Fungidb: an Integrated Bioinformatic Resource for Fungi and Oomycetes
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Journal of Fungi Tutorial FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes Evelina Y. Basenko 1,*,† ID , Jane A. Pulman 1,†, Achchuthan Shanmugasundram 1,†, Omar S. Harb 2, Kathryn Crouch 3 ID , David Starns 1 ID , Susanne Warrenfeltz 4, Cristina Aurrecoechea 4, Christian J. Stoeckert Jr. 5, Jessica C. Kissinger 4, David S. Roos 2 and Christiane Hertz-Fowler 1,* ID 1 Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; [email protected] (J.A.P.); [email protected] (A.S.); [email protected] (D.S.) 2 Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] (O.S.H.); [email protected] (D.S.R.) 3 Wellcome Trust Centre for Molecular Parasitology, Glasgow G12 8TA, UK; [email protected] 4 Center for Tropical and Emerging Global Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA; [email protected] (S.W.); [email protected] (C.A.); [email protected] (J.C.K.) 5 Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] * Correspondence: [email protected] (E.Y.B.); [email protected] (C.H.-F.) † These authors contributed equally to this work. Received: 31 January 2018; Accepted: 15 March 2018; Published: 20 March 2018 Abstract: FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD), The Broad Institute, Joint Genome Institute (JGI), Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.). This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records. Keywords: fungi; pathogen; bioinformatics; omics; genomics; transcriptomics; proteomics; sequence analysis; RNA-Seq; Galaxy 1. Introduction The Eukaryotic Pathogen Bioinformatics Resource Center (eupathdb.org) comprises a family of bioinformatics resources that include an integrated functional genomics database for fungi and oomycetes—FungiDB [1,2]. FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis. It provides an easy-to-use, interactive interface to explore genomes, annotation, functional data (e.g., transcriptomics, proteomics, phenomic data for selected species), metabolic pathways, and results from numerous genome-wide analyses (i.e., InterPro scan, signal peptide and transmembrane domain predictions, orthology, etc.). FungiDB contains J. Fungi 2018, 4, 39; doi:10.3390/jof4010039 www.mdpi.com/journal/jof J. Fungi 2018, 4, 39 2 of 28 an expanding number of genomes from various taxa including, but not limited to, plant, animal, and human pathogens. FungiDB contains nearly 100 genomes obtained from GenBank [3], Ensembl [4], Joint GenomeJ. Fungi Institute 2018, 4, 39 (JGI) [5], Aspergillus Genome Database (AspGD) [6], Candida Genome2 of 28 Database (CGD) [7], Saccharomyces Genome Database (SGD) [8], PomBase [9], and The Broad Institute [10]. FungiDB continuespathogens. toFungiDB acquire contains new genomes nearly 100 and genomes datasets obtained from from data GenBank repositories, [3], Ensembl other [4] fungal, Joint databases, Genome Institute (JGI) [5], Aspergillus Genome Database (AspGD) [6], Candida Genome Database and individual(CGD) providers. [7], Saccharomyces The loadedGenome genomesDatabase (SGD) and related[8], PomBase datasets [9], and can The be Broad investigated Institute [10] via. a number of search strategiesFungiDB continues and FungiDB to acquire website-embedded new genomes and tools.datasets Presented from data hererepositories, is an overview other fungal of FungiDB resourcesdatab andases, several and individual tutorials providers. on how The to loaded mine genomes FungiDB and bioinformatic related datasets can resources be investigated by creating in silico experiments.via a number of search strategies and FungiDB website-embedded tools. Presented here is an overview of FungiDB resources and several tutorials on how to mine FungiDB bioinformatic resources by creating in silico experiments. 2. Overview of the FungiDB Home Page and its Features The home2. Overview page of of the FungiDB FungiDB canHome be Page divided and its intoFeatures four sections: the header (Figure1a), the grey menu bar (FigureThe 1homeb), the page side of FungiDB bar on thecan leftbe divided (Figure into1c), four and sections: the main the header central (Figure section 1a), withthe grey three large menu bar (Figure 1b), the side bar on the left (Figure 1c), and the main central section with three panels: Search for Genes (left), Search for Other Data Types (middle), and Tools (right) (Figure1d). large panels: Search for Genes (left), Search for Other Data Types (middle), and Tools (right) (Figure 1d). Figure 1. FungiDBFigure 1. FungiDB Home Home page page and and its features.its features. The The home page page comprise comprisess (a) the ( aheader) the headersection with section with Gene ID search highlighted in purple, (b) the main menu in grey, (c) the side bar with links and Gene ID b c searchvarious highlighted information insections, purple; and ( (d))the the mainmain component menu in grey;offering ( )Search the sidefor Genes bar, withSearch linksfor Other and various informationData sections; Types, and and Tools (d )sections. the main Find component a search box fr offeringom SearchSearch for Genes for component Genes, Search is highlighted for Other in Data Types, and Tools sections.purple. Find a search box from Search for Genes component is highlighted in purple. The header section offers quick access to the Gene ID and Gene Text search and a list of useful The headerlinks (Figure section 1a). To offers quickly quick navigate access to a specific to the geneGene record ID pageand, Genea user can Text enter search a singleand Gene a list ID of useful links (Figure(e.g.1,a). NCU06306) To quickly into navigatethe Gene ID to search a specific box at genethe top record of the main page, page auser (Figure can 1a). enter Alternatively, a single Gene ID (e.g., NCU06306)searching intofor chromatin the Gene in the ID Genesearch Text Search box at box the adjacent top of to thethe Gene main ID pagesearch (Figurebox will return1a).Alternatively, a list of genes from fungal and oomycete organisms that have matches to the searched term in any of the searchingfollowing for chromatin gene fields:in the enzymeGene commission Text Search (EC)box description, adjacent Gene to theID, Gene notes, ID search gene product, box will return a list of genesgene fromname, fungalgene ontology and oomycete (GO) terms organismsand definitions, that metabolic have matches pathway tonames the and searched descriptions, term in any of the followingphenotype, gene fields:protein domain enzyme names commission and descriptions, (EC) description,PubMed, and user Gene comments. ID, Gene The notes,links located gene product, gene name,directly gene under ontology the search (GO) boxes terms provide and quick definitions, access to information metabolic about pathway the FungiDB names project, and login descriptions, and registration, social media links, YouTube tutorial channel, and the Contact Us email form. phenotype,Support protein inquiries domain can namesalso be sent and to descriptions,[email protected] PubMed,(Figure 1a). and user comments. The links located directly underThe the grey search menu bar boxes is preserved provide across quick almost access all FungiDB to information pages and provides about easy the navigation FungiDB project, login andto registration, all database sections social mediawhen a user links, navigates YouTube away tutorial from the channel, main page and (Figure the 1b).Contact The side Us baremail form. Support inquiriessection (Figure can also1c) consists be sent of the to [email protected] Summary, News (Figureand Tweets1,a). Community Resources, Education and Tutorials, and About FungiDB sections. The grey menu bar is preserved across almost all FungiDB pages and provides easy navigation to all database sections when a user navigates away from the main page (Figure1b). The side bar section (Figure1c) consists of the Data Summary, News and Tweets, Community Resources, Education and Tutorials, and About FungiDB sections. J. Fungi 2018, 4, 39 3 of 28 The central section is the largest section of the home page and consists of three panels: Search for Genes, Search for Other Data Types, and Tools panels (Figure1d). The Search for Genes panel contains links to searches organized into seventeen intuitive categories allowing the user to quickly navigate toJ. Fungi a desired 2018, 4, 39 search. Each search initiated from this panel will return lists of genes3 of