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

2. Iowa State University Animal Science Department 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

3. Iowa State University Animal Science Department Bioinformatics & Computational Biology Program - 01/16/06 3 Importance of ATO journal articles other sources books experts

4. Iowa State University Animal Science Department 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

5. Iowa State University Animal Science Department Bioinformatics & Computational Biology Program - 01/16/06 5 Biological Questions 1)Are QTL conserved across species? 2)Are QTL pleiotrophic across species? 3)Are categories of trait QTL related across species? 4)How many traits are common across species? 5)Based on traits that are related in ATO, what are phenotypic and genetic correlations? 6)Based on all traits available, how well can genetics explain the variation within a category (e.g. fertility, meat quality)? 7)Given several QTL studies for a particular trait, what is the minimal number of genes that have a major affect on a particular trait?

6. Iowa State University Animal Science Department 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

7. Iowa State University Animal Science Department Bioinformatics & Computational Biology Program - 01/16/06 7 Stanford University Dec. 1-2, 2006 PATO Meeting

8. Iowa State University Animal Science Department 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)

9. Iowa State University Animal Science Department 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 a plasma membrane which is part_of a spermatocyte GO-CCOBO-RELCell GenusDifferentia

10. Iowa State University Animal Science Department Bioinformatics & Computational Biology Program - 01/16/06 10 Advantage: Automatic DAG calculation a plasma membrane which is part_of a spermatocyte a membrane which is part_of a germ cell

11. Iowa State University Animal Science Department 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

12. Iowa State University Animal Science Department 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

13. Iowa State University Animal Science Department 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?

14. Iowa State University Animal Science Department 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)