OBO-Edit: The Browser
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Transcript of OBO-Edit: The Browser
OBO-Edit: The Browser
The BrowserJohn Day-Richter
Berkeley Bioinformatics and Ontology Project / Gene Ontology
Before We Do Anything!
When in doubt, check the User's Guide!
Intro to the OBO-Edit Interface
● How to read the ontology editor panel● How to split the ontology editor panel● Viewing term details
Searching: Keywords
● The simplest OBO-Edit search is a “keyword” search. Keyword searches work kind of like a google search.
Search Example: Keywords
Keyword search: kinase
Working with Search Results
● Selecting search results● Sorting search results● Naming sets of search results● Tabs or windows?● Closing results
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)
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
Search Example: Full Term Search
● Term search: Find terms with comments that contain the word “kinase”
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
Search Example: The “Aspect” Field
Term search: Find all children of “development”
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.
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”
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.
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
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.
Rendering
● Rendering allows you to specify a special visual style for terms that match your search.
Rendering Example
● If a term name contains the word “kinase”, draw that term in red
Filtering
● Filtering changes the main OBO-Edit display so that only matching terms (or links) are shown.
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
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.
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
● See the User's Guide for information on configuring OBO-Edit to use your installation of GraphViz
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
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
How to Get OBO-Edit
● http://sourceforge.net/projects/geneontology
Acknowledgments
Acknowledgments
● 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...
More Acknowledgments
Logan Isaac – August 22nd, 2006