This document introduces the use of the OWL Web Ontology
Language for
medical and biosciences applications. The focus is basic ideas
and the approach for creation of collaborative
applications. Use of Protégé Java API's for accessing data within
OWL documents is demonstrated using the BioPax Level 2 Ontology.
The
intended audience is people in science, medicine, or software
engineering wanting to
understand the basics of this area and software developers new to the
technology.
The Web Ontology Language OWL represents the meanings of terms
in
vocabularies and the relationships between those terms in a way that is
suitable for processing by software. Organizing information using OWL
can be very powerful because it can eliminate the need for applications
to embed logic specific to their own software. The logic can be
externalized to the OWL data, which can be authored by subject matter
experts and updated without changing application source code. OWL
is particularly useful for representing large volumes of complex data,
such as that found in medicine and biosciences. In
this introductory article I will describes the basics of OWL and
demonstrate it somes uses with medical and biology examples.
The representation of terms from vocabularies together with the relationships is called an ontology. Here the term ontology has been borrowed from philosophy where it refers to the art of describing the various kinds of things that exist and how they are related to one another. OWL is developed as an extension of the Resource Description Framework (RDF), which is a language for representing resources, such as RSS feeds. See this site's Frequently Asked Questions for more detail on RSS feeds.
OWL differs from most other XML variants and XML Schema itself in that they are use to define the structure of information within a document but not to support reasoning outside their own context. One of goals of the OWL initiative from the W3C is to encourage the development of ontologies by various groups with specific subject matter expertise, such as medical and bioscience groups, and at the same time encourage the development of generic OWL processing and reasoning tools that process and the specific ontologies.
There are a number of ontology projects that exist at present. Here
are some of them.
| Project | Ontology |
|---|---|
| BioPAX Level 2 covers metabolic pathways16 | Metabolic Pathways |
| US National Library of Medicine, Unified Medical Language System18 | General Medical Knowledge |
| The Open Biomedical Ontologies21 project has a number of ontologies in medical and biological areas. It is sponsored by The National Center for Biomedical Ontology24 | Animal natural history and life history |
| Arabidopsis development and gross anatomy | |
| Biological imaging methods | |
| Biological process | |
| BRENDA tissue / enzyme source | |
| C. elegans development and gross anatomy | |
| Cell type | |
| Cellular component | |
| Cereal plant development, gross anatomy, and traits | |
| Chemical entities of biological interest | |
| Dictyostelium discoideum anatomy | |
| Drosophila development and gross anatomy | |
| Event (INOH pathway ontology) and codes | |
| eVOC (Expressed Sequence Annotation for Humans) | |
| FlyBase Controlled Vocabulary | |
| Fungal gross anatomy | |
| Habronattus courtship | |
| Human developmental anatomy and disease | |
| Loggerhead nesting | |
| Maize gross anatomy | |
| Mammalian phenotype | |
| Medaka fish anatomy and development | |
| MESH | |
| Microarray experimental conditions | |
| Molecular function | |
| Molecule role (INOH Protein name/family name ontology) | |
| Mosquito gross anatomy | |
| Mouse adult gross anatomy | |
| Mouse gross anatomy and development | |
| Mouse pathology | |
| Multiple alignment1 | |
| NCBI organismal classification and | |
| Thesaurus | |
| Pathways | |
| Physico-chemical methods, properties, and processes | |
| Plant environmental conditions, growth, developmental stage, and structure | |
| Plasmodium life cycle | |
| Protein covalent bond, domain, and Protein-protein interaction | |
| Sequence types and features | |
| Systems Biology | |
| UniProt taxonomy | |
| Zebrafish anatomy and development | |
| The Gene Ontology Project22 | Genes |
| Standards and Ontologies for Functional Genomics27 | Human and mouse anatomies |
| MGED Open Source Projects28 | Microarray Gene Expression Data |
| Plant Ontology™ Consortium27 | Plant structures and growth and developmental stages |
| The Trial Bank Project30 | Clinical trial database |
| Case Western Reserve University, Matthias Samwald37 | Psychoactive Drug Screening Program Ki database |