EuPathDB: the eukaryotic pathogen genomics database resource

Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

EuPathDB's extensive record system documents integrated data and analysis results for entities such as Genes, Genomic Sequences, SNPs, Isolates, Compounds and Metabolic Pathways. Record pages have a new streamlined look, contain improved navigation tools, and are reorganized to reflect EDAM-based categories ( Figure 4) . To view the gene page for PF3D7 0905700, autophagy-related protein 3, putative that is highlighted in Figure 4 , go to http://plasmodb.org/plasmo/app/record/ gene/PF3D7 0905700. For example, in gene record pages, gene IDs and product descriptions are prominently displayed in the upper left corner of the page with other pertinent gene information and links directly below ( Figure 4A ). Also at the top of the page are 'Shortcuts' ( Figure 4B ) which serve two functions--clicking on the Shortcut's magnifying glass icon offers a larger view of the data, while clicking on the image (or its title) navigates to the data within the gene page. 'View in Genome Browser' links (e.g. above and below the Gene Models image in Figure 4D ) accompany data that are also available for dynamic viewing in the Genome Browser. These links open the Genome Browser (GBrowse) (32) with the pertinent data track added to the user's current browser session. The collapsible and interactive 'Contents' section reflects the new EDAM-based categories and features a search function for quickly locating a category ( Figure 4C ). The contents section remains stationary and visible while scrolling the gene page data ( Figure 4D) . A section indicator (small blue circle) appears to the left of the category name of the data currently in view. Clicking a category name directs the page to that data section. The check boxes to the right of the category names can be used to customize the data display. Data from categories with empty check boxes will be hidden from view.