Overview of Animal Trait Ontology and PATO concepts

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Overview of Animal Trait Ontology and PATO
concepts

• LaRon Hughes
• Ph.D. student Iowa State University

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Why use bio-ontologies?

• The need for bio-ontologies has increased in
  recent years in large part due to several
  biological databases
• Provide a shared vocabulary for biologist so that
  results can be communicated effectively
• Allow computational approaches such as data
  exploration, inference, and mining
• e.g. Gene Ontology (GO) project, Mammalian
  Phenotype (MP) Ontology

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Importance of ATO
journal articles
other sources
books
experts
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Options for development

• Protégé
• COBrA
• OBO-edit
• COB

Allows researchers to edit, browse, query, and
visualize data in an ontology
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Biological Questions

• Are QTL conserved across species?
• Are QTL pleiotrophic across species?
• Are categories of trait QTL related across
  species?
• How many traits are common across species?
• Based on traits that are related in ATO, what are
  phenotypic and genetic correlations?
• Based on all traits available, how well can
  genetics explain the variation within a category
  (e.g. fertility, meat quality)?
• Given several QTL studies for a particular trait,
  what is the minimal number of genes that have a
  major affect on a particular trait?

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National Center for Biomedical Ontology (NCBO)

• Purpose
• Advance biology and medicine with tools and
  methodologies for the structured organization of
  medicine
• Create technologies to allow scientist to create,
  disseminate, and manage biomedical information
  and knowledge in machine-processable form
• Composed of biologist, clinicians,
  informaticians, and ontologist
• Resources available
• Open Biomedical Ontologies (OBO) library
• Open Biomedical Data (OBD) repositories
• Other tools to access and use biomedical
  information

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PATO Meeting

• Stanford University
• Dec. 1-2, 2006

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Compositionality

• Important for describing phenotypes
• Compositionality is a principle for good ontology
  design
• a.k.a. building blocks, cross-products,
  normalized/modular design
• Create complex descriptions (definitions) from
  simpler ones
• Descriptions can be composed at any time
• Ontology construction time (pre-composition)
• Annotation time (post-composition)

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An example of compositionality

• Plasma membrane of spermatocyte
• Plasma membrane GO CC
• Spermatocyte OBO Cell
• Formal means of composition
• Genus-differentia

Genus
Differentia
a plasma membrane which is part_of a spermatocyte
GO-CC
OBO-REL
Cell
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Advantage Automatic DAG calculation
a membrane which is part_of a germ cell
a plasma membrane which is part_of a spermatocyte
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The building blocks of phenotype descriptions EQ

• Entities and qualities (EQ)
• (Bearer) Entity
• E.g compound eye, spermatocyte, blood, wing
  growth, scale morphogenesis
• Quality (aka property, attribute)
• A kind of dependent continuant
• Defined in PATO
• E.g green, hot, squamous, rugose, edematous,
  light-sensitivity, luminescent, ectopic,
  arrested, decomposed

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PATO vs. ATO system

• Early? ATO
• Pre-composed phenotype definitions
• MP0000017 big ears
• TO0000227 root length
• TO0000029 chlorine sensitivity
• Advantage end user understands terminology
• Late? PATO
• Post-composed phenotype definitions
• E MAear Q PATObig
• E POroot Q PATOlength
• E organism Q PATOsensitivity E2
  CHEBIchlorine
• Advantage querying is more comprehensible

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Conclusions

• PATO will be beneficial to present and future
  ontology projects
• The ATO will benefit from PATO
• Will use both pre post composition?
• Questions?

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Acknowledgments

• Dr. Reecy (Iowa State University)
• Dr. Honovar (Iowa State University)
• Dr. Hu, Jie Bao (Iowa State University)
• Chris Mungall Suzanna Lewis (PATO)