OCDM Change Log

This page is intended to give a brief summary of the content changes to the Ontology of Craniofacial Development and Malformation (OCDM) by version.

Version 1.1.0

Summary of work on CHO musculoskeletal system

In version 1.1 of the OCDM, we have extended content in Craniofacial Human Ontology (CHO) to include the taxonomic and spatio-structural representation of the entire musculoskeletal system of the head (muscles, bones, cartilages, skeletal ligaments and joints). The work entailed the addition of over 1500 classes (represented by >2000 terms, either as preferred term, synonym or non-English equivalent) and the instantiation of about 15000 relationships between the classes using 34 properties, such as parthood (regional partonomy, constitutional partonomy and membership), connectivity (articulation, attachment, continuity, innervation [nerve supply]) and location (qualitative coordinate relationships such as anterior to, posterior to, superior to, inferior to, medial to, lateral to, etc., and containment).

Version 1.2.0

Summary of work on CMO musculoskeletal system

In version 1.2 of the OCDM, we have extended content in Craniofacial Mouse Ontology (CHO) to include the taxonomic and spatio-structural representation of the musculoskeletal system of the head (muscles, bones, cartilages, skeletal ligaments and joints). The work entailed the deletion of 809 classes, which represent anatomical entities derived from the CHO that are not found in the mouse (e.g. canine tooth, glabella, uvula)and the addition of over 790 classes which represent anatomical entities that are in the mouse but not in the human (squamosal bone, zygomaticomandibularis, intermolar eminence) and the instantiation of about 2000 relationships between the classes using spatio-structural properties, such as parthood (regional partonomy, constitutional partonomy and membership), connectivity (articulation, attachment, continuity (qualitative coordinate relationships such as anterior to, posterior to, superior to, inferior to, medial to, lateral to, etc., and containment).

Version 1.3.0

In version 1.3 of the OCDM, a new sub-ontology, the Craniofacial Zebrafish Ontology (CZO) was created and added to the OCDM. Its ontological framework is based on the CHO and CMO and was populated with the same high-level classes as in the CHO and CMO to build its class hierarchy. In this work we focused on the taxonomic and spatio-structural representation of the canonical musculoskeletal system of the adult head (muscles, bones, cartilages, skeletal ligaments and joints). The work entailed the creation of 624 classes, using specific zebrafish terms from the Zebrafish Anatomy Ontology (ZFIN) where applicable, and the instantiation of about 2900 relationships between the classes using 26 spatio-structural properties (object properties), such as parthood (regional partonomy, constitutional partonomy and membership), connectivity (articulation, attachment, continuity (qualitative coordinate relationships such as anterior to, posterior to, superior to, inferior to, medial to, lateral to, etc., and containment), as well data-type properties, such as dimension, mass and species.

Version 1.4.0

Summary of work on CHO musculoskeletal system development

We have extended content in Craniofacial Human Ontology (CHO) to include the taxonomic, spatio-structural and developmental representation of fetal musculoskeletal system of the head (muscles, bones, cartilages, skeletal ligaments and joints) and their embryonic precursors and predecessors. The work focused on the parthood and spatial relationships of fetal bones, muscles, cartilages and sutures, as well as on the developmental properties of these structures, such as derivation, transformation and maturation.

In this version of the OCDM, we have also incorporated mouse and zebrafish terms that were requested or suggested by some members of the FACEBASE consortium.

Version 1.5.0

Summary of work on CMO musculoskeletal system development

We have extended content in Craniofacial Mouse Ontology (CMO) to include the taxonomic, spatio-structural and developmental representation of fetal musculoskeletal system of the head (muscles, bones, cartilages, skeletal ligaments and joints) and their embryonic precursors and predecessors where available. The work focused on the parthood and spatial relationships of fetal bones, muscles, cartilages and sutures, as well as on the developmental properties of these structures, such as derivation, transformation and maturation. We have likewise updated representation of mouse embryo days and Theiler stages and their correspondences.

In this version of the OCDM, we have also incorporated mouse and zebrafish anatomy terms and human malformation phenotypes that were requested or suggested by some members of the FACEBASE consortium.

Version 1.6.0

Summary of work on CZO musculoskeletal system development

We have extended content in Craniofacial Zebrafish Ontology (CZO) to include the taxonomic, spatio-structural and developmental representation of developmental musculoskeletal system of the head (muscles, bones, cartilages and joints) and their precursors and predecessors where available. The work focused on the parthood and spatial relationships of developmental (embryonic and larval) bones, muscles, cartilages and sutures, as well as on the developmental properties of these structures, such as derivation, transformation and maturation. We likewise added muscle insertion and muscle origin relationships between muscles and bones during embryonic, larval, juvenile and adult stages. We updated representation of developmental ages and stages based on the suggestions of FaceBase zebrafish domain experts.

In this version of the OCDM, we have also incorporated mouse and zebrafish anatomy terms that were requested or suggested by some members of the FaceBase consortium.

Version 1.7.0 - January 30, 2017

Summary of work on CHMMO comparative anatomy mapping

The work focused on homology mappings between human and mouse developmental and postnatal anatomical entities in Craniofacial Human Mouse Mouse Ontology (CHMMO). The mappings for developmental entities include embryonic development from zygote to embryonic precursors, where available, of components of musculoskeletal system of the head (muscles, bones, cartilages, skeletal ligaments and joints). Sources for mapping information was derived from our domain experts, as well as from established published work, such as textbooks and journal publications. For this deliverable, mappings were carried out at the gross anatomical level but can be extended to microscopic level if and when required.

Version 1.8.0 - June 27, 2017

Summary of work on CHZMO comparative anatomy mapping

The work primarily focused on homology mappings between human and zebrafish developmental and adult anatomical entities in Craniofacial Human Zebrafish Mouse Ontology (CHZMO). Mappings include developmental entities, from the zygote to larval structures at progressive stages of development, with emphasis on embryonic and larval precursors of components of the musculoskeletal system of the head (muscles, bones, cartilages, skeletal ligaments and joints). Provisional mappings were initially carried out based on similar or same names and then submitted to FaceBase domain experts for verification. We likewise consulted the literature for homology evidence, either based on direct molecular studies or inferred vertebrate Bauplan. Bi-directional one to one and uni-directional one to null mappings were recorded in this work. Additional homology mappings for human and mouse structures (CHMMO) were also included in this version.

Version 1.9.0 - Nov 29, 2017

Summary of work on CHMO

In this work the emphasis is on cranial dysmorphologies, and in particular, the ontological representation of the phenotypic and genotypic abnormalities associated with craniofacial microsomias which are observed in a number of genetic syndromes, such as Apert’s, and Treacher-Collins syndromes. We initially focused on creating a proof of concept whereby we described a number of syndromes (e.g. Apert’s) and expressed their attributes as phenotypic abnormalities (e.g. bicoronal craniosynostosis) and as genotypic abnormalities (e.g. Fibroblast Growth Factor Receptor 2 [FGFR2] abnormality). Where available, we used external sources, such as HPO and DOID, for phenotypic terms and used their IRIs as the primary identifiers. We also elucidated on the attributes of these phenotypic abnormalities in terms of identifying the structures involved in the malformation. For genotypic abnormalities, we created links to external databases such as UnitPro to identify the protein involved and all other relevant genotypic information or data associated with that particular abnormality. This exercise allowed us to refine our objective for this milestone, which is to create a comprehensive representation of phenotypic abnormalities, using existing ontologies or inventing our own, that can serve as search terms to external sources, such as OMIM and London Dysmorphology database, which would then provide the possible candidate syndromes associated with those abnormalities.

Version 1.10.0 - March 30, 2018

Summary of work on CMMO

In this work we created the craniofacial mouse malformation ontology. As in the human version, the emphasis was on cranial dysmorphologies, and in particular, the ontological representation of the phenotypic abnormalities as reported in the literature, starting with published reports from members of the FaceBase consortium. Where available, we used MPO (Mammalian Phenotype Ontology) terms and their IRIs as the primary identifiers. Although the main focus of work was on description of the different phenotypic abnormalities and pathological entities associated with craniofacial microsomias, we likewise established the ontological framework for incorporating functional disorders associated with the abnormalities, such as hearing loss and blindness. We have also created properties (is_pathological_transformation_of and has_location) that link both phenotypic abnormalities and pathological structures to the corresponding canonical anatomical structures to provide correlation of these pathologies to developmental and cross-species associations.

Version 1.11.0 - August 30, 2018

Summary of work on CZMO

In this work we created the ontology of craniofacial malformation ontology for the zebrafish, called Craniofacial Zebrafish Malformation Ontology or CZMO in short. We applied the same ontological framework we used for the human and mouse versions in representing phenotypic abnormalities and pathological anatomical entities in the zebrafish. The focus was on cranial dysmorphologies, with emphasis largely on the malformation of craniofacial bones, cartilages, muscles and joints, from developmental to adult stages. Since there is no established zebrafish ontology on phenotypic abnormalities, we largely derived content from publications and inputs from domain experts.