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OBO Foundry

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Chris Mungall
Chris Mungall

The document discusses the Open Biomedical Ontologies (OBO) Foundry, which is a collection of reference ontologies in biology and biomedicine that follow a set of principles to ensure logical structure and interoperability. It outlines the motivation and history of OBO Foundry, describes how the ontologies are organized, and provides examples of ontologies in the Foundry and their scopes. The goal of OBO Foundry is to facilitate sharing, integration and analysis of biological data through standardized ontologies.

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The OBO Foundry Chris Mungall Lawrence Berkeley Laboratory NCBO GO Consortium May 2007
The Open Biomedical Ontologies (OBO) Foundry ,[object Object],[object Object]
Outline ,[object Object],[object Object],[object Object],[object Object],[object Object]
http://obofoundry.org http://www.bioontologies.org (NCBO)
Why is the OBO Foundry necessary? ,[object Object],[object Object],[object Object],[object Object]
Origins of OBO: The Gene Ontology (GO) ,[object Object],[object Object],[object Object],[object Object],[object Object]
Annotation and GO ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
GO and the need for OBO ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],ChEBI Cell Anatomy quality
Organisation of the OBO Foundry ,[object Object],[object Object],[object Object],[object Object]
Partitions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
Connecting the Foundry: The OBO Relation Ontology ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
OBO Foundry Principles ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],http://obofoundry.org/crit.shtml
Results ,[object Object],[object Object],[object Object],[object Object],[object Object]
Genotype-Phenotype Annotation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
OBI: Ontology for Biomedical Investigations ,[object Object],[object Object],[object Object],[object Object]
Results: GO cross-products ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Anatomy Ontologies ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Finding out more and participating ,[object Object],[object Object],[object Object]
Acknowledgements NCBO/Berkeley Nicole Washington Mark Gibson John Day-Richter Suzanna Lewis NCBO/Stanford Nigam Shah Daniel Rubin Archana Verbakam Lynn Murphy Michael J Montague Mark Musen Ontologies Amelia Ireland Jane Lomax Jen Clark Midori Harris David Hill Karen Eilbeck Seth Carbon Judith Blake & GO NCBO/Buffalo Fabian Neuhaus Werner Ceusters Louis Goldberg Barry Smith NCBO/Eugene Melissa Haendel Monte Westerfield NCBO/Cambridge Michael Ashburner George Gkoutos NCBO/Victoria Chris Callender Margaret-Anne Storey NCBO/Mayo James Buntrock Chris Chute NIH Peter Good Carol Bean David Sutherland Oliver Hofmann Sue Rhee Johnathan Bard Lindsay Cowell Erik Segerdell Alan Rector Cynthia Smith Jannan Eppig Rex Chisholm Pascale Gaudet Paula de Matos Rafael Alcantra Kirill Degtyarenko Pankaj Jaiswal Onard Mejino Cornelius Rosse William Bug Alan Ruttenberg Trish Whetzel Jennifer Fostel & OBI Consortium NCBO/UCSF Simona Carini Ida Sim Nation Heart, Lung and Blood Institute
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 

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OBO Foundry

  • 1. The OBO Foundry Chris Mungall Lawrence Berkeley Laboratory NCBO GO Consortium May 2007
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  • 20. Acknowledgements NCBO/Berkeley Nicole Washington Mark Gibson John Day-Richter Suzanna Lewis NCBO/Stanford Nigam Shah Daniel Rubin Archana Verbakam Lynn Murphy Michael J Montague Mark Musen Ontologies Amelia Ireland Jane Lomax Jen Clark Midori Harris David Hill Karen Eilbeck Seth Carbon Judith Blake & GO NCBO/Buffalo Fabian Neuhaus Werner Ceusters Louis Goldberg Barry Smith NCBO/Eugene Melissa Haendel Monte Westerfield NCBO/Cambridge Michael Ashburner George Gkoutos NCBO/Victoria Chris Callender Margaret-Anne Storey NCBO/Mayo James Buntrock Chris Chute NIH Peter Good Carol Bean David Sutherland Oliver Hofmann Sue Rhee Johnathan Bard Lindsay Cowell Erik Segerdell Alan Rector Cynthia Smith Jannan Eppig Rex Chisholm Pascale Gaudet Paula de Matos Rafael Alcantra Kirill Degtyarenko Pankaj Jaiswal Onard Mejino Cornelius Rosse William Bug Alan Ruttenberg Trish Whetzel Jennifer Fostel & OBI Consortium NCBO/UCSF Simona Carini Ida Sim Nation Heart, Lung and Blood Institute
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Editor's Notes

  1. NCORB s/core4/core1