Post on 06-May-2015
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Collaborative Ontology Development
Natasha NoyStanford University
Monday, July 15, 13
The ontology development that we grew up with
Courtesy of Mark Musen
Monday, July 15, 13
Lots of databases and sources
The data is in different silos
Need to integrate them
Considerable benefit if you can integrate the data
Ontologies are essential to science
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Many ontologies today are largeand there are lots of them
• Gene ontology: 28K classes• Foundational Model of Anatomy: >80K classes• NCI Thesaurus: 80K classes• SNOMED CT: >300K classes
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There are lots of ontologies and more to come
BioPortal has more than 350 ontologiesonly in the field of
biomedicine
Users uploaded more than 230 ontologies to
WebProtégé in the first two months after its release
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To provide canonical representation of scientific knowledge
To annotate experimental data to enable interpretation, comparison, and discovery across databases
To facilitate knowledge-based applications for decision support, natural language-processing, data integration
and other applications
Scientists have adopted ontologies
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Ontology development has changed, too
or to any number ofusers anywhere
in the world
from a loneknowledge engineer
to a few distributed
users
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Courtesy of Mark Musen
Monday, July 15, 13
Collaborative Ontology Development
• Collaborative• Several users contribute to a single developing
ontology• There are mechanisms to carry out discussions and
to reach consensus
• Ontologies• From simple taxonomies• To expressive OWL ontologies
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Ontologies That Are Being Developed Collaboratively
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Gene Ontology (GO)
• Developed by the Gene Ontology Consortium• Goal: create a single terminological resource
for annotating genes and gene function from different model organisms:• drosophilla, mouse, e.coli, homo sapiens, ...
• GO: 38,000 classes
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Key Resource: GO Annotations
Manually curated over the past 10 yearsPublicly available
345,000 annotations for homo sapiens
TP53
Gene productGO:0007569
cell aging
GO Term
PubMed article
ManualGO
Annotation
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The Gene Ontology
Terminology for consistent description of gene products
Issue Tracker
Curators of biomedical
databases
GO Curators 3 full-time curators have access to edit GO
Anyone in the community can submit an issue or request
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Monday, July 15, 13
The NCI Thesaurus
A reference ontology for cancer biology, translational science, and clinical oncology
~20 full-time editors making changes
Changes are not immediately visible
A “lead editor” who approves the changes, and assigns new tasks
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International Classification of Diseases (ICD)
Have you looked at your medical insurance bill lately?
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International Classification of Diseases
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ICD – Why should you care?
Certificate of death
Policy making
Medical bills
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Developing ICD-10: Revision process in the 20th century
8 Annual Revision Conferences (1982 - 89)
17 – 58 Countries participated
1- 5 person delegations
Mainly Health Statisticians
Manual curation
List exchange
Index was done later
"Decibel” Method of discussion
Output: Paper Copy
Work in English only
Limited testing in the field
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ICD-11: the 21st century
• ICD-11 is being developed as an OWL ontology• Being developed collaboratively, in an open
editing process• Links to other ontologies, such as SNOMED CT• 33,000 classes
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Over 250 domain experts from around the world
Organized in groups, which edit different parts of the ontologyT. Tudorache, S. Falconer, C. Nyulas, N. F. Noy and M. A. MusenWill Semantic Web Technologies Work for the Development of ICD-11?International Semantic Web Conference (ISWC 2010), In-Use Track, Shanghai, China
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ICD-11 development process
• Each night a snapshot of the commonly edited ontology is published in a public platform to encourage feedback from the larger community http://apps.who.int/classifications/icd11/browse/f/en
• Editorial workflow• Centrally overseen by WHO• Peer-reviewed process for the content and structure• Experts may add change proposals• WebProtégé used as the collaborative ontology
development platform
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Modeling ICD-11: Different views
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Linearization
Foundation:ICD categories with
Definitions, synonymsClinical descriptionsDiagnostic criteriaCausal mechanismFunctional impact
Primary care
Morbidity
Mortality
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Multi-Linguality
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Links to Other Terminologies
Search in BioPortal
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All properties are reified
Multi-lingualityExternal references
MetadataEvidence
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related to
linguisticEntity : LinguisticEntity
LanguageTerm
id : xsd:stringlinearizationSpecification* :
LinearizationSpecificationdefinition : DefinitionTermsynonym* : LanguageTermbodyPart* : BodyPartTerm ...
ICDCategory
source : xsd:string label : LinguisticEntity ...
ReferenceTerm
label : xsd:stringlanguage : xsd:string
LinguisticEntity linearizationView : LinearizationValueSetlinearizationParent : ICDCategoryType ...
LinearizationSpecification
id : xsd:string
Term
DomainConceptsubclass of
Courtesy of Tania Tudorache
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Monday, July 15, 13
Ontology Development as a Collaborative Process
• Ontology development is an inherently collaborative process
• It is also inherently modular, so “stepping on someone else’s toes” is not a big issue
• Users expect Web 2.0-style interaction: • feeds, emails• watched entities• Web interface• social-networking features
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Dimensions of Collaborative Workflows
• Ontology size• from 100s to 10,000s of concepts
• Size of the community• Contributors (in some form): from 2-3
to dozens
• Editors: from 1-2 to 20
• Control mechanisms• Variety of roles
• Gatekeepers, etc.
• Client-server editing
• Discussion tools• mailing lists, message boards
• face-to-face meetings, telecons
• Synchronization and editing mechanisms• CVS, SVN
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WebProtégé
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“Google docs” for ontologies
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Collaboration Features
• Simultaneous editing• Change tracking• Threaded discussions for ontology entities and changes
(notes, discussions, proposals, reviews)• Watching ontology entities and branches and notifications• Upload and sharing of ontologies• Download any revision of the ontology• Access policies• User interface customization for domain experts• Change analysis and statistics
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Notes and discussions
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Change tracking
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Watching entities and branches
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Download any snapshot in time
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Research Challenges
• Human-Computer Interaction:• How do we enable domain experts to contribute effectively?
• What are the minimal sets of constructs necessary?
• Change analysis:• Are there patterns in how users edit ontologies?
• Can we use these patterns to guide user interfaces?
• Community dynamics:• What are the dynamics in groups that develop ontologies
collaboratively?
• Are there explicit or implicit roles?
• Do roles change over time?
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