OLSVisMore info
OLSVis ("oh-el-es vis") is an interactive visualisation of EBI's Ontology Lookup Service (OLS).
It is an application of WordVis' visualiser (see also WordVis' About page).

OLSVis was developed at NTNU university in Norway in 2011, by Steven Vercruysse [1,2] ("vər krəj sə").
Feature List
What is shown
  • OLSVis visualises the contents of the publicly available OLS-data. OLS is a combination of several biomedical ontologies. These are 'official' terminology lists (often hierarchies) that are used to unambiguously describe and share information on various biological topics.
  • The OLS database is updated weekly. OLSVis detects this usually within a few hours and updates automatically as well. Current version = ....

    [Update]: OLSVis stopped receiving updates since EBI profoundly changed how new OLS-data is published.
    [Update2]: Somewhere on/after April 2016, OLSVis will probably be able to receive updates again, after some future software development work.

    • Term Searching
  • While typing a term part or identifier (e.g. "mito" or "PO:0009001") in the search box, a selection of best known matches is shown. This includes both preferred terms and synonyms. For each autosuggested term, its ontology (short)name and identifier is shown. The ontology's full name appears when the mouse hovers the term.
    Press arrow-down to show the autosuggestions again after they were hidden.
  • Selecting a specific ontology in the ontology list, confines the autosuggested terms to that ontology.
  • Pressing Enter in the search box, 'expands' the term that is selected in the autosuggestion list. I.e. the term and its environment are shown in the visualiser. Pressing Enter without selecting a term, will take the first term in the autosuggestion list (whether shown or not).
    • Basic Visualisation
  • Clicking on any term in the visualiser expands that term instead. This enables browsing through the graph.
  • A term is expanded in the visualiser as follows: 1) Its parents and ancestor terms are shown up till the 'root' terms of the ontology. By default, all paths to all roots are shown (all based on OLS data). Terms are originally placed into hierarchical levels on top. Relations are shown as labelled arrows, with lengths adjusted for good hierarchy positioning. 2) In addition, all child terms of the expanded term are shown. These are first placed on a half-circle under it.
  • After original placement, the visualiser shows a force-based-layout animation. This makes terms slide to positions that are more optimal, using electrical repulsion forces between the terms, and spring forces on the relation arrows. Also the user can reorganize term positions, by dragging them around.
  • Hovering a term makes its definition pop up. For a relation arrow, its non-abbreviated name pops up. Leaf terms (=without child terms) get a little more orange background. The three most prevalent relations (is a, part of, develops from) get a slightly blue/red/green arrow.
  • In the left pane, information about the last expanded term is shown: 1) On top the term and its identifier (hovering this show the ontology's full name). 2) Then a list of synonyms, annotations and cross-references (all coming from the OLS database). 3) Then the child terms (each clickable to expand) - this makes child terms more clearly visible when they are many.
    • Customized Visualisation
  • Clicking on "+ filters", makes a panel appear where some filters can be set. These narrow down the expanded node's environment (ancestors+children). Turning off "obsolete terms" will also hide them in the autosuggestions panel.
    Any relation type can be excluded; this means that they are omitted when building e.g. the paths-to-roots. Initially the three most common relation types are shown; and the list grows each time the visualiser encounters new relation types. Relations types currently in the visualiser are shown in blue.
  • The graph in the visualiser can be modified in detail via the mouse, keyboard, and toolbar buttons. Individual terms can be dragged around. Dragging the background moves the entire graph. Mouse-scrolling zooms. Any item can be removed, connection lengths changed, and terms anchored. (See toolbar-button tooltips for instructions). Multiple items can be selected and modified together.
    Undo and redo (accessible via the buttons top-left of the visualiser panel, not the browser!) are available.
    Earlier expanded terms (+their environment) can be automatically removed, or all kept in the visualiser (changeable via a toolbar button).
    • More features
  • Click on "roots" (this link appears when selecting a specific ontology) to expand the ontology's root terms: i.e. showing them with their child terms. This enables easy top-down ontology exploration. Note, some ontologies don't have root terms defined in the OLS database.
  • Multiple terms/IDs can be entered in the search box: separate them with a comma (example). Because commas are used to separate terms, a comma in a term must be preceded by a backslash. E.g. type \, for a comma in a term (and \\ for a backslash).
  • A right-click on a term in the visualiser shows its context-menu, i.a. to google the term directly.
  • 1) Any term can be expanded immediately, via an URL like: http://ols.wordvis.com/q=GO:0005739. The part behind "q=" will be automatically typed + launched in the search box.
    2) A specific ontology can be preselected via an URL like: http://ols.wordvis.com/ont=GO. The part behind "ont=" is the ontology's short name (as shown in the ontology selection list).
    3) With both "q" and "ont", an URL like http://ols.wordvis.com/ont=GO&q=mitochondrion, sarcoplasm starts OLSVis with the given term(s) expanded. (Here: both the first result of an autocomplete-search limited to the GO ontology).
    4) As some ontologies use non-standard prefixes in term-identifiers (e.g. NEWT has none, or ZFA can use ZFS), term identifiers after the "q=" can always be prefixed by the ontology's shortname, for disambiguation. E.g. /q=NEWT:1234, /q=ZFA:ZFS:0000019, or /q=GO:GO:0005739.
    • In perspective
    We created OLSVis as a better way to explore ontologies, especially for biocurators. [Biocuration is the translation of information relevant to biology (e.g. from scientific literature), into a structured format (e.g. into a database).]
    OLS is a combined dictionary of over 1 million biological/biomedical terms. With OLSVis, biocurators have a user-friendly tool to find 'official' terminology, and to explore related or more precise concepts.
    Acknowledgements
    S.V. is thankful to :
    Contact
    Please send your constructive comments, feature suggestions, bug reports, etc. to this address:
    .