GulfDoctor.net - A site for dermatologists & bioinformaticians by Bell Raj Eapen

ONTODerm
A Step towards semantic dermatology...

Ontology is an explicit formal specifications of the terms in a particular domain and relations among them. ONTODerm is a specialty specific ontology for dermatology. Dermatology is different in many ways from the other medical specialties with a semantics of its own. Hence having a specialty specific ontology is essential to integrate dermatology with other medical software systems.
ONTODerm is prepared in OWL - DL using the Protege OWL plugin. This is by no means a complete and stable ontology. ONTODerm is an ongoing project hosted at SourceForge.net. Hopefully over a period of time, with the contribution from many domain experts, ONTODerm will emerge as a stable ontology which can be integrated into various software systems. The latest version of ONTODerm including the protege project is available here. The stable version can be directly imported to protege using the URL http://www.gulfdoctor.net/ontoderm/ontoderm.owl#.
ONTODerm Tools:

Virtual Dermatologist: A diagnostic application for Dermatology.

SLISED: Semantic LIterature SEarch for Dermatology. (Planning)

TERM LOOKUP: Search ONTODerm for dermatological terms.

Contributions from other project members will be posted here. A stable ONTODerm may become part of ontology based guideline systems in the future.

ONTODerm Schema

Please cite this article if you use ONTODerm in your project.

Eapen BR. ONTODerm - A domain ontology for dermatology. Dermatology Online Journal (2008) 14 (6): 16 [Full Text]

Other articles and books citing ONTODerm.

Leila Kefi-Khelif, Michel Demarchez, Martine Collard, A Knowledge Base Approach for Genomics Data Analysis, Proc. International Conference on Semantic Systems, I-Semantics 2008, Graz, Austria, September 2008.
Evolving Application Domains of Data Warehousing and Mining: Trends and Solutions by Pedro Nuno San-Banto Furtado
Conceptual Development of Mental Health Ontologies by JS Deogun
Ontology-Driven Method for Ranking Unexpected Rules. Mohamed Said Hamani and Ramdane Maamri

Other websites citing ONTODerm

An ontology will never be complete if it is developed by a single person. I can't do it alone and I don't want to do it alone! If you are a domain expert in dermatology or a software developer interested in ontology related tools you can also contribute by joining the ONTODerm project. Refer below for details and contact me for further clarification.

If you are a dermatologist...
ONTODerm is not a software. It is a compilation of dermatological definitions (Well, sort of). Hence the most important skill needed to be part of Core ontoderm development is the thorough understanding of dermatological terms. However it is not like writing a book. Terms are defined in a particular way using a software tool called protégé. Hence a technical mind and a basic knowledge of software tools are essential.

How do I start?
Please go through the primary publication on ONTODerm. Don't worry even if you do not understand everything mentioned about ontology. Download and install Protégé on your computer. Read the guide to build OWL ontologies using Protege [PDF]. Read the OWL Biomedical Ontology Tutorial [PDF]. At this juncture you will be able to assess your suitability for the project.

What next?
Download the current version of ONTODerm and open it in protégé. Once you are ready to add new terms to ONTODerm or modify or improve the terms already present in ONTODerm contact me. For combined development, software professional use a system called cvs. I use the same system to track changes (Since many contributors add to the code we have to keep track of who added what) to ontoderm. Initial setup of cvs may be tricky for a dermatologist. But once you reach this far, I can guide you through the rest of the steps needed to install and use cvs.

If you are a software developer...
ONTODerm is a domain ontology for dermatology which may be useful for ontology driven biomedical applications. I am presently working on 3 tools.

Virtual Dermatologist: A diagnostic application for Dermatology which I wrote during the pre-ontology days, but based on the core ontology principles. I am planning to redesign the entire application using ONTODerm. (Java Servlet)
SLISED: Semantic LIterature SEarch for Dermatology. (Planning) This is a literature search application using Sesame from openrdf.org. (Java Servlet + Sesame)
TERM LOOKUP: Search ONTODerm for dermatological terms using the RDF::Core PERL library. (PERL + RDF::Core)

The source codes of all the above applications are available to those interested in combined development from the cvs server www.freepository.com . Please register there and send me a request with your background and proposals.