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A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it.

Abstract : The EDAM Browser is a client-side web-based visualization javascript widget for the navigation of the EDAM ontology (Ison et al. 2013). EDAM is a structured and controlled vocabulary describing bioinformatics and computational biology concepts. It is used to annotate resource descriptions (tools, web services) for discovery (Ison et al. 2015) and integration in platforms such as galaxy (Afgan et al. 2016). The EDAM Browser provides users a simple and performant interface to explore EDAM when annotating or searching for bioinformatics resources. User interface and functionalities The user interface (see Fig. 1) is divided in two main panels, a tree representation of the ontology on the left, and a properties card on the right. The tree on the left represents the different parts of the ontology (formats, data, operations and topics). By expanding or closing the nodes, users explore the hierarchy of the EDAM concepts. The selected concept is displayed in bold, and all the path(s) leading from the root to it are highlighted. The properties card panel on the right displays the main properties of the concept, such as its definition, comments, synonyms, and its non-hierarchical relations to other concepts (e.g. an operation has inputs, outputs, and belongs to a given topic). It also includes counts and links to entries in various databases that use this term, such as bio.tools, BioSphere (Brancotte et al. 2017), BioWeb and TeSS. The user may directly suggest a modification on a concept by clicking on the "edit" icons at the top-right corner of this panel ; creating a new concept is also possible thanks to the "add a child" button. Both lead the user to a form that directly formats suggestions as github issues ready to be submitted by the user (see Fig. 2). Additional components of the interface include a full-text search box to search for concepts on their names, synonyms or descriptions; a navigation toolbar to toggle the display of specific parts of the ontology only, or load locally modified versions of the ontology; and a history stack of the concepts that have been seen previously to the one currently selected, below the properties card panel.
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Submitted on : Thursday, June 4, 2020 - 11:35:23 AM
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Bryan Brancotte, Christophe Blanchet, Hervé Ménager. A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it.. Journal of Open Source Software, Open Journals, 2018, 3 (27), pp.698. ⟨10.21105/joss.00698⟩. ⟨pasteur-02770161⟩

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