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:
- Human craniofacial anatomy and development
- Mouse craniofacial anatomy and development
- Zebrafish craniofacial anatomy and developmemnt
- Craniofacial malformations in human, mouse and zebrafish
- Mappings between human, mouse and zebrafish anatomy
- 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.
- Download latest release: OCDM version 2.0.0.
- You can also download the latest OCDM release from this link: http://sig.biostr.washington.edu/share/downloads/ocdm/release/latest/ocdm.zip
- Change log
The OCDM is written in OWL 2, and consists of an umbrella ontology, which imports a set of sub-ontologies. Currently these ontologies are:
|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
For further information and to download the latest version see the project webpage.