1. Core 2: Bioinformatics NCBO-Berkeley

2. Core 2 Specific Aims 1.Apply ontologies  Software toolkit for describing and classifying data 2.Capture, manage, and view data annotations  Database (OBD) and interfaces to store and view annotations 3.Investigate and compare implications  Linking human diseases to model systems 4.Maintain  Ongoing reconciliation of ontologies with annotations

3. Core 2 Specific Aims 1.Apply ontologies  Software toolkit for describing and classifying data 2.Capture, manage, and view data annotations  Database (OBD) and interfaces to store and view annotations 3.Investigate and compare implications  Linking human diseases to model systems 4.Maintain  Ongoing reconciliation of ontologies with annotations

4. Elicitation of Requirements for Annotation Tools  Applications pull from pioneer users in Core 3  ZFIN  FlyBase  Trial Bank  Study these groups currently annotate data  Determine how our Core 2 tools can integrate with existing data flows and databases  Evaluate the commonalities and differences among approaches

5. Development of Data-Annotation Tool  Develop plug-in architecture  Default user interface for generic data-annotation tasks  Custom-tailored interfaces for particular biomedical domains  Enable interoperability with existing ontology- management platforms  Integrate ontology-annotation tool with BioPortal  Access ontologies for data annotation from OBO  Store data annotations in OBD

6. Creating associations context environment genetic Phenotypic observation publication figures evidence assay sequence ID ontology

7. Association = Genotype Phenotype Environment Assay Phenotype = Stage* Entity Attribute Entity* Measurement* Measurement = Unit Value (Time) Entity = OBOClassID Attribute = PATOVersion2ClassID Definition of an association

8. Our Annotation Task  Annotation: describing an instance with a set of associated ontological terms  Genotype, environmental, assay, evidence, and phenotype  For an association we need to capture the following data: 1.A name or tag for the instance 2.The evidence for the observation  For example, the URL of an image 3.A list of associated terms comprising the annotation

9. The pieces of an Annotation Kit 1.Instance browser 2.Evidence browser and selector 3.Environmental context specifier 4.Entity genotype specifier 5.Assay specifier 6.Instance phenotype editor 7.Ontology recognizer 8.Ontology term locator

10. The pieces of an Annotation Kit 1.Instance browser 2.Evidence browser and selector 3.Environmental context specifier 4.Entity genotype specifier 5.Assay specifier 6.Instance phenotype editor 7.Ontology recognizer 8.Ontology term locator

11. Phenotype from published evidence

12. Ontologies enable users to describe assays

13. Ontologies enable users to describe environments

14. Ontologies enable users to describe genotypes

15. Demo

16. Planning ahead