Submissions tagged with ontology
(67 documents)
A Bayesian Hierarchical Model to Derive Novel Gene Networks from Gene Ontology Fingerprints
We developed a Bayesian hierarchical model to identify gene networks based on the similarity score generated from comparing the gene ontology fingerprints of gene pairs. Genes in this network were …
Received 29 July 2009 15:15 UTC; Posted 29 July 2009
Posted to: Bioinformatics
Using Ontology Fingerprints to Evaluate Genome-wide Association Results
We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes…
Received 29 July 2009 15:37 UTC; Posted 29 July 2009
Posted to: Genetics & Genomics, Bioinformatics
An Advanced Clinical Ontology
This article discusses a fundamental issues of medical ontology based on ontological theory. We focus on “anatomical structure of organs” and “abnormal states in the human body”. On the basis of th…
Received 29 July 2009 08:19 UTC; Posted 29 July 2009
Posted to: Bioinformatics
Concurrent, Collaborative Ontology Building with Collaborative Protégé (CP)
Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology’s developers. An obvious solution ther…
Received 29 July 2009 16:29 UTC; Posted 29 July 2009
Posted to: Bioinformatics
Cross-Product Extensions of the Gene Ontology
The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference o…
Received 28 July 2009 21:38 UTC; Posted 29 July 2009
Posted to: Genetics & Genomics, Bioinformatics
Evolution of the Sequence Ontology terms and relationships
The Sequence Ontology is undergoing reform to meet the standards of the OBO Foundry. Here we report some of the incremental changes and improvements made to SO. We also propose new relationships to…
Received 28 July 2009 21:10 UTC; Posted 29 July 2009
Posted to: Bioinformatics
An Ontology-Based Framework for Clinical Research Databases
The Ontology-Based eXtensible data model (OBX) was developed to serve as a framework for the development of a clinical research database in the Immunology Database and Analysis Portal (ImmPort) sys…
Received 27 July 2009 22:48 UTC; Posted 28 July 2009
Posted to: Bioinformatics
An exercise on developing an ontology-epistemology about schizophrenia and neuroanatomy
This paper describes preliminary ideas on formalizing some concepts of neuroanatomy into ontological and epistemological terms. We envisage the application of this ontology on the assimilation of f…
Received 28 July 2009 01:54 UTC; Posted 28 July 2009
Posted to: Neuroscience, Bioinformatics
SNOMED CT’s Ontological Commitment
SNOMED CT is a clinical terminology that describes the meaning of terms by logical axioms. This requires an ontological commitment, i.e. precise agreements about the ontological nature of the entit…
Received 25 July 2009 19:15 UTC; Posted 27 July 2009
Posted to: Bioinformatics
Clonal Complexes in Biomedical Ontologies
An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Se-quence Typing (MLST) is a genetic techniqu…
Received 27 July 2009 19:17 UTC; Posted 27 July 2009
Posted to: Bioinformatics
