This document provides an overview tutorial of the OBO-Edit ontology editing environment. It describes advantages like standardized annotation systems and intuitive browsing. Disadvantages include less expressivity than OWL. It demonstrates basic functions like browsing, editing, searching, and using reasoners to check for errors and classify terms.

1. OBO-Edit tutorial David Osumi-Sutherland, [email_address] FlyBase / Virtual Fly Brain / OBO-Edit Working Group

23. Demo – OBO-Edit basics

27. Brief discussion of tutorial ontology

28. Browsing

29. Browsing - Trees The ontology tree editor is a good way to browse down the ontology graph, but not all are parents visible in one view Click to expand or contract branch

30. Preferences help save a picture Quick Filtering

32. Browsing - parents The parent editor provides a quick way to check all parental relationships – usually these are not all visible in a single tree view

33. Browsing - graphs A good way to view and browse ancestral relationships, graphs of ancestors via transitive relations answer questions e.g.- what is X? What is X part of? What does X develop from? Note – in version 2.1 beta, requires link pile reasoner to be turned on.

34. Preferences help save a picture

35. Graph viewer setup For an uncluttered view:

36. Browsing – The Text Editor

37. Browsing - Graph Editor

39. Basic Searching - single leg

40. Basic searching – multi-leg Add new leg AND/OR Remove leg nesting (parentheses)

41. All searches can also be filters or renders

42. Editing

44. Global vs local selection modes local mode -selection in other components doesn’t affect selection here global mode - 2 way auto sync with other components

46. Drag and drop term move

47. Drag and drop term move

48. Drag and drop term move

49. Drag and drop term merge

53. Committing Check this box to commit text edits automatically. Note, committing will not change your ontology file

54. Deletion, obsoletion, destruction … deletes the relationship between the selected term and its immediate parent in the ontology tree editor. When the selected term has only one parent, this option switches to: OTE – right click menu: … changes the status of term to obsolete. The OBO file retains the ID for future reference and to prevent re-use. To indicate replacement terms, drag suitable terms to the obsoleted term => Within the context of a single editing session, or a pre-release file, you may wish instead to destroy the term completely (BUT BE CAREFUL!)

55. Parent Editor Delete parent relationship Does what it says. But be careful it adds is_a parents by default. For other relations, switch after adding

56. Managing multiple inheritance

66. Detecting redundancy with the reasoner Redundant relationship Use the Rule Base Reasoner* *Link pile reasoner over-flags redundancy when cross-product terms are present

69. Logical queries The first leg of the search finds all subtypes of sensillum. The second leg finds all parts of the head. The ‘matches all’ radio button ensures the two legs are combined by a boolean AND. OWL-DL: sensillum and part_of some head ** Note – reasoner required ** Find all sensilla that are part of some head:

70. Logical queries How is sensillum classified? What does adPN DL1 develop_from ? Note – this query has no OWL-DL equivalent ** Note – reasoner required **

74. Slides showing features not demonstrated in tutorial

80. Saving helper terms

81. Saving helper terms Check filter terms Make sure “allow dangling parents” is NOT checked Record version of foreign ontology here Avoid importing foreign ID rules

82. Saving helper terms Load helper term filter