Protege Feature Requirements

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This page is for editors to list issues and hurdles they experience using Protege in their editing pipeline.

Specs doc is here: https://docs.google.com/document/d/17tph3jwrDGEaa7DyYPOK8HCi2dCDdJxi3VrTWNQpbqc/edit

Alpha version of OBO annotation plugin is here: https://github.com/simonjupp/protege-obo-plugins

{DOS planning add doc here on editing GO in Protege - check back in April}

Wish List

  1. More easily interpreted Diffs. The Owl diffs are very difficult to interpret. This might not be a Protege issue per se, but does have an impact on the workflow. Some of us look at a diff every time we edit.
  2. Good search functionality. The searching features in OBO-Edit that allow an user to pick which fields to search etc are quite nice and are used all the time. The scrollable sub-window that is saved is very helpful when working on an entire set of related term.
  3. Good display of search results. Show all results that match a search string. Is this already possible in some plugin? For example, everything that ends with 'morphogenesis'.
  4. Graphical drag and drop editing. Not essential, but really nice. These days I have been using the parent editor more and more, but when moving terms around the tree editor is quite handy. This is particularly true since you can have two windows open, highlight your term in one and then search the ontology in the other window to find an appropriate parent or child. It is impossible to know the entire ontology and having the tree-view is quite helpful when searching for an existing term. Although much of the additional parent additions will go away with better axiomatization.
  5. Better visualization. The visualization in the tree editor and and the graphical editor allow users to visualize the term and all of its relationships. Although this can get quite complicated, it is very useful. Being able to toggle which relationships are shown/hidden would be great.
  6. Easier term addition. All of the required fields are easily viewed and edited in a single sub-window in OBO-Edit; term name, def, dbxref, synonyms, comments. QC checks are in place to be sure all of the required fields are in place before a term is accepted.
  7. When adding a term in Protege, automatically add the 'created_by:' and 'creation_date:' fields to the term.
  8. We need to enable Protege to look up the latest ID in the ID range that is being used in the ontology and use the next available ID. Right now editors will need to have separate ID subranges for Protege and OBO-edit.