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