A Tool for Collaborative Construction of Large Biological Ontologies

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Jie Bao

Technologie Bildung

Outline ,[object Object],[object Object],[object Object],[object Object]

Large Biological Ontologies Gramineae Taxonomy Plant Ontology Gene Ontology MGED Ontology (microarray)

Non-collaborative Ontology Building Download Ontology Local Editing Upload Ontology (single curator) (Protégé) (OBO-Edit)

Collaboration In Need Example: Gene Ontology Consortium

Collaboration In Need (2) Swine Cattle Chicken Horse Each group works on an ontology module for a particular species (according to the group’s best expertise) Example 2: an animal trait ontology that involves multiple research groups across the world

Challenges ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Solutions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],<= Very limited collaboration <= Collaboration with high cost <= Our approach

CVS-based Ontology Building Get GO CVS Account Get Source Forge Account Set Up CVS Access Submit Change Request Track the Request User submit change suggestion (in natural language) Get Source Forge Account Take a Change Request Curator Download Whole GO Flat File Local Editing Make Local Log File Save GO Flat File Version Control Commit Whole New Ontology to CVS

Unprincipled Authorization and Organization ,[object Object],[object Object]

Risk of Inconsistency ,[object Object],[object Object]

Lack of Partial Editing/Reuse ,[object Object],[object Object],[object Object],[object Object]

Expensive History Maintenance ,[object Object],[object Object]

Limited Participation ,[object Object],[object Object],[object Object],[object Object]

Basic Strategy ,[object Object],[object Object],[object Object]

Package-based Ontologies ,[object Object],[object Object],[object Object],Egg Chicken Reproduction General General Cattle Pig Chicken Animal Trait ontology

Package Nesting ,[object Object],[object Object],[object Object],[object Object],General Pig Pig Health Animal trait ontology

Division of Labor ,[object Object],[object Object],[object Object],[object Object]

Partial Reuse General Cattle Pig Chicken Animal Trait Ontology (Centralized) Pork General Pig Cattle Chicken Pork Animal Trait Ontology (Package-based) Semantic importing Knowledge incorporated in Pork ontology Knowledge not presented in Prok ontology Legend :

Scaleability ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Broadened Participation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

The COB Editor Pig Package Cattle Package Chicken Package [BIDM06 Paper] a.k.a [8]

Collaborative Ontology Building ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Work with COB Editor ,[object Object],[object Object],[object Object],Get Ontology Account Check out a package Curator Create new package or Lock Package Edit the Package Commit the Package (Auto) Server Change Log

More Features ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Conclusions ,[object Object],[object Object],[object Object]

Future Work ,[object Object],[object Object],[object Object],[object Object]

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