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Core 2: Bioinformatics

Core 2: Bioinformatics. NCBO-Berkeley. Core 2 Specific Aims. Apply ontologies Software toolkit for describing and classifying data Capture, manage, and view data annotations Database (OBD) and interfaces to store and view annotations Investigate and compare implications

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Core 2: Bioinformatics

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  1. Core 2: Bioinformatics NCBO-Berkeley

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

  3. Core 2 Specific Aims • Apply ontologies • Software toolkit for describing and classifying data • Capture, manage, and view data annotations • Database (OBD) and interfaces to store and view annotations • Investigate and compare implications • Linking human diseases to model systems • 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 Phenotypic observation evidence publication environment figures assay genetic sequence ID ontology

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

  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: • A name or tag for the instance • The evidence for the observation • For example, the URL of an image • A list of associated terms comprising the annotation

  9. The pieces of an Annotation Kit • Instance browser • Evidence browser and selector • Environmental context specifier • Entity genotype specifier • Assay specifier • Instance phenotype editor • Ontology recognizer • Ontology term locator

  10. The pieces of an Annotation Kit • Instance browser • Evidence browser and selector • Environmental context specifier • Entity genotype specifier • Assay specifier • Instance phenotype editor • Ontology recognizer • 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

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