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.