Home

Biological Ontologies

Various Biologial Ontology Websites, vr.153, April 2006, Oliver Bromley
  Link Description
BioCASE Thesaurus
 Lists of Taxa and Collections
Biological Process
 5029 metabolic terms
Neuronal Neurotransmission - at the levels of the molecule, the supra-molecular assembly, the neuronal cell and the neuronal network
Genes A controlled vocabulary that can be applied to all organisms even as knowledge of gene and protein roles in cells is accumulating and changing
Plants
 Plant Anatomy (morphology, organs, tissue and cell types)
Growth stages (plant growth and developmental stages)
Gene Ontology (GO)*
Molecular function, Biological process, Cellular component
Gene Browser
 Gene_Ontology
biological_process [GO:0008150] (9770 genes, 18833 annotations)
behavior + biological_process unknown cellular process + development + obsolete biological process + physiological process + regulation of biological process + viral life cycle +
Biological Ontology
In view of the diversity and complexity of biological information, it is extremely unlikely that a single, overarching biological ontology will be developed. Rather, it is the case that ontologies describing discrete areas of biology are being developed.
Tambis Project
 TAMBIS aims to provide transparent information retrieval and filtering from biological information services by building a homogenising layer on top of the different sources. This layer uses a mediator and many source wrappers to create the illusion of one all encompassing data source.
     
  Tools  
     
Owl The OWL Plugin is a comprehensive OWL Editor (OWL = Web Ontology Language) based on the Protégé ontology development platform
Owl XML Example OWL defines syntax and semantics for an ontology language that can be used on the web for these purposes.

OWL documents are typically stored in terms of an XML/RDF file. However, these files are awkward to read, and few people will want to edit them directly. Much more relevant than the syntax of OWL documents is the catalog of modeling elements that it provides. OWL ontologies roughly contain three types of resources:

Classes define concepts from the domain (e.g., the class Koala)
Individuals represent specific instances of classes (e.g., the pink Koala I just saw in my garden)
Properties define the values that each individual can take (e.g., the specific Koala has the color pink)
Other modeling languages such as UML or XML have similar modeling constructs, and basically OWL can be compared to them. However, the strength of OWL is that it allows us to specify the meaning of classes and properties in various ways, so that intelligent programs can reason about it.