The ontology of craniofacial development and malformation for translational craniofacial research

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

Recent insights into the morphological diversity in the amniote primary and secondary palates

“…Many recent reviews have performed an exemplary job of covering the underlying molecular signaling in primary and secondary palate development (Cox, 2004; Hilliard et al, 2005; Szabo-Rogers et al, 2010; Dixon et al, 2011; Bush and Jiang, 2012; He and Chen, 2012; Brinkley et al, 2013; Hall, 2014; Lane and Kaartinen, 2014). Therefore, this commentary will instead compare the mechanisms of facial morphogenesis during amniote ontogeny.…”

The FaceBase Consortium: A comprehensive resource for craniofacial researchers

“…As part of FaceBase 1, this group designed and partially implemented the ontology of craniofacial development and malformation (OCDM), based on their foundational model of anatomy ontology (FMA). The FaceBase 1 version of the OCDM consisted of components for representing human and mouse adult and developmental anatomy and malformations, as well as mappings between homologous structures in the two organisms, with emphasis on those structures involved in cleft lip and palate ( Brinkley et al, 2013 ; Mejino et al, 2013 ; Wang et al, 2014 ; Koul, 2015 ). In FaceBase 2, the OCDM is being enhanced to include conditions of interest to FaceBase 2 researchers, such as human, mouse and zebrafish facial, palatal and cranial vault development, and dysmorphology such as craniosynostosis, midface hypoplasia, frontonasal dysplasia, craniofacial microsomia and microtia ( Mejino et al, 2015 ).…”

The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data

“…In addition, concerted efforts to compile craniofacial data, across broad scientific fields, are also underway, notably through the FaceBase Consortium (https://www.facebase.org) (Hochheiser et al, 2011) and Jackson Laboratories to maintain specific stocks of craniofacial mutations (https://www.jax.org/research-and-faculty/tools/mouse-resource-for-craniofacial-research). Such resources provide a comprehensive database of developmental, anatomical, and genetic information related to both human and animal models of craniofacial development (Brinkley et al, 2013a; Brinkley et al, 2013b; Eames et al, 2013). …”