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The ontology of craniofacial development and malformation for translational craniofacial research.

ABSTRACT: 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.

SUBMITTER: Brinkley JF

PROVIDER: S-EPMC4041627 | biostudies-other | 2013 Nov

REPOSITORIES: biostudies-other

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The ontology of craniofacial development and malformation for translational craniofacial research.

Brinkley J F JF Borromeo C C Clarkson M M Cox T C TC Cunningham M J MJ Detwiler L T LT Heike C L CL Hochheiser H H Mejino J L V JL Travillian R S RS Shapiro L G LG

American journal of medical genetics. Part C, Seminars in medical genetics 20131004 4

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 crani ...[more]

PMID: 24124010

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Project description:BackgroundWeb-based resources and social media platforms play an increasingly important role in health-related knowledge and experience sharing. There is a growing interest in the use of these novel data sources for epidemiological surveillance of substance use behaviors and trends.ObjectiveThe key aims were to describe the development and application of the drug abuse ontology (DAO) as a framework for analyzing web-based and social media data to inform public health and substance use research in the following areas: determining user knowledge, attitudes, and behaviors related to nonmedical use of buprenorphine and illicitly manufactured opioids through the analysis of web forum data Prescription Drug Abuse Online Surveillance; analyzing patterns and trends of cannabis product use in the context of evolving cannabis legalization policies in the United States through analysis of Twitter and web forum data (eDrugTrends); assessing trends in the availability of novel synthetic opioids through the analysis of cryptomarket data (eDarkTrends); and analyzing COVID-19 pandemic trends in social media data related to 13 states in the United States as per Mental Health America reports.MethodsThe domain and scope of the DAO were defined using competency questions from popular ontology methodology (101 ontology development). The 101 method includes determining the domain and scope of ontology, reusing existing knowledge, enumerating important terms in ontology, defining the classes, their properties and creating instances of the classes. The quality of the ontology was evaluated using a set of tools and best practices recognized by the semantic web community and the artificial intelligence community that engage in natural language processing.ResultsThe current version of the DAO comprises 315 classes, 31 relationships, and 814 instances among the classes. The ontology is flexible and can easily accommodate new concepts. The integration of the ontology with machine learning algorithms dramatically decreased the false alarm rate by adding external knowledge to the machine learning process. The ontology is recurrently updated to capture evolving concepts in different contexts and applied to analyze data related to social media and dark web marketplaces.ConclusionsThe DAO provides a powerful framework and a useful resource that can be expanded and adapted to a wide range of substance use and mental health domains to help advance big data analytics of web-based data for substance use epidemiology research.

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Dataset Information

The ontology of craniofacial development and malformation for translational craniofacial research.

Publications

The ontology of craniofacial development and malformation for translational craniofacial research.

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