visant.bu.edu/ [open in a new window]

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Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Networks & Interactions, Pathways and Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

links directory index: 372
TitlePublication YearGoogle Scholar Citation Count
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology200947
Towards zoomable multidimensional maps of the cell200749
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction200754
VisANT: data-integrating visual framework for biological networks and modules2005107
VisANT: an online visualization and analysis tool for biological interaction data2004115
NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

XML Central of DDBJTool Content

http://www.xml.nig.ac.jp/index.html [open in a new window]

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Computer Related > Web Services
Education > Directories and Portals

XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.

links directory index: 41
TitlePublication YearGoogle Scholar Citation Count
Web API for biology with a workflow navigation system200912
Biological SOAP servers and web services provided by the public sequence data bank200329
NAR Web Server Issue 2003
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tagsbiology nucleic acid databases systems integration

YPADatabase Content

http://ypa.ee.ncku.edu.tw/ [open in a new window]

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DNA > Databases
Model Organisms > Databases

The Yeast Promoter Atlas (YPA) database collects promoter features in Saccharomyces cerevisiae. YPA integrates nine kinds of promoter features including promoter sequences, genes' transcription boundaries-transcription start sites (TSSs), five prime untranslated regions (5'-UTRs) and three prime untranslated regions (3'UTRs), TATA boxes, transcription factor binding sites (TFBSs), nucleosome occupancy, DNA bendability, transcription factor (TF) binding, TF knockout expression and TF-TF physical interaction. In YPA, various promoter features can be accessed in a centralized and organized platform.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
YPA: an integrated repository of promoter features in Saccharomyces cerevisiae20113
NAR Database Issue 2011
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tagsbinding sites genetic promoter regions nucleic acid databases saccharomyces cerevisiae systems integration transcription factors

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