Transcript NCBIO-Berkeley

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 ontologymanagement platforms
 Integrate ontology-annotation tool with
BioPortal
 Access ontologies for data annotation from OBO
 Store data annotations in OBD
Creating associations
context
Phenotypic
observation
environment
evidence
publication
figures
assay
genetic
sequence ID
ontology
Definition of an association
Association = Genotype Phenotype Environment Assay
Phenotype = Stage* Entity Attribute Entity* Measurement*
Measurement = Unit Value (Time)
Entity = OBOClassID
Attribute = PATOVersion2ClassID
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.
2.
3.
4.
5.
6.
7.
8.
Instance browser
Evidence browser and selector
Environmental context specifier
Entity genotype specifier
Assay specifier
Instance phenotype editor
Ontology recognizer
Ontology term locator
The pieces of an Annotation
Kit
1.
2.
3.
4.
5.
6.
7.
8.
Instance browser
Evidence browser and selector
Environmental context specifier
Entity genotype specifier
Assay specifier
Instance phenotype editor
Ontology recognizer
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