Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Dec 15;26(24):3112-8.
doi: 10.1093/bioinformatics/btq578. Epub 2010 Oct 22.

Interoperability between phenotype and anatomy ontologies

Robert Hoehndorf  1 , Anika Oellrich, Dietrich Rebholz-Schuhmann
Affiliations

Interoperability between phenotype and anatomy ontologies

Robert Hoehndorf et al. Bioinformatics. .

Abstract

Motivation: Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning.

Results: We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge.

Availability: http://bioonto.de/pmwiki.php/Main/PheneOntology.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
The first distinction is drawn between phenes of objects and phenes of processes. We primarily classify phenes of objects into four main categories: structural, functional, qualitative and participatory phenes. Under the structural phenes, we show possible further classifications based on the relations we use in our method. Qualitative phenes can be further distinguished into those where only the quality is relevant and those where the quality's value is considered.
See this image and copyright information in PMC

References

    1. Adams N, et al. The ontology of primary immunodeficiency diseases (PIDs): using PIDs to rethink the ontology of phenotypes. In: Herre H, et al., editors. Proceedings of “Ontologies in Biomedicine and Life Sciences”. Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig; 2010.
    1. Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000;25:25–29. - PMC - PubMed
    1. Bult CJ, et al. The mouse genome database (MGD): mouse biology and model systems. Nucleic Acids Res. 2008;36:D724–D728. - PMC - PubMed
    1. Courtot M, et al. Dolbear C, et al., editors. The OWL of biomedical investigations. Proceedings of the Fifth OWLED Workshop on OWL: Experiences and Directions. 2008;432 of CEUR Workshop Proceedings. Availabe at http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-432/ (last accessed date October 29, 2010)
    1. Environment Ontology Consortium. Environment Ontology (EnvO). 2008 Available at: http://www.obofoundry.org/cgi-bin/detail.cgi?id=envo (last accessed date October 29, 2010)

Publication types