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Review
. 2013 Nov;163C(4):232-45.
doi: 10.1002/ajmg.c.31377. Epub 2013 Oct 4.

The ontology of craniofacial development and malformation for translational craniofacial research

J F Brinkley, C Borromeo, M Clarkson, T C Cox, M J Cunningham, L T Detwiler, C L Heike, H Hochheiser, J L V Mejino, R S Travillian, L G Shapiro
Review

The ontology of craniofacial development and malformation for translational craniofacial research

J F Brinkley et al. Am J Med Genet C Semin Med Genet. 2013 Nov.

Abstract

We introduce the Ontology of Craniofacial Development and Malformation (OCDM) as a mechanism for representing knowledge about craniofacial development and malformation, and for using that knowledge to facilitate integrating craniofacial data obtained via multiple techniques from multiple labs and at multiple levels of granularity. The OCDM is a project of the NIDCR-sponsored FaceBase Consortium, whose goal is to promote and enable research into the genetic and epigenetic causes of specific craniofacial abnormalities through the provision of publicly accessible, integrated craniofacial data. However, the OCDM should be usable for integrating any web-accessible craniofacial data, not just those data available through FaceBase. The OCDM is based on the Foundational Model of Anatomy (FMA), our comprehensive ontology of canonical human adult anatomy, and includes modules to represent adult and developmental craniofacial anatomy in both human and mouse, mappings between homologous structures in human and mouse, and associated malformations. We describe these modules, as well as prototype uses of the OCDM for integrating craniofacial data. By using the terms from the OCDM to annotate data, and by combining queries over the ontology with those over annotated data, it becomes possible to create "intelligent" queries that can, for example, find gene expression data obtained from mouse structures that are precursors to homologous human structures involved in malformations such as cleft lip. We suggest that the OCDM can be useful not only for integrating craniofacial data, but also for expressing new knowledge gained from analyzing the integrated data.

Keywords: craniofacial development and malformation; data integration; knowledge representation; ontologies.

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Figures

Figure 1
Figure 1
Schematic diagram of the regional parts of the upper lip
Figure 2
Figure 2
OCDM component ontologies
Figure 3
Figure 3
Regional (R) and constitutional (C) parts of the upper lip as shown in our OCDM ontology viewer. Clicking a horizontal arrow opens up more detail.
Figure 4
Figure 4
Class inheritance (is_a) hierarchy of developmental structures
Figure 5
Figure 5
Schematic diagram of the development of the hard palate and upper lip as represented in the OCDM. Grey boxes are classes, labeled lines are relations.
Figure 6
Figure 6
Classes and relations involved in the genesis of cleft upper lip, as represented in the OCDM.
Figure 7
Figure 7
FaceBase search interface. Clicking on one of the categories in the top row (e.g. Anatomy) brings up a set of terms from the OCDM. The user has checked one of these terms (Medial nasal process), which retrieves the three mouse datasets annotated with this term.
See this image and copyright information in PMC

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