The mouse-human anatomy ontology mapping project - PubMed (original) (raw)

The mouse-human anatomy ontology mapping project

Terry F Hayamizu et al. Database (Oxford). 2012.

Abstract

The overall objective of the Mouse-Human Anatomy Project (MHAP) was to facilitate the mapping and harmonization of anatomical terms used for mouse and human models by Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI). The anatomy resources designated for this study were the Adult Mouse Anatomy (MA) ontology and the set of anatomy concepts contained in the NCI Thesaurus (NCIt). Several methods and software tools were identified and evaluated, then used to conduct an in-depth comparative analysis of the anatomy ontologies. Matches between mouse and human anatomy terms were determined and validated, resulting in a highly curated set of mappings between the two ontologies that has been used by other resources. These mappings will enable linking of data from mouse and human. As the anatomy ontologies have been expanded and refined, the mappings have been updated accordingly. Insights are presented into the overall process of comparing and mapping between ontologies, which may prove useful for further comparative analyses and ontology mapping efforts, especially those involving anatomy ontologies. Finally, issues concerning further development of the ontologies, updates to the mapping files, and possible additional applications and significance were considered. DATABASE URL: http://obofoundry.org/cgi-bin/detail.cgi?id=ma2ncit.

PubMed Disclaimer

Figures

Figure 1.

Figure 1.

Preliminary identification of equivalent terms using a combination of automated and manual curation approaches.

Figure 2.

Figure 2.

Task-specific performance features at the time of the tools evaluation. Since that time, both OBO-Edit and Protégé have added functionality in the form of new features as well as with plug-ins.

Figure 3.

Figure 3.

Mouse and human anatomy ontology terms, and corresponding matched sets of terms, at start of study (A), after extension and harmonization of the ontologies (B) and after recent updates to the files (C).

Figure 4.

Figure 4.

Example of the extension and harmonization process. (A) Representation of the urinary bladder in the MA (left) and NCIt (right) prior to the revision process. Terms in black, linked by blue lines, represent matched sets of terms; terms in red are those not shared by the other ontology. (B) Urinary bladder concept subtrees after extension and harmonization of the ontologies. Terms in blue are those that have been added, with blue lines indicating corresponding terms in the other ontology.

Figure 5.

Figure 5.

Summary of results from cross-analysis using Uberon xrefs.

Similar articles

Cited by

References

    1. von Eschenbach AC, Buetow K. Cancer informatics vision: caBIG. Cancer Inform. 2006;2:22–24. - PMC - PubMed
    1. Finger JH, Smith CM, Hayamizu TF, et al. The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res. 2011;39(Suppl. 1):D835–D841. - PMC - PubMed
    1. Hayamizu TF, Mangan M, Corradi JP, et al. The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol. 2005;6:R29. - PMC - PubMed
    1. Schofield PN, Bard JB, Booth C, et al. Pathbase: a database of mutant mouse pathology. Nucleic Acids Res. 2004;32:D512–D515. - PMC - PubMed
    1. Smith CL, Goldsmith CW, Eppig JT. The Mammalian Phenotype Ontology as a tool for annotating, analyzing and comparing phenotypic information. Genome Biol. 2005;6:R7. - PMC - PubMed

Publication types

MeSH terms

LinkOut - more resources