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

publicationfigures

evidence

assaysequence ID

ontology

Association = Genotype Phenotype Environment AssayPhenotype = Stage* Entity Attribute Entity* Measurement*Measurement = Unit Value (Time)Entity = OBOClassIDAttribute = 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 instance2.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 browser2. Evidence browser and selector3. Environmental context specifier4. Entity genotype specifier5. Assay specifier6. Instance phenotype editor7. Ontology recognizer8. Ontology term locator

The pieces of an Annotation Kit

1. Instance browser2. Evidence browser and selector3. Environmental context specifier4. Entity genotype specifier5. Assay specifier6. Instance phenotype editor7. Ontology recognizer8. 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