• HCLS
• OntologyTaskForce

Mission and Scope

Key Questions

• What is an ontology?

  • NIST, OMG, NCBO, W3C .... any others ...

  • NIST Ontology Definitions

• What information should be represented in an ontology?

• How should information be represented in an ontology?

• How could ontologies be created?

• How should ontologies be accessed and used?

• How should ontologies be maintained?

• How should ontologies be evaluated?

Active Tasks

• Harmonization of the representation of labels, descriptions and definitions of entities in biomedical ontologies

• Finding a common standard for the representation of bibliographic information

• Clarification of BFO Process Definition

• Mapping Clinical Observations across Clinical Practice and Clinical Trials

• A uniforma representation and reasoning approach for Evidence across HCLS

Resources

• Mappings from Gene Ontology to other ontologies

Work products

Members of the Task Force share the responsibility for preparation of deliverables, with the assistance of collaborators.

• Re-use and Cross Mapping of DCM and SDTM Models

• Notes Prepared for W3C

• Use Cases

  • Parkinson's Disease

  • Alzheimer's Disease

  • Integration of AD and PD Use Cases with extension to Bedside

• Ontology Building Experiences of Various Groups (Use Cases, Gotchas, Questions, Hacks, Solutions)

  • Experiences with building the Problem Oriented Medical Record Ontology

  • Clinical Element Models at IHC

  • Experiences with building SWAN Ontology

  • Experiences with building ACPP Ontology

  • Experiences with building Brainstage Ontology

  • Experiences with building the bio-zen Ontology

  • Kei - present his work on Neuron DB ontology
• Examples of using Ontologies
  • Sub Task 1: Write up U. Manchester examples for using ontologies

    • Owner: Alan Ruttenberg see Ontologization for Transitive Closure Inferences ==> Examples

  • Sub Task 2: Write up L and C examples for ontologization of Snomed

    • Owner: Davide Zaccagnini

  • Sub Task 3: Incorporate, align or extend use case based on these examples

    • Owner: Donald Doherty and Kensaku Kawamoto

  • Sub Task 4: Create Bridging Ontology between NeuronDB and CoCoDat databases and UMLS Common Vocabulary

    • Owner: Donald Doherty

* Seed Ontology

• Design Choices and Issues in creating an ontology

• List of Statements from Research articles and their representation

* Amsterdam F2F Presentation of Goals, Status and Collaboration Opportunities

* Ontology Fragments

• Coordinator: John Madden

• Sub Task 1: Ontologization for Annotation Inferences

  • Owner: Michael Miller

• Sub Task 2: Ontologization for Classification Inferences

• Sub Task 3: Ontologization for Transitive Closure Inferences

• Sub Task 4: Ontologization for Change Propagation Inferences
• Sub Task 5: Experimenation with different design patterns

• Mappings to BIORDF Data Sources

  • Coordinator: Xiaoshu Wang

  • Sub Task 1: Rewrite BIORDF queries using Snomed (or any other ontology)
  • Sub Task 2: Coordinate with Tonya, Alan and Susie to see which of the BIORDF data sources can address the questions identified in the use case.

    • Owner: Vipul Kashyap

• Best practice descriptions

  • Sub Task 1: Best practice for Ontology URI specifications

• Demonstration implementations of Semantic Web technology in biomedicine

Teleconferences

Our weekly teleconference occurs on Tuesdays, from 1600h-1700h GMT (1100h-1200h US Eastern Time).

Our archived teleconference minutes are available.

Active participants

The following HCLS members are actively involved in the activities of this task force. (Please feel free to add or remove your name. We've put your names as a WikiName, so it will generate a link to your WikiHomePage.) All HCLS participants are welcome to join in the activity of this task force.

• BudakArpinar

• JohnBarkley

• BillBug

• KeiCheung

• DonaldDoherty

• VipulKashyap

• KensakuKawamoto

• JoanneLuciano

• JohnMadden

• MichaelMiller

• AlanRuttenberg

• MatthiasSamwald

• AmitSheth

• SamirTartir

• XiaoshuWang

Resources

We set up a public Connotea group for the Task Force, where we can maintain references of interest to all.

• You can view the page without a Connotea username; to add references you will need to (1) get a Connotea username (free) and (2) send John an email with you username so he can add you to the group as a contributor.

Feel free to add to our useful links page.

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