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.