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Overview of Animal Trait Ontology and PATO concepts

Overview of Animal Trait Ontology and PATO concepts. LaRon Hughes Ph.D. student – Iowa State University. Why use bio-ontologies?. The need for bio-ontologies has increased in recent years in large part due to several biological databases

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Overview of Animal Trait Ontology and PATO concepts

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  1. Overview of Animal Trait Ontology and PATO concepts LaRon Hughes Ph.D. student – Iowa State University Bioinformatics & Computational Biology Program - 01/16/06

  2. 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 Bioinformatics & Computational Biology Program - 01/16/06

  3. Importance of ATO journal articles other sources books experts Bioinformatics & Computational Biology Program - 01/16/06

  4. Options for development • Protégé • COBrA • OBO-edit • COB Allows researchers to edit, browse, query, and visualize data in an ontology Bioinformatics & Computational Biology Program - 01/16/06

  5. 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? Bioinformatics & Computational Biology Program - 01/16/06

  6. 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 Bioinformatics & Computational Biology Program - 01/16/06

  7. PATO Meeting • Stanford University • Dec. 1-2, 2006 Bioinformatics & Computational Biology Program - 01/16/06

  8. 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) Bioinformatics & Computational Biology Program - 01/16/06

  9. An example of compositionality • Plasma membrane of spermatocyte • Plasma membrane[GO CC] • Spermatocyte[OBO Cell] • Formal means of composition • Genus-differentia Genus Differentia aplasma membranewhichispart_ofaspermatocyte GO-CC OBO-REL Cell Bioinformatics & Computational Biology Program - 01/16/06

  10. Advantage: Automatic DAG calculation amembranewhichispart_ofagerm cell aplasma membranewhichispart_ofaspermatocyte Bioinformatics & Computational Biology Program - 01/16/06

  11. 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 Bioinformatics & Computational Biology Program - 01/16/06

  12. PATO vs. ATO system • Early? ATO • Pre-composed phenotype definitions • MP:0000017 “big ears” • TO:0000227 “root length” • TO:0000029 “chlorine sensitivity” • Advantage: end user understands terminology • Late? PATO • Post-composed phenotype definitions • E= MA:ear Q= PATO:big • E= PO:root Q= PATO:length • E= organism Q= PATO:sensitivity E2= CHEBI:chlorine • Advantage: querying is more comprehensible Bioinformatics & Computational Biology Program - 01/16/06

  13. Conclusions • PATO will be beneficial to present and future ontology projects • The ATO will benefit from PATO • Will use both pre & post composition? • Questions? Bioinformatics & Computational Biology Program - 01/16/06

  14. Acknowledgments • Dr. Reecy (Iowa State University) • Dr. Honovar (Iowa State University) • Dr. Hu, Jie Bao (Iowa State University) • Chris Mungall & Suzanna Lewis (PATO) Bioinformatics & Computational Biology Program - 01/16/06

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