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Found 7 result(s)

FlyReactome

a curated knowledgebase of drosophila melanogaster pathways

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<<<!!!<<< This repository is no longer available. This record is out dated >>>!!!>>>- eir fields, maintained by the FlyReactome staff.

Genomic Expression Archive

GEA

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Genomic Expression Archive (GEA) is a public database of functional genomics data such as gene expression, epigenetics and genotyping SNP array. Both microarray- and sequence-based data are accepted in the MAGE-TAB format in compliance with MIAME and MINSEQE guidelines, respectively. GEA issues accession numbers, E-GEAD-n to experiment and A-GEAD-n to array design. Data exchange between GEA and EBI ArrayExpress is planned.

Genomic Observatories MetaDatabase

GEOME

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The Genomic Observatories Meta-Database (GEOME) is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. GEOME helps users with the following goals: ensure the metadata from your biological samples is findable, accessible, interoperable, and reusable; improve the quality of your data and comply with global data standards; and integrate with R, ease publication to NCBI's sequence read archive, and work with an associated LIMS. The initial use case for GEOME came from the Diversity of the Indo-Pacific Network (DIPnet) resource.

mentha

the interactome browser

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mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome". mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global network that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users. Source databases are: MINT, IntAct, DIP, MatrixDB and BioGRID.

WikiPathways

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WikiPathways was established to facilitate the contribution and maintenance of pathway information by the biology community. WikiPathways is an open, collaborative platform dedicated to the curation of biological pathways. WikiPathways thus presents a new model for pathway databases that enhances and complements ongoing efforts, such as KEGG, Reactome and Pathway Commons. Building on the same MediaWiki software that powers Wikipedia, we added a custom graphical pathway editing tool and integrated databases covering major gene, protein, and small-molecule systems. The familiar web-based format of WikiPathways greatly reduces the barrier to participate in pathway curation. More importantly, the open, public approach of WikiPathways allows for broader participation by the entire community, ranging from students to senior experts in each field. This approach also shifts the bulk of peer review, editorial curation, and maintenance to the community.

BioVel

Biodiversity Virtual e-Laboratory

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<<<!!!<<< This repository is no longer available. >>>!!!>>> BioVeL is a virtual e-laboratory that supports research on biodiversity issues using large amounts of data from cross-disciplinary sources. BioVeL supports the development and use of workflows to process data. It offers the possibility to either use already made workflows or create own. BioVeL workflows are stored in MyExperiment - Biovel Group http://www.myexperiment.org/groups/643/content. They are underpinned by a range of analytical and data processing functions (generally provided as Web Services or R scripts) to support common biodiversity analysis tasks. You can find the Web Services catalogued in the BiodiversityCatalogue.

Protein Data Bank in Europe

PDBe

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PDBe is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - we work to collate, maintain and provide access to the global repository of macromolecular structure data. We develop tools, services and resources to make structure-related data more accessible to the biomedical community.