Difference between revisions of "Evolutionary Biology and Ontologies"

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== Introduction ==
 
== Introduction ==
  
This workshop will be held in conjunction with the [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008] meeting in Minneapolis, MN, 20 June 2008. It is organized under the auspices of the [http://ncbo.us National Center for Biomedical Ontologies] (NCBO) in collaboration with the [http://www.nescent.org/ National Evolutionary Synthesis Center] (NESCent). Please disseminate widely using the URL for this page, or the [http://www.nescent.org/documents/EBO_Flyer.pdf workshop flyer].  
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This workshop will be held in conjunction with the [http://www.cce.umn.edu/conferences/evolution/ Evolution 2008] meeting in Minneapolis, MN on June 20, 2008. It is organized under the auspices of the [http://ncbo.us National Center for Biomedical Ontologies] (NCBO) in collaboration with the [http://www.nescent.org/ National Evolutionary Synthesis Center] (NESCent).  
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; [https://wiki.phenoscape.org/wiki/Training_and_Workshops NESCent wiki]
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; [https://wiki.phenoscape.org/wg/phenoscape/images/7/71/EBO_Flyer.pdf Workshop flyer]
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; [http://www.cce.umn.edu/conferences/evolution/ Venue]
  
 
; Organizers: Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)
 
; Organizers: Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)
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; Registration: Registration will be open to attendees of the Evolution 2008 conference at no additional cost.
 
; Registration: Registration will be open to attendees of the Evolution 2008 conference at no additional cost.
  
== Draft Agenda ==
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== Agenda ==
 
   
 
   
*9:00-10.00 Barry Smith, Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo; Lead Scientist of the National Center for Biomedical Ontology: Tutorial: An Introduction to Ontology for Evolutionary Biology
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*8:00 '''''Registration'''''
*10.00-10.30 Break
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*10.30-11.00 Chris Mungall, University of California, Berkeley: An Introduction to the PATO Phenotype Ontology
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*8:30-9:30 '''''Tutorial: An Introduction to Ontology for Evolutionary Biology''''' [https://wiki.phenoscape.org/wg/phenoscape/images/2/22/Smith.ppt Slides]
*11:00-11:30 Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases
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:Barry Smith, NCBO / Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo  
*11:30-12:00 Paula Mabee, University of South Dakota: An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics
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*12:00-1:00 lunch
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*9:30-10:00 '''''An Introduction to the PATO Phenotype Ontology''''' [https://wiki.phenoscape.org/wg/phenoscape/images/b/b7/Mungall.ppt Slides]
*1.00-1:45 Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, Oregon: An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies
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:Chris Mungall, NCBO / University of California, Berkeley  
*1:45-2:15 Anne Maglia, University of Missouri-Rolla: Developing an Ontology for Amphibians using NLP  
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*10:00-10:30 '''''Morning Break'''''
*2:15-2:45 Coffee
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*2:45-3:15 Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina: Ontologies, Image Databases, and Evolutionary Biology
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*10:30-11:00 '''''Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases'''''
*3.15-3:45 Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina: An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits
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:Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, OR
*3:45-4:45 Roundtable & Discussion
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*4.45-5:00 Suzanna Lewis and Paula Mabee: Wrap-Up Session: Next Steps
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*11:00-11:20 '''''An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics'''''
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:Paula Mabee, University of South Dakota
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*11:20-11:30 '''''Phenote: Curation Software for Evolutionary Phenotypes''''' [https://wiki.phenoscape.org/wg/phenoscape/images/e/ee/Balhoff.pdf Slides]
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:James Balhoff, NESCent, Duke University
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*11:30-12:00 '''''An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies'''''
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:Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, OR
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*12:00-1:00 Lunch
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*1:00-1:30 '''''Lightning Talks from Workshop Participants'''''
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*1:30-2:00 '''''Developing an Ontology for Amphibians using NLP''''' [https://wiki.phenoscape.org/wg/phenoscape/images/1/12/Maglia.ppt Slides]
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:Anne Maglia, University of Missouri-Rolla
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*2:00-2:30 '''''Ontologies, Image Databases, and Evolutionary Biology''''' [https://wiki.phenoscape.org/wg/phenoscape/images/9/94/Ramirez.pdf Slides]
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:Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina
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*2:30-2:45 Afternoon Break
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*2:45-3:15 '''''An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits''''' [https://wiki.phenoscape.org/wg/phenoscape/images/a/a4/Vision_evont08.pdf Slides]
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:Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina
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*3:15-3:45 '''''Names, Ranks, Clades, and Taxonomy Ontologies''''' [https://wiki.phenoscape.org/wg/phenoscape/images/5/5b/Midford.ppt Slides]
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: Peter Midford, Department of Ecology and Evolutionary Biology, University of Kansas
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*3:45-4:00 '''''Synthesis'''''
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:Suzanna Lewis, NCBO / University of California, Berkeley and Paula Mabee
  
 
== Background Reading ==
 
== Background Reading ==
  
 
[http://obofoundry.org The OBO Foundry]
 
[http://obofoundry.org The OBO Foundry]
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Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith b. (2008) CARO - The common anatomy reference ontology
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http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf
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In Anatomy Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson and R. Baldock (eds).
  
 
Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) [http://dx.doi.org/10.1016/j.tree.2007.03.013 Phenotype ontologies: the bridge between genomics and evolution]. Trends in Ecology and Evolution 22, 345-50.
 
Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) [http://dx.doi.org/10.1016/j.tree.2007.03.013 Phenotype ontologies: the bridge between genomics and evolution]. Trends in Ecology and Evolution 22, 345-50.
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Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
 
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
 
(2007) [http://dx.doi/org/10.1080/10635150701313848 Text linking of digital images to phylogenetic data matrices using a morphological ontology]. Systematic Biology 56, 283-94.
 
(2007) [http://dx.doi/org/10.1080/10635150701313848 Text linking of digital images to phylogenetic data matrices using a morphological ontology]. Systematic Biology 56, 283-94.
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Smith B,  Ashburner M,  Rosse C, et al. [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration], Nature Biotechnology 2007; 25 (11): 1251-1255.
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Smith B, Ceusters W, Klagges B, et al., [http://genomebiology.com/2005/6/5/R46 Relations in biomedical ontologies], Genome Biology (2005), 6 (5), R46.
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== Additional Resources ==
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Michael Bada and Larry Hunter did an analysis of the glossary of terms for the book ''Being Alive'' (by Larry Hunter, forthcoming from MIT Press) found 189 terms that were not mappable to any OBO ontology.  About half of these terms were related to evolution or population biology.  The  [[list of unmatched glossary terms]] is available and may be useful for ensuring the comprehensiveness of an evolutionary biology ontology.

Latest revision as of 08:48, 7 September 2017

Evolution2008-OntologyWorkshop.png

Contents

[edit] Introduction

This workshop will be held in conjunction with the Evolution 2008 meeting in Minneapolis, MN on June 20, 2008. It is organized under the auspices of the National Center for Biomedical Ontologies (NCBO) in collaboration with the National Evolutionary Synthesis Center (NESCent).

NESCent wiki
Workshop flyer
Venue
Organizers
Barry Smith (Buffalo), Paula Mabee (University of South Dakota), Todd Vision (University of North Carolina, Chapel Hill), Monte Westerfield (University of Oregon)
Focus
This meeting is focused on the application of ontologies to studies in evolutionary biology and related disciplines, with a particular emphasis on studies of the phenotype.
Goals
  1. Introducing what ontologies are, how they should be built, what makes an ontology useful, and how ontologies help people collaborate across disciplines;
  2. Giving illustrations of ontologies actually being used to address problems of interest to evolutionary biologists;
  3. Networking and planning: what do we do next in order to advance ontology-based information integration in evolutionary biology?
Registration
Registration will be open to attendees of the Evolution 2008 conference at no additional cost.

[edit] Agenda

  • 8:00 Registration
  • 8:30-9:30 Tutorial: An Introduction to Ontology for Evolutionary Biology Slides
Barry Smith, NCBO / Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo
  • 9:30-10:00 An Introduction to the PATO Phenotype Ontology Slides
Chris Mungall, NCBO / University of California, Berkeley
  • 10:00-10:30 Morning Break
  • 10:30-11:00 Using Ontologies in the NCBO Project to Link Fish and Fly Mutants to Human Diseases
Monte Westerfield, Director, Zebrafish Information Network and Institute of Neuroscience, Eugene, OR
  • 11:00-11:20 An Introduction to the Use of Ontologies in Linking Evolutionary Phenotypes to Genetics
Paula Mabee, University of South Dakota
  • 11:20-11:30 Phenote: Curation Software for Evolutionary Phenotypes Slides
James Balhoff, NESCent, Duke University
  • 11:30-12:00 An Introduction to the CARO Anatomy Reference Ontology; Multispecies Ontologies
Melissa Haendel, Anatomy Curator, Zebrafish Information Network, Eugene, OR
  • 12:00-1:00 Lunch
  • 1:00-1:30 Lightning Talks from Workshop Participants
  • 1:30-2:00 Developing an Ontology for Amphibians using NLP Slides
Anne Maglia, University of Missouri-Rolla
  • 2:00-2:30 Ontologies, Image Databases, and Evolutionary Biology Slides
Martin Ramirez, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Buenos Aires, Argentina
  • 2:30-2:45 Afternoon Break
  • 2:45-3:15 An Introduction to the Use of Anatomy Ontologies for the Identification of Genes Underlying Complex Traits Slides
Todd Vision, Associate Director, National Evolutionary Synthesis Center and Dept. of Biology, University of North Carolina
  • 3:15-3:45 Names, Ranks, Clades, and Taxonomy Ontologies Slides
Peter Midford, Department of Ecology and Evolutionary Biology, University of Kansas
  • 3:45-4:00 Synthesis
Suzanna Lewis, NCBO / University of California, Berkeley and Paula Mabee

[edit] Background Reading

The OBO Foundry

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith b. (2008) CARO - The common anatomy reference ontology http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf In Anatomy Ontologies for Bioinformatics: Principles and Practice, A. Burger, D. Davidson and R. Baldock (eds).

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall C, Westerfield M (2007) Phenotype ontologies: the bridge between genomics and evolution. Trends in Ecology and Evolution 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) An anatomical ontology for amphibians. Pacific Symposium on Biocomputing 12: 367-378.

Midford PE (2004) Ontologies for behavior. Bioinformatics 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J, Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC (2007) Text linking of digital images to phylogenetic data matrices using a morphological ontology. Systematic Biology 56, 283-94.

Smith B, Ashburner M, Rosse C, et al. The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration, Nature Biotechnology 2007; 25 (11): 1251-1255.

Smith B, Ceusters W, Klagges B, et al., Relations in biomedical ontologies, Genome Biology (2005), 6 (5), R46.

[edit] Additional Resources

Michael Bada and Larry Hunter did an analysis of the glossary of terms for the book Being Alive (by Larry Hunter, forthcoming from MIT Press) found 189 terms that were not mappable to any OBO ontology. About half of these terms were related to evolution or population biology. The list of unmatched glossary terms is available and may be useful for ensuring the comprehensiveness of an evolutionary biology ontology.

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