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|  Oregon Health and Science University |
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| Oregon Health and Science University |
The OHSU ontology development group is an interdisciplinary group lead by Assistant Professors Dr. Carlo Torniai and Dr. Melissa Haendel. An ontology is a formal representation about a set of concepts and relationships between those concepts within a given domain. Ontologies are developed in many different domains, but share four common goals: 1) Represent what is known, 2) Infer what is not otherwise obvious, 3) promote the discovery of new insights from exploration and manipulation of complex data and 4) provide context and intuitive navigation during the exploration process.
The Ontology Development Group was brought together at the OHSU Library to build ontologies for the eagle-i resource discovery platform (eagle-i.net). The group contributes to ontology development within the context of the Open Biological Ontologies Foundry consortium of ontologies, and participates in a diversity of projects to represent knowledge and analyze data in biomedicine. Our research is currently directed towards ontological representation of persons and their roles and expertise in research, biological specimens and pathological anatomy, reagents and cell lines, cross-species anatomy, best practices for use of ontologies in software applications and publication of Linked Open Data, and ontology reuse and interoperability.
The OHSU Ontology Development Group serves the OHSU research community in support of their data management and analysis needs.
Member:
Haendel, Melissa, PhD
Role:
Associate Professor
Member:
Vasilevsky, Nicole, PhD
Role:
Project Manager & Biocurator
An ontology is a formal representation about a set of concepts and relationships between those concepts within a given domain. Ontologies are developed in many different domains, but share four common goals: 1) Represent what is known, 2) Infer what is not otherwise obvious, 3) promote the discovery of new insights from exploration and manipulation of complex data and 4) provide context and intuitive navigation during the exploration process.
The members of the Ontology Development Group are available for de novo ontology development or consultation on existing projects.
Building Nipype pipeline to perform image registration and annotations for MRI images.
The ontologically based molecular signature (OBAMS) is a method to identify novel biomarkers and infers biological functions as characteristic of particular immune cell types. This method finds molecular signatures for cell types based on mapping biological samples to the Cell Ontology (CL) and navigating the space of all possible pairwise comparisons between cell types to find genes whose expression is core to a particular cell type’s identity. Expression data available from the Immunological Genome project (IGP) (www.immgen.org) was evaluated to identify unique biomarkers of mature B cell subtypes. The Gene Ontology was used to cluster cell types by shared biological processes in order to find candidate genes responsible for somatic hypermutation in germinal center B cells. This algorithm can be applied to other cell types as well.
"Protégé is a free, open source ontology editor and knowledge-base framework.
The Protégé platform supports two main ways of modeling ontologies via the Protégé-Frames and Protégé-OWL editors. Protégé ontologies can be exported into a variety of formats including RDF(S), OWL, and XML Schema.
Protégé is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development."