EuPathDB: the eukaryotic pathogen genomics database resource

The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful...

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Bibliographic Details
Published in:	Nucleic acids research Vol. 45; no. D1; pp. D581 - D591
Main Authors:	Aurrecoechea, Cristina, Barreto, Ana, Basenko, Evelina Y, Brestelli, John, Brunk, Brian P, Cade, Shon, Crouch, Kathryn, Doherty, Ryan, Falke, Dave, Fischer, Steve, Gajria, Bindu, Harb, Omar S, Heiges, Mark, Hertz-Fowler, Christiane, Hu, Sufen, Iodice, John, Kissinger, Jessica C, Lawrence, Cris, Li, Wei, Pinney, Deborah F, Pulman, Jane A, Roos, David S, Shanmugasundram, Achchuthan, Silva-Franco, Fatima, Steinbiss, Sascha, Stoeckert, Jr, Christian J, Spruill, Drew, Wang, Haiming, Warrenfeltz, Susanne, Zheng, Jie
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 04-01-2017
Subjects:	Computational Biology - methods Database Issue Databases, Genetic DNA Copy Number Variations Eukaryota Gene Expression Profiling Genomics - methods Host-Pathogen Interactions - genetics Metagenome Metagenomics - methods Proteomics Software Web Browser
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Summary:	The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host-pathogen interactions.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0305-1048 1362-4962
DOI:	10.1093/nar/gkw1105