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MEBI 534 , Autumn 2008
Biology and Informatics

Anatomy: Informatics 

Assignment

1.  Read the following and be prepared to discuss in class

Rosse, C. and Mejino, J. L. V. (2003) A Reference Ontology for Bioinformatics: The Foundational Model of Anatomy. Journal of Biomedical Informatics. 

Shadbolt, N., W. Hall, and T. Berners-Lee, The semantic web revisited. IEEE Intelligent Systems, 2006. 21(3): p. 96-101.

Optional: Detwiler, L.T., D. Suciu, and J.F. Brinkley, Regular paths in SparQL: Querying the NCI thesaurus, in Proceedings, Fall Symposium of the American Medical Informatics Association. In Press. 2008.


2. Provide written answers to the following questions, to be turned in prior to the Wed class, as per these instructions.


a. Define the meaning of the terms in the following high level definition of the FMA:

FMA=(AT,ASA,ATA,Mk)

b. In the FMA explain why the Brain and Spinal cord are not classified as Organs, but rather as Organ parts.

c. Using the Foundational Model Explorer, look up the parent class in the subclass navigation tree type of each of these respiratory system structures in the FMA: pharynx, right lung, inferior margin of right lung. For each of these specify whether they are also anatomical structures.

d. Define the meaning of the following semantic web terms RDF, OWL and SparQL.

e. The following is a semantic web SparQL query that finds the transitive closure of the regional parts of the Temporal lobe of the brain (ie parts of parts) in the OWL version of the FMA ontology.

 
CONSTRUCT 
         {
         fma:Temporal_lobe  fma:part ?object . 
}
         WHERE
         {
         fma:Temporal_lobe  gleen:OnPath("[fma:regional_part]+" ?object) .
}
       
 

Cut and paste this query into the following web site, subsituting Left_lung for Temporal_lobe, to find the transitive closure of the regional parts of the Left lung.

http://fma.biostr.washington.edu:8080/FMA_OWL_Client/

Cut and paste the list of parts to your answer.

f. The string "[fma:regional_part]+" in the above query is called a regular path expression, which causes the query to traverse one or more regional_part links starting with Temporal_lobe in order to find rhe transitive closure. Modify the path expression in your Left_lung query to return only the top level parts of the Left_lung, ie the regional parts that can be reached by following just one link. You might need to read page 3 of the optional reference above.


Cut and paste the list of top-level parts to your answer.

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 Last Updated 9/25/08

Contact the instructor at: brinkley@u.washington.edu