What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species

Basenko, E. Y. et al. (2024) What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species. Genetics, (doi: 10.1093/genetics/iyae035) (PMID:38529759) (Early Online Publication)

Abstract

FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species.

• Item Type: Articles
• Additional Information: FungiDB project is supported in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, the National Institutes of Health, the Department of Health and Human Services, under contract no. 75N93019C00077, and the Wellcome Trust UK (212929/A/18/Z). No NIAID contract funds were used to fund the planning, preparation, submission, or publication of this manuscript. Funding for the open-access charge was provided through the University of Liverpool Open Access Publisher Agreement and Membership.
• Status: Early Online Publication
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Crouch, Dr Kathryn
• Authors: Basenko, E. Y., Shanmugasundram, A., Böhme, U., Starns, D., Wilkinson, P. A., Davison, H. R., Crouch, K., Maslen, G., Harb, O. S., Amos, B., McDowell, M. A., Kissinger, J. C., Roos, D. S., and Jones, A.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
• Journal Name: Genetics
• Publisher: Oxford University Press
• ISSN: 0016-6731
• ISSN (Online): 1943-2631
• Published Online: 26 March 2024
• Copyright Holders: Copyright © 2024 The Author(s)
• First Published: First published in Genetics 2024
• Publisher Policy: Reproduced under a Creative Commons license