SWUG:OBO-Edit Report 2008-04

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Documentation and Installer

  • Updated a lot of the userguide, including adding new pages for some new components.
  • Included a sample ontology in the distribution and added it to the default history so new users can load it easily.
  • Fixed some problems with installer (wasn't creating desktop icon; wasn't applying user's chosen memory setting).
  • Installers will now keep separate install histories for OE1, OE2, and Phenote, to avoid misleadingly prompting you to install any of them on top of each other. (In fact, it will now explicitly warn you if you try to do that.)

I/O and command-line options

  • Associated scripts (e.g. obomerge) now support both OBO_1_0 and OBO_1_2 formats (with 1_2 the default).
  • Can specify on the command line an obo file to load.
  • Handle dangling references correctly in both input and output.
  • OBO_1_2 writer now outputs dates in ISO 8601 format. Reader can handle both old and new date formats.
  • converted map2slim to java


  • Fixed buggy delete/destroy behavior. Clarified difference between "delete term" and "delete relationship". Pop up appropriate warnings if a term is about to be made obsolete.
  • Fixed sub-selection problem where you couldn't change the sub-selection without de-selecting most of the other selected terms.
  • Made sub-selection behavior more consistent: the sub-selection is now the term that you most recently selected (rather than the one that happened to be alphabetically first, or a random one).
  • Searches were sensitive to whitespace at the end of the search string, so if you searched for "term ", rather than "term", it wouldn't find anything. Now whitespace is trimmed from the beginning and end of the search string.
  • Title of search results window is configurable (can include search string and/or number of matches found) and settings persist.
  • Width of search results columns can now be adjusted by user.
  • Save words that user adds to dictionary.
  • Fixed problem that sometimes made it impossible to save ontologies that generated warnings during the checks that are performed before saving. (The issue was that the warning generator created vestigial windows that grabbed the focus.)
  • Improved support for ontologies with dangling references (which were causing all sorts of problems). "Allow dangling refs" is now true by default, so you can load ontologies that have dangling refs. (Dangling refs result in a warning message when you load and when you save.)
  • Added GUI for selecting a reasoner.
  • Added support for 'regulates' relationships. Removed default global filter "Select links where Type that have a 'Is Transitive'" in order to let regulates relationships show up. (This global filter can be re-added by the user if desired.)
  • Added CheckMemoryThread that runs in the background and warns user if the available memory is >95% used up.
  • Made file browser for load/save open at last used directory (rather than always at your home directory).
  • Fixed Windows-only problem where built-in relationship icons wouldn't show up.
  • Now autosave will only save if there are unsaved edits, and it won't grab the focus and pop to the front.

GUI look and feel

  • Improved the look of various components in terms of colors, styles, and layout.
  • Pop-up help windows that appear when you click the ? icon on a panel titlebar are now real windows, which can be dragged around, resized, or destroyed.
  • Main OE window title now includes the text "(REASONER ON)" if the reasoner is turned on.
  • Changed some confusing component names as follows:

Ontology Editor Panel -> Ontology Tree Editor
Graph Editor -> (Graph Editor) (unchanged)
Graph DAG View -> Graph Viewer
DAG Viewer -> Tree Viewer
Graphviz Viewer -> (Graphviz Viewer) (unchanged)

  • Significantly rearranged configuration options and tabs in the Configuration Manager. The new layout makes the user config directory much more obvious, and is more logical in general.
  • Made TextIcons (black & white icons used in the Ontology Tree Editor for unknown relationships) readable. Font is now based on user's preferred font. (Note: not yet fixed in Graph Editor.)
  • Ontology Tree Editor now uses your preferred font for the text in the tree. (Note: not yet fixed in Graph Editor and other components.)

Software / architecture