HCLS/OntologyTaskForce

Mission and Scope

The mission of the Ontology Task Force is to facilitate creation, evaluation and maintenance of "core vocabularies and ontologies to support cross-community data integration and collaborative efforts.” [[FootNote(HCLS Charter)]]

Activities will focus on the theme of best practices in the context of well defined use cases that are of interest to the broader HCLS community.

Towards this end, this group will collaborate with other task forces within HCLS and with the National Center for Biomedical Ontology (NCBO).

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

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
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

  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).

Phone

IRC

Browser-based IRC client

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.

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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