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Ontology of Craniofacial Development and Malformation (OCDM) | FaceBase

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Ontology of Craniofacial Development and Malformation (OCDM)

To satisfy the need for standardized terminologies and intelligent data integration, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including:

Project Features

Project Lead:
Onard Mejino
Project members:
Todd Detwiler
Related projects:
Foundational Models of Anatomy , OCDM Browser
Funding Sources
FaceBase 1, FaceBase 2
See Publications section of the project page.


The Ontology of Craniofacial Development and Malformation (OCDM) is 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 human, mouse and zebrafish, mappings between homologous structures in the different species, and associated malformations. 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.

OCDM version 2.0.0

Here is some information on the latest version of OCDM (2.0.0): The Craniofacial Human Zebrafish Malformation Mapping Ontology (CHZMMO) was created to capture the homology or similarities between the human and the zebrafish phenotypic abnormalities. The CHZMMO incorporates both the Craniofacial Human Malformation Ontology (CHMO) and the Craniofacial Zebrafish Malformation Ontology (CZMO) and we used the same mapping tab that allowed us to previously correlate human and mouse phenotypic malformations and pathological structures. As in the CH3MO we generated the mapping by first selecting the human phenotypic abnormality from the CHMO (e.g. Craniosynostosis), then identifying the corresponding homologous zebrafish phenotype from the CZMO (e.g. Craniosynostosis [Danio rerio]). The process can start either from the human or the zebrafish phenotype. Mapping validation based on published report/s are recorded in the reference annotation field.

Important Links:

Related Ontologies

The OCDM is written in OWL 2, and consists of an umbrella ontology, which imports a set of sub-ontologies. Currently these ontologies are:

Category Name Description
OCDM Ontology of Craniofacial Development and Malformation Umbrella ontology that imports all of the other sub-ontologies
CHO Craniofacial Human Ontology Normal human craniofacial anatomy, both adult and developmental, derived from our Foundational Model of Anatomy (FMA)
CMO Craniofacial Mouse Ontology Normal mouse craniofacial anatomy, both adult and developmental
CZO Craniofacial Zebrafish Ontology Normal zebrafish craniofacial anatomy, both adult and developmental
CHMO Craniofacial Human Malformation Ontology Abnormal human craniofacial anatomy and phenotypes
CMMO Craniofacial Mouse Malformation Ontology Abnormal mouse craniofacial anatomy and phenotypes
CHMMO Craniofacial Human-Mouse Mappings Ontology Mappings of classes in the CHO to related (homologous) structures in the CMO
CHM3O Craniofacial Human-Mouse Malformation Mappings Ontology Mappings of classes in the CHMO to related (homologous) structures in the CMMO
AEO Attribute Entity Ontology Ontology which contains measurements and other descriptors
CET Craniofacial External Terminology Mappings from external ontologies that don't easily fit into the OCDM

All ontologies are in Protege OWL format, and can be loaded into the latest version of Protege . Ontologies refer to other ontologies via the OWL import mechanism.

For further information and to download the latest version see the project webpage .