Toward Distributed
Development of Ontologies
Mark A. Musen
Stanford University
Manual, top–down development of
ontologies is the norm
• Yahoo! taxonomy of Web
pages
• Most clinical terminologies
• All the worlds’ upper-level
ontologies
– SUMO
– Open CYC
– HL7 RIM
The Open Directory Project
• Started by Netscape in 1999
• “Editors” volunteer to develop
categorizations of their domains of
expertise
• There are explicit expectations of
editors and review of their work
• At present, thousands of editors, yet
only 0.5 FTE of paid management!
Gene Ontology Consortium
• Outstanding example of communitydriven ontology development
• Small group of volunteer developers
work tirelessly to expand their work
• A new version of GO is released every
30 minutes!
• But there are lots of tensions in the GO
community
 Carole Goble
Prologue
— Carole Goble
Two households, both alike in dignity,
In fair genomics, where we lay our scene,
(One, comforted by its logic’s rigour,
Claims ontology for the realm of pure,
The other, with blessed scientist’s vigour,
Acts hastily on models that endure),
From ancient grudge break to new mutiny,
When “being” drives a fly-man to blaspheme.
From forth the fatal loins of these two foes
Researchers to unlock the book of life;
Whole misadventured piteous overthrows
Can with their work bury their clans’ strife.
The fruitful passage of their GO-mark'd love,
And the continuance of their studies sage,
Which, united, yield ontologies undreamed-of,
Is now the hours' traffic of our stage;
The which if you with patient ears attend,
What here shall miss, our toil shall strive to mend.
Based on an idea by Shakespeare
A Portion of the OBO Library
Moving from cottage industry
to the industrial age
• There must be widely available tools that are opensource, that are easy to use, and that adhere to
knowledge representation standards
• There must be a large user user community of
developers who use the tools and who can provide
feedback to one another and to the core team of tool
builders
• There must be an organizational structure to
provide a modicum of coordination and quality control
• If all these pieces are in place, people can do great
work from their cottages!
The NCI Thesaurus
NCI Thesaurus Today:
Three Critical Pieces
Deployed
(Real)
Integrative,
Experimental,
Collaborative
Scaleable, End -toEnd Production
Process
NCI Thesaurus Production
Environment with History
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N C I T h e s a u ru s
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P ro d u c tio n
00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
D T S S e rv e rs
Egyptian Crop Pests
A thousand flowers are
blooming!
• Ontologies are being developed by interested groups
from every sector of academia, industry, and
government—often “on the cheap”
• Many of these ontologies have been proven to be
extraordinarily useful to wide communities
• Many of these same ontologies have been shown to
have structural flaws
• We finally are at the stage where we have opensource tools and standard representation languages
that can help us to create durable and maintainable
ontologies with rich semantic content
Research Questions
• How do we measure the “quality” of ontologies
developed via industrial engineering and by grassroots efforts?
• Can we perform controlled studies to compare the
cost-effectiveness of top–down versus bottom–up
approaches?
• Can we evaluate the cost-effectiveness of alternative
management structures to facilitate distributed
ontology development?
• Can we develop correlates of peer review to ensure
open quality control of ontologies created in a
distributed fashion?