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InnateDB: facilitating systems-level analyses of the mammalian innate immune response.

Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought of in terms of simple linear pathways. InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune response. InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with centralized annotation on the broader human and mouse interactomes. To date, more than 3500 innate immunity-relevant interactions have been contextually annotated through the review of 1000 plus publications. Integrated into InnateDB are novel bioinformatics resources, including network visualization software, pathway analysis, orthologous interaction network construction and the ability to overlay user-supplied gene expression data in an intuitively displayed molecular interaction network and pathway context, which will enable biologists without a computational background to explore their data in a more systems-oriented manner.

Pubmed ID: 18766178 RIS Download

Mesh terms: Animals | Computational Biology | Databases, Factual | Humans | Immunity, Innate | Internet | Signal Transduction | Software | Systems Biology

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This is a list of tools and resources that we have found mentioned in this publication.


Integrating Network Objects with Hierarchies

INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form. The system provides pathway information as a composite of biological events, since functional knowledge is usually described as a set of fragmented processes. Each event is annotated with entries of a event ontology, which also has links to GO.

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Ensembl

A collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. The goal of Ensembl is to automatically annotate the genome, integrate this annotation with other available biological data and make the data publicly available via the web. The range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl allows users to: upload and analyze data and save it to an Ensembl account; search for a DNA or protein sequence using BLAST or BLAT; fetch desired data from the public database, using the Perl API; download the databases via FTP in FASTA, MySQL and other formats; and mine Ensembl with BioMart and export sequences or tables in text, HTML, or Excel format. The DNA sequences and assemblies used in the Ensembl genebuild are provided by various projects around the world. Ensembl has entered into an agreement with UCSC and NCBI with regard to sequence identifiers in order to improve consistency between the data provided by different genome browsers. The site also links to the Ensembl blog with updates on new species and sequences as they are added to the database.

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Pathway Interaction Database

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 27, 2016. Curated database of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. All interactions are assembled into pathways, and can be accessed by performing searches for biomolecules, or processes, or by viewing predefined pathways. This was a collaborative project between the NCI and Nature Publishing Group (NPG) from 2006 until September 22nd, 2012, and is no longer being updated. PID is aimed at the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. The database focuses on the biomolecular interactions that are known or believed to take place in human cells. It can be browsed as an online encyclopedia, used to run computational analyses, or employed in ways that combine these two approaches. In addition to PID''''s predefined pathways, search results are displayed as dynamically constructed interaction networks. These features of PID render it a useful tool for both biologists and bioinformaticians. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is supplemented by a concise editorial section that includes specially written synopses of recent important research articles in areas related to cancer research, and specially commissioned Bioinformatics Primers that provide practical advice on how to make the most of other relevant online resources. The database and editorial content are updated monthly, and users can opt to receive a monthly email alert to stay informed about new content. Note: as of September 23, 2012 the PID is no longer being actively curated. NCI will maintain the PID website and data for twelve months beyond September 2012 to allow interested parties to obtain the previously curated data before the site is retired in September 2013.

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