The goal of the proposed project is to develop a community driven, open source Disease Ontology (DO) that can be used to link disparate datasets through disease concepts. We will provide a computable structure of inheritable, environmental and infectious origins of human disease to facilitate the connection of genetic data, clinical data, and symptoms through the lens of human disease. To achieve this, we will garner and encompass the lessons learned and best practices generated by the Gene Ontology (GO) Consortium. The Gene Ontology is a humanreadable, formal ontology that is community driven and provides a focal point for organizing human understanding of molecular function, biological process, and cellular localization from the perspective of a gene. Biomedical ontologies are increasingly important in biomedical research where complex data in disparate resources need to be integrated. Development of these ontologies has led to consistent standards for annotation between disparate, heterogeneous datasets, across species, and has provided a framework for computational inference and semantic interoperability. Along with GO, the Open Biomedical Ontologies (OBO) Foundry is a project designed to provide best practices for ontology development, and be a clearinghouse of ontologies that meet the Foundry's requirements. We have developed the Disease Ontology during the past few years to the point where it has been accepted to the OBO Foundry. However, there are several important hurdles that the Disease Ontology needs to overcome in order to gain widespread community acceptance and live up to its potential as a cornerstone ontology in biomedical research.
The specific aims of this project are designed to overcome these barriers to acceptance.
The aims are to: (i) develop the core Disease Ontology, organized by anatomical location, environment, infectious agent and by aberrant process, (ii) develop community engagement activities and hold annual DO design and annotation workshops, (iii) define and validate mappings between DO, UMLS, ICD, and SNOMED, (iv) based on community input, develop additional scientific use cases to further drive design and validation of DO, and (v) expanding and extending DO deeply through the merging of disease-focused ontologies such as the BIRN neurological disease ontology into the genetic/environmental and infectious disease branches of the Disease Ontology. Through scientific meetings and collaborations (for example with sequence annotation groups) DO will be distributed and vetted by the wider scientific community to ensure that DO is useful and widely adopted. We believe that DO will be an important part of the arsenal of tools that will unravel the role of genes, nutrition and environment in the development and progression of disease by providing dynamic, `arbitrarily granular'computable relationships between disease and concepts that can be mapped to disease, such as genetic associations to disease, infectious agents, symptoms and aberrant biological process.
The Disease Ontology (DO) is an open source ontology organized around inheritable diseases, environmental factors leading to disease and infectious origins of disease. The ontology will provide a computable structure to facilitate the connection of genetic data, clinical data, and symptoms from multiple databases and datasets through the lens of human disease. The Disease Ontology is a part of the Open Biomedical Ontologies (OBO) collection and is also a reference ontology in the OBO Foundry. This project is designed to extend the Disease Ontology to include community disease-focused ontologies. The DO project will also validate mappings to standard terminologies containing disease concepts such as UMLS, SNOMED-CT and ICD-9-CM.
| Peng, Kai; Xu, Wei; Zheng, Jianyong et al. (2013) The Disease and Gene Annotations (DGA): an annotation resource for human disease. Nucleic Acids Res 41:D553-60 |
| Schriml, Lynn Marie; Arze, Cesar; Nadendla, Suvarna et al. (2012) Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res 40:D940-6 |
| Xu, Wei; Wang, Huisong; Cheng, Wenqing et al. (2012) A framework for annotating human genome in disease context. PLoS One 7:e49686 |
