Ontology (Chrisine Fennema-Notestine)

Background of Ontology Project:

• The overarching goals are to create an ontology prototype that relates brain structure and function through neuroanatomical regions, neuropsychological and cognitive terms, and clinical assessments.
• The current MBIRN testbed goal is to extend examples of clinical assessments from the Multi-site AD project to a relationship-based ontology extending UMLS. Our preliminary focus is a basic neuropsychological ontology as it relates to clinical assessments and neuroanatomy in the multi-site AD study sample, with future branching into neuropsychiatric measures (e.g., fBIRN schizophrenia interviews, etc.).
• For a view of the existing BIRN tool in nbirn.net, login to the portal and select Advanced Data Integration and KNOW-ME UMLS.

Description of Development Plan:

• Terms and relationships will include those already in UMLS and those that will be defined through Bonfire, for a graphical interface. Since the UMLS now automatically includes APA Thesaurus terms, we will not be adding any additional existing data sources. Bonfire allows the creation of new terms and new relationships/links between terms.
• Currently, existing assessment terms in UMLS are not linked to cognitive or anatomical terms. Therefore, each assessment and subscore will be linked to basic cognitive functions and theoretical anatomical bases (where appropriate), with new relationships to be defined.
• “Missing” assessment names and acronyms will be “added” to our KNOW-ME ontology browser UMLS (via Bonfire) to provide unique IDs for each assessment and its subscores.
• For the initial work, CFN will provide addditional new terms and create new relationships via Bonfire to test scope of ontology development.

Development Goals and Progress:

• BIRN-CC’s AG and XQ will develop web interface for adding new terms and creating new relationships via Bonfire, extending the existing KNOW-ME UMLS browser.

  2005.02.02 Current goal is mid-February for testing, with the aim to display this work at the March meeting.

• In addition to the ontological structure, we need simple “look up” tables with task descriptions, including information on score interpretation, etc. CFN has sent AG the updated descriptions for the basic clinical assessments for reference in the search engine.
• AG's team is extending the current KNOW-ME ontology browser to include the extensions to UMLS. It would also extend the capabilities of the current browser to issue HID and mediator queries with one or more selected terms from the KNOW-ME interface.
• DK and CFN have spoken regarding the scope of the ontology project development once the information entry interface is in place.
  • Initial proposal is to start small with a select 10 experienced neuropsychologist types to assist in growing the database with valid information. Ultimately, input resources could grow to a larger set of individuals in which case curation becomes a much more significant issue.
  • DK mentioned Platypus (http://platypuswiki.sourceforge.net/), similar to a “semantic WIKI,” that allows relational links between objects and the creation of new terms, as well as some potential graphical presentation tools.

    2005.02.02 DK and CFN will coordinate a demo of some of these existing tools so that we can gauge their usefulness.