Aurrecoechea, C. et al. (2017) EuPathDB: the eukaryotic pathogen genomics database resource. Nucleic Acids Research, 45(D1), D581-D591. (doi: 10.1093/nar/gkw1105) (PMID:27903906) (PMCID:PMC5210576)
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132177.pdf - Published Version Available under License Creative Commons Attribution Non-commercial. 7MB |
Abstract
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.
| Item Type: | Articles |
|---|---|
| Keywords: | EuPathDB, database, parasitology, functional genomics. |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Crouch, Dr Kathryn |
| Authors: | Aurrecoechea, C., Barreto, A., Basenko, E. Y., Brestelli, J., Brunk, B. P., Cade, S., Crouch, K., Doherty, R., Falke, D., Fischer, S., Gajria, B., Harb, O. S., Heiges, M., Hertz-Fowler, C., Hu, S., Iodice, J., Kissinger, J. C., Lawrence, C., Li, W., Pinney, D. F., Pulman, J. A., Roos, D. S., Shanmugasundram, A., Silva-Franco, F., Steinbiss, S., Stoeckert Jr, C. J., Spruill, D., Wang, H., Warrenfeltz, S., and Zheng, J. |
| Subjects: | Q Science > QH Natural history > QH301 Biology Q Science > QH Natural history > QH426 Genetics |
| College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity |
| Journal Name: | Nucleic Acids Research |
| Journal Abbr.: | NAR |
| Publisher: | Oxford University Press |
| ISSN: | 1362-4962 |
| ISSN (Online): | 1362-4962 |
| Published Online: | 29 November 2016 |
| Copyright Holders: | Copyright © 2016 The Authors |
| First Published: | First published in Nucleic Acids Research 2016 |
| Publisher Policy: | Reproduced under a Creative Commons License |
| Related URLs: |
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