FaceBase

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.

Abstract: The mouse, as a genetically defined and easily manipulated model organism, has played a critical role in unraveling the mechanisms of craniofacial development and dysmorphology. While numerous gene knockout strains that display craniofacial abnormalities and essential recombinase tool strains with craniofacial-specific expression have been generated, many are absent from public repositories. Large-scale, international resource-generating initiatives promise to address this concern, providing a comprehensive set of targeted mutations and a suite of new Cre driver strains. In addition, panels of genetically defined strains provide tools to dissect the multigenic, complex nature of craniofacial development, adding to the foundation of information gained from single gene studies. Continued progress will require awareness and access to these essential mouse resources. In this review, current mouse resources, large-scale efforts, and potential future directions will be outlined and discussed.

Abstract: Different interpretations of the term “Cleft Lip” by clinicians and developmental biologists referred to by Wang et al. (2014) in the introduction of their article on evaluation and integration of disparate classification systems for clefts of the lip, mirrors my observations in an article on nomenclature in craniofacial embryology (Koul, 2006). In that article, I had proposed a change of terminology of pre-palate/primary palate/anterior palate to Antenasal Segment, to remove the ambiguity of interpretations of differing terms for components that are involved in “Cleft Lip” formation. This antenasal segment comprises of (1) antenasal labium, (2) antenasal gnathia, (3) and antenasal palate in the completed face. This new terminology accurately identifies the embryological origin (naso-medial process) and structural precedence of this segment to the nasal frame of reference. The term antenasal segment reconciles the pre-natal and post-natal terminologies, facilitating a correct interpretation of the term “Cleft Lip” for classification and registration of the clefts of this segment in a manner that would reflect its etiologic and phenotypic variability. Evaluation and integration of various classification systems of “Cleft Lip” by Wang et al. is an important contribution to the process of making informed decisions for a cleft lip patient or a group of patients. The ontology of craniofacial development and malformation (OCDM) being developed as a part of NIDCR funded research network, Facebase will facilitate integration of such data for translational craniofacial research (Brinkley et al., 2013; Mejino et al., 2013). A standardized and uniform recording and retrieval of patient data is of fundamental importance for permitting interoperability with multiple resources in an efficient and effective manner. Toward this end, the classification schemes of cleft lip and palate need to be evaluated not only for their accuracy but also for optimization with electronic data registration and retrieval for multiple applications. With the introduction of medical information technology in clinical medicine, a global computerized classification system for cleft lip and palate is a prerequisite for achieving standardization and uniformity. Koul's classification of cleft lip and palate (Koul, 2007) expresses clinical data with a universally accepted natural language that corresponds to the nomenclature of the affected structures of the clefts. The use of this natural language in upper and lower case formats in combination with other keyboard signs and symbols makes this system of classification computer- processable. These are interpretation of facts, further verification and comparison studies are required to arrive at definitive conclusions. A universal, computerized classification system of cleft lip and palate will facilitate efficient and effective recording and retrieval of craniofacial data for translational research.

Abstract: In this paper we describe an ontological scheme for representing anatomical entities undergoing morphological transformation and changes in phenotype during prenatal development This is a proposed component of the Anatomical Transformation Abstraction (ATA) of the Foundational Model of Anatomy (FMA) Ontology that was created to provide an ontological framework for capturing knowledge about human development from the zygote to postnatal life It is designed to initially describe the structural properties of the anatomical entities that participate in human development and then enhance their description with developmental properties, such as temporal attributes and developmental processes This approach facilitates the correlation and integration of the classical but static representation of embryology with the evolving novel concepts of developmental biology, which primarily deals with the experimental data on the mechanisms of embryogenesis and organogenesis This is important for describing and understanding the underlying processes involved in structural malformations In this study we focused on the development of the lips and the palate in conjunction with our work on the pathogenesis and classification of cleft lip and palate (CL/P) in the FaceBase program Our aim here is to create the Craniofacial Human Development Ontology (CHDO) to support the Ontology of Craniofacial Development and Malformation (OCDM), which provides the infrastructure for integrating multiple and disparate craniofacial data generated by FaceBase researchers