The usual info

Project topicComparative Anatomy Information System
SchoolUniversity of Washington
Realted groupsStructural Informatics Group
Dept. of Medical Education & Biomedical Infromatics
Dept. of Computer Science & Engineering
MentorDr. Linda Shapiro
PeopleRavensara (Raven) S. Travillian - this is her project
Katarzyna (Kasia) Wilamowska - helping Raven with programming and development
Related papers
  1. Travillian, R.S. and Rosse, C. and Shapiro, L.G. An Approach to the Anatomical Correlation of Species through the Foundational Model of Anatomy

  2. Shapiro, L. G. and Chung E. and Detwiler, L. T. and Mejino Jr., J. L. V. and Agoncillo, A. V. and Brinkley, J. F. and Rosse, C. (2004) Processes and Problems in the Formative Evaluation of an Interface to the Foundational Model of Anatomy Knowledge Base

Details, details...


The following is information about the project that I have put together from the papers I have read; most of it is quoted or paraphrased from a paper titled "Of Mice and Men: Design of a Comparative Anatomy Information System" by Ravensara Travillian MS, MA, John H. Gennari PhD, and Linda G. Shapiro PhD.

Raven, one of Dr. Shapiro's graduate students, is working on the design of a comparative anatomy information system that allows users to issue queries to determine the similarities and differences between two species. The system will serve as a pilot project for cross-species anatomical information collection, storage, and retrieval.

In the paper titled An Approach to the Anatomical Correlation of Species through the Foundational Model of Anatomy, the authors desribe an approach called the Structural Difference Method (SDM), in which each of two species is represented by an attributed graph, and graph matching is used to determine the similarities and differences.

Using the Foundational Model of Anatomy (FMA) for humans as a framework, Raven and the other authors of the "Of Mice and Men" paper have developed a partial mouse anatomy ontology (MAO) that can be used for comparisons. To compare two species, a mapping between them must be constructed and represented as a computer data structure. Since both the FMA and the MAO are implemented in the Protégé 2000 frame-based knowledge system, the mappings between mouse and human have been designed as Protégé classes that can link the two ontologies and provide a resource for a query system.

Thus, the implementation of this version of the comparative anatomy system will be a single database of mappings, which will be accessed by a query engine and which will provide a result set.

Our goals

From what Tenjinder and I know right now, Kasia has developed the mapping database and our goal will be to create a Java application that will accept queries, access the database through the Protégé API and return a result set. Part of the project will be developing the application to retrieve data from the database, and part of it will be creating a user interface and coming up with a useful way of reprsenting the query results.

We are meeting with Dr. Shapiro and Kasia on Monday, July 18, to discuss how far Kasia is into the project, and to develop a specific design for our part of the project. Raven is working in Philadelphia for the summer, but we are keeping in touch with her by email.

Why is this important?

As the authors of An Approach to the Anatomical Correlation of Species through the Foundational Model of Anatomy point out, research in bioinformatics, genomics, and animal models of human disease, as well as other fields, has shown an increasing need for extrapolating information from one species to another. Basically, this means that it would be very helpful for contemporary researchers to be able to compare anatomical entities of two different species. For example, if experiments are conducted on a certain part of a mouse, it is critical to know how closely the relevant anatomical entity of the mouse models the corresponding human entity, so that it is easier to evaluate the significance of the results for humans.

Furthermore, the amount of anatomical and related medical data emerging from animal modeling experiments is growing at an exponential rate, calling for innovative methods of evaluating, organizing and managing this information.

What is the FMA?

According to the FMA website:

"The Foundational Model of Anatomy(FMA) is an evolving computer-based knowledge source for bioinformatics; it is concerned with the representation of classes and relationships necessary for the symbolic modeling of the structure of the human body in a form that is understandable to humans and is also navigable by machine-based systems. Specifically, the FMA is a domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy."

Emily: an interface to the FMA

In the paper titled Processes and Problems in the Formative Evaluation of an Interface to the Foundational Model of Anatomy Knowledge Base, the authors describe Emily as a relation-centric query interface that is able to query the entire range of classes and relationships in the FMA.

Since the system we will be working on is similar to Emily, Tejinder and I have been doing some reading about Emily. The main difference between the system we will be working on and Emily is the fact that Raven's system will handle two-species queries involving comparisons between anatomical structures across two different species, whereas Emily deals with single-species queries.

More information about Emily and a demo can be found at this Structural Informatics Group website.