VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms

Abstract

VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health. VectorBase includes genomics and functional genomics data from bed bugs, biting midges, body lice, kissing bugs, mites, mosquitoes, sand flies, ticks, tsetse flies, stable flies, house flies, fruit flies, and a snail intermediate host. Tools include the Search Strategy system and MapVEu, enabling users to interrogate and visualize diverse 'omics and population-level data using a graphical interface (no programming experience required). Users can also analyze their own private data, such as transcriptomic sequences, exploring their results in the context of other publicly-available information in the database. Help Desk: help@vectorbase.org.

Figure 1

Redesigned VectorBase home page. (a) Left-hand panel provides access to all available searches, categorized by datatype. (b) Header on all site pages, including Site Search box and access to My Strategies, Searches, Tools, My Workspace, Data, About, Help (educational materials, arrow) and Contact Us sections. Release date and version adjacent to the logo at left; social media, login, registration, and user profile links at right. (c) Central section provides an overview of resources and tools, including vignettes to help users get started on specific topics of likely interest. (d) News & Tweets section is an expandable tab (collapsed by default), providing access to recent announcements. (e) Links to more detailed step-by-step exercises. (f) Hyperlinked logos to other VEuPathDB components and affiliated sites, and community chat button enabling users to ask questions and share information.

Figure 2.. Population data in MapVEu, a tool for visualizing, analyzing, and downloading geographic data. (a) Select MapVEu from the Tools menu on the home page (arrow). (b) Select Abundance ‘view’ from the dropdown menu below the map search bar (violet arrow). Select sampling location on the map or, enter into the search bar and select from the autocomplete menu (Manatee County used in this example). Date Search set = July 2018 to July 2019. Open/collapse blue arrowhead in legend panel (green box) to set: Collection Protocol = CDC light trap & Attractant = carbon dioxide, in the same panel select Species & Optimize Colors options. A point was selected (indicated in color, center of the map), to explore it in more detail. The icon at the left (orange arrow) defines graph type (bars in this example); ‘EpiWeekly’ is set as temporal resolution. Left panel size can be adjusted (red box). The orange box indicates other ‘view’ specific data visualizations, metadata details, raw data download, and so on. Login to VectorBase and follow this link to recreate the image shown: https://tinyurl.com/InsectGx2021VectorBaseFig2.

Figure 3.

Search strategies as in silico experiments. (a) Site Search, a box that can be accessed from the header, returns site-wide hits, in the results page filters can be applied. Search strategies (for Genes, Organisms, Pathways, etc.) can be run from the Searches pull-down menu or the Search for . . . panel at the left. (b) Search filter can help to locate searches of interest, for example, identifying ‘text’ searches of Genes or Compounds. (c) Search results constitute one Step in a Search Strategy, which can be combined with other searches (+ Add a step; green arrow) using Boolean operators (e.g. union, intersection, subtraction). Results may be downloaded (black arrow), and searches edited, saved, shared, or published (icons at right; blue arrow). To retrieve this sample search for A. gambiae proteases expressed in the midgut with a specific promotor region DNA motif, see: https://vectorbase.org/vectorbase/app/workspace/strategies/import/bc4d101022805435. Publicly shared strategies are available from the menu at the top (orange arrow; https://vectorbase.org/vectorbase/app/workspace/strategies/public).