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      VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

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      Nucleic Acids Research
      Oxford University Press

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          Abstract

          The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

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          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            Basic local alignment search tool.

            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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              The Protein Data Bank.

              The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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                Author and article information

                Contributors
                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                07 January 2022
                28 October 2021
                28 October 2021
                : 50
                : D1
                : D898-D911
                Affiliations
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Genetics, School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                Wellcome Centre for Integrative Parasitology, University of Glasgow , Glasgow G12 8TA, UK
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Department of Pathology, School of Veterinary Medicine, University of Pennsylvania , Philadelphia, PA, USA
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Genetics, School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Genetics, School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                Department of Life Sciences , Imperial College London, South Kensington Campus, London SW7 2AZ, UK
                Wellcome Centre for Integrative Parasitology, University of Glasgow , Glasgow G12 8TA, UK
                Center for Research Computing, University of Notre Dame , Notre Dame, IN 46556, USA
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Center for Research Computing, University of Notre Dame , Notre Dame, IN 46556, USA
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Genetics, School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                Center for Research Computing, University of Notre Dame , Notre Dame, IN 46556, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame , Notre Dame, IN 46556, USA
                Departamento de Ciencias Biológicas y Departamento de Ciencias Básicas Médicas, Universidad Icesi , Calle 18 No. 122-135, Cali, Colombia
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Center for Research Computing, University of Notre Dame , Notre Dame, IN 46556, USA
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Genetics, School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Life Sciences , Imperial College London, South Kensington Campus, London SW7 2AZ, UK
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Department of Genetics, University of Georgia , Athens, GA 30602, USA
                Institute of Bioinformatics, University of Georgia , Athens, GA 30602, USA
                Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame , Notre Dame, IN 46556, USA
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Department of Life Sciences , Imperial College London, South Kensington Campus, London SW7 2AZ, UK
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Center for Research Computing, University of Notre Dame , Notre Dame, IN 46556, USA
                European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Life Sciences , Imperial College London, South Kensington Campus, London SW7 2AZ, UK
                European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame , Notre Dame, IN 46556, USA
                Center for Research Computing, University of Notre Dame , Notre Dame, IN 46556, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame , Notre Dame, IN 46556, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Genetics, School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Center for Tropical & Emerging Global Diseases, University of Georgia , Athens, GA 30602, USA
                Center for Research Computing, University of Notre Dame , Notre Dame, IN 46556, USA
                Institute of Systems, Molecular & Integrative Biology, University of Liverpool , Liverpool L69 7ZB, UK
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Biology, University of Pennsylvania , Philadelphia, PA 19104, USA
                Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Department of Genetics, School of Medicine, University of Pennsylvania , Philadelphia, PA 19104, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 215 746 7019; Fax: +1 215 573 3111; Email: oharb@ 123456upenn.edu
                Author information
                https://orcid.org/0000-0002-5489-6557
                https://orcid.org/0000-0001-9310-4762
                https://orcid.org/0000-0002-3897-7955
                https://orcid.org/0000-0001-6118-9327
                https://orcid.org/0000-0002-9789-8878
                Article
                gkab929
                10.1093/nar/gkab929
                8728164
                34718728
                2db013a0-96f8-4c21-9cf8-e8c2f899e054
                © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License ( https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                : 04 October 2021
                : 21 September 2021
                : 15 September 2020
                Page count
                Pages: 14
                Funding
                Funded by: National Institute of Allergy and Infectious Diseases, DOI 10.13039/100000060;
                Funded by: National Institutes of Health, DOI 10.13039/100000002;
                Funded by: Department of Health and Human Services, DOI 10.13039/100000016;
                Award ID: 75N93019C00077
                Funded by: Wellcome Trust, DOI 10.13039/100010269;
                Award ID: 218288/Z/19/Z
                Award ID: 212929/Z/18/Z
                Funded by: University of Pennsylvania, DOI 10.13039/100006920;
                Categories
                AcademicSubjects/SCI00010
                Database Issue

                Genetics
                Genetics

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