1. OBO-Edit: The Browser The Browser John Day-Richter Berkeley Bioinformatics and Ontology Project / Gene Ontology

2. Before We Do Anything! When in doubt, check the User's Guide!

3. Intro to the OBO-Edit Interface ● How to read the ontology editor panel ● How to split the ontology editor panel ● Viewing term details

4. Searching: Keywords ● The simplest OBO-Edit search is a “keyword” search. Keyword searches work kind of like a google search.

5. Search Example: Keywords Keyword search: kinase

6. Working with Search Results ● Selecting search results ● Sorting search results ● Naming sets of search results ● Tabs or windows? ● Closing results

7. The DAG Viewer ● The DAG Viewer displays every single path from a term to the root. ● This view can get very confusing in complex ontologies. There are a number of ways to simplify the view. (See the User's Guide)

8. Searching: Full Term Search ● It is possible to do a much more precise search using the full-featured search capabilities. ● The full-featured search works by specifying: – “NOT” (whether or not to negate the search) – A search aspect (we'll talk about this later) – Which field to search (term name, comment, id, namespace, whatever) – What comparison to use (equals, contains, starts with, >, etc) – The value to look for

9. Search Example: Full Term Search ● Term search: Find terms with comments that contain the word “kinase”

10. Searching: The “Aspect” Field ● The “Aspect” field allows you to specify which OTHER terms should be looked at to determine whether a term should be matched. (OR: Sometimes you need to look at terms A, B, C, and D to see if term X matches your search) ● The available aspects are – Self: X is included in the search results if X satisfies the search criteria – Ancestor: X is included in the search results if any ancestor of X satisfies the search criteria – Descendant: X is included in the search results if any descendant of X satisfies the search criteria

11. Search Example: The “Aspect” Field Term search: Find all children of “development”

12. Searching: Compound Searches ● It is possible to create complex search criteria by combining simpler searches with boolean operators ● OBO-Edit's interface defines a complex search using prefix notation (sometimes called reverse polish notation) rather than the more common infix notation. The infix statement “a AND (b OR C)” would be written “AND a (OR b c)” in prefix notation.

13. Searching: Compound Searches ● Keyword search: kinase AND cell ● Term search: Term name contains the words “kinase” OR “activity” ● Term search: Term name contains the word “kinase” AND contains the words “activity” OR “complex”

14. Searching: Link search ● Term searches find terms (duh). Link searches find relationships between terms. ● Links searches can be defined in terms of a link's child, a link's parent, a link's type, or properties of the link itself.

15. Search Example: Link search ● Link search: Find all “part_of” links ● Link search: Find all links with type “part_of” that occur in the molecular function branch of the GO

16. Saving/Loading Searches ● Searches can be saved to disk as an XML file, and loaded later. ● This can be really useful for frequently used or complex searches. Share your favorite search with your spouse or rabbi! ● Saved searches can be used by the obo2obo command line tool to do quick, file-based ontology filtering.

17. Rendering ● Rendering allows you to specify a special visual style for terms that match your search.

18. Rendering Example ● If a term name contains the word “kinase”, draw that term in red

19. Filtering ● Filtering changes the main OBO-Edit display so that only matching terms (or links) are shown.

20. Filtering Example ● Only show terms that belong to the molecular_function ontology ● Only show terms that belong to goslim_generic ● Only show is_a links

21. Root Detection Algorithm ● The Root Detection Algorithm decides what counts as a root. There are (currently) 2 different Root Detection Algorithms: – GREEDY: Anything that has no visible parents should be displayed as a root. – STRICT: Only display a term as a root if it actually has no parents. ● STRICT will sometimes hide terms that actually match a filter. GREEDY will never do that.

22. The Graph Viewer Plugin ● The Graph Viewer Plugin uses AT&T's GraphViz library to draw a graphical version of the information shown in the DAG Viewer ● This plugin requires GraphViz, which can be downloaded for your platform from http://www.graphviz.org http://www.graphviz.org ● See the User's Guide for information on configuring OBO-Edit to use your installation of GraphViz

23. Graph Viewer Demo ● How the Graph Viewer displays selections ● Selecting terms using the Graph Viewer ● Saving pictures ● If time permits: Future directions for the Graph Viewer

24. Oh the Things You Can Do! ● Filtered save using the Advanced Save Dialog ● Filtered save using obo2obo ● All kinds of cool filtering & searching options when you use the OBO-Edit reasoner

25. How to Get OBO-Edit ● http://sourceforge.net/projects/geneontology http://sourceforge.net/projects/geneontology

26. Acknowledgments

27. ● The Good People at Berkeley BOP – Seth Carbon – Karen Eilbeck – Mark Gibson – Chris Mungall – Suzi Lewis – She Shengqiang – Nicole Washington ● The Gene Ontology Consortium ● AND...

28. More Acknowledgments Logan Isaac – August 22nd, 2006