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
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.
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.