Core 2: Bioinformatics NCBO-Berkeley

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

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

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

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

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

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

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

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

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

Phenotype from published evidence

Ontologies enable users to describe assays

Ontologies enable users to describe environments

Ontologies enable users to describe genotypes

Demo

Planning ahead