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Skeletome Ontology

The main role of the Skeletome ontology is improve the highly static and rigid format of the ISDS Nosology, by enabling a more flexible classification of the disorders and the integration with existing Web resources, such as the Gene Ontology, the Human Phenotype Ontology, or the NCI Thesaurus. The actual requirements of the ontology emerged from its planned application within the underlying Skeletome project, and include the following:

Common terminology
The diagnosis and management of skeletal dysplasias depends on highly specialised domain knowledge across a number of disciplines (radiography, genetics, orthopaedics, physiotherapy), which is not easily comprehensible to individual communities or hospitals. In order to enable the exchange of knowledge between experts (across languages and disciplines), patients, their families and medical staff, a common terminology is required, hence leading to a shared conceptualisation of the domain.

Data integration
Large datasets containing rich information on molecules (genes, proteins) already exist and the information relevant to skeletal dysplasias needs to be extracted and cross-referenced with the clinical data and knowledge produced by Skeletome. This requires integration both at conceptual level, as well as, at actual data/instance level.

Capturing provenance and expertise
The contributed content may take several forms, ranging from personal observations to scientific publications. Independently of the form, Skeletome requires a mechanism to keep track of the provenance of the data and knowledge (to ensure proper privacy and access control), to provide a measure of certainty of derived data and to leverage expertise from the content and to streamline the delivery of the most relevant information/queries to the most appropriate person.

While the above elements assemble a conceptual perspective of the requirements, from a technical perspective, the existence of the Skeletome ontology will enable the development of the following services:

  • semantically enhanced content annotation and integration services (eg, a repository of patient case studies linked to related evidence and Web resources - publications, radiographic data, gene databases, etc);
  • automatic ontology-driven text processing of publications leading to rich semantic annotations;
  • enhanced image classification, search and retrieval via ontology-based annotation tools;
  • creation of social networking graphs that enable identification of specific domain experts.


The latest OWL version of the ontology (Version 1.0) can be found on the following websites:

(NB: We're currently working on publishing the ontology in the NCBO BioPortal.)

High-level Description

The Skeletome ontology is an upper-level ontology re-using concepts and instances from well-known vocabularies, such as SNOMED or HPO. The structure of the ontology comprises two conceptual layers:

  • an abstract layer describing the generic features of skeletal dysplasias, such as, well established gene mutations or phenotypic characteristics
  • an instance layer modelling patient features with a possible bone dysplasia diagnosis
Both layers contain elements capturing context, provenance and temporality, in order to provide an accurate view of the facts. This structure enables the description of real-world patient cases, and, in the context of a skeletal dysplasia knowledge base: (i) tracking the evolution and medical history of a patient, (ii) connecting the patient characteristics to the generic features of the disorders, and (iii) the discovery of new generic features via statistical inference.

Bone Dysplasia




Patient–Phenotypic Characteristic


Patient–Gene Mutation




Event Context


State Context