The Infectious Disease Ontology in the age of COVID-19
Abstract Background Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially for those ontologies built on the design pr...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-07-01
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| Series: | Journal of Biomedical Semantics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13326-021-00245-1 |
| _version_ | 1819105348517101568 |
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| author | Shane Babcock John Beverley Lindsay G. Cowell Barry Smith |
| author_facet | Shane Babcock John Beverley Lindsay G. Cowell Barry Smith |
| author_sort | Shane Babcock |
| collection | DOAJ |
| description | Abstract Background Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially for those ontologies built on the design principles of the Open Biomedical Ontologies Foundry. These principles are exemplified by the Infectious Disease Ontology (IDO), a suite of interoperable ontology modules aiming to provide coverage of all aspects of the infectious disease domain. At its center is IDO Core, a disease- and pathogen-neutral ontology covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is extended by disease and pathogen-specific ontology modules. Results To assist the integration and analysis of COVID-19 data, and viral infectious disease data more generally, we have recently developed three new IDO extensions: IDO Virus (VIDO); the Coronavirus Infectious Disease Ontology (CIDO); and an extension of CIDO focusing on COVID-19 (IDO-COVID-19). Reflecting the fact that viruses lack cellular parts, we have introduced into IDO Core the term acellular structure to cover viruses and other acellular entities studied by virologists. We now distinguish between infectious agents – organisms with an infectious disposition – and infectious structures – acellular structures with an infectious disposition. This in turn has led to various updates and refinements of IDO Core’s content. We believe that our work on VIDO, CIDO, and IDO-COVID-19 can serve as a model for yielding greater conformance with ontology building best practices. Conclusions IDO provides a simple recipe for building new pathogen-specific ontologies in a way that allows data about novel diseases to be easily compared, along multiple dimensions, with data represented by existing disease ontologies. The IDO strategy, moreover, supports ontology coordination, providing a powerful method of data integration and sharing that allows physicians, researchers, and public health organizations to respond rapidly and efficiently to current and future public health crises. |
| first_indexed | 2024-12-22T02:20:49Z |
| format | Article |
| id | doaj.art-94c2163a9fc84d63aa3428b74163cf79 |
| institution | Directory Open Access Journal |
| issn | 2041-1480 |
| language | English |
| last_indexed | 2024-12-22T02:20:49Z |
| publishDate | 2021-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biomedical Semantics |
| spelling | doaj.art-94c2163a9fc84d63aa3428b74163cf792022-12-21T18:42:08ZengBMCJournal of Biomedical Semantics2041-14802021-07-0112112010.1186/s13326-021-00245-1The Infectious Disease Ontology in the age of COVID-19Shane Babcock0John Beverley1Lindsay G. Cowell2Barry Smith3Department of Philosophy, Niagara UniversityNational Center for Ontological Research, University at BuffaloNational Center for Ontological Research, University at BuffaloNational Center for Ontological Research, University at BuffaloAbstract Background Effective response to public health emergencies, such as we are now experiencing with COVID-19, requires data sharing across multiple disciplines and data systems. Ontologies offer a powerful data sharing tool, and this holds especially for those ontologies built on the design principles of the Open Biomedical Ontologies Foundry. These principles are exemplified by the Infectious Disease Ontology (IDO), a suite of interoperable ontology modules aiming to provide coverage of all aspects of the infectious disease domain. At its center is IDO Core, a disease- and pathogen-neutral ontology covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is extended by disease and pathogen-specific ontology modules. Results To assist the integration and analysis of COVID-19 data, and viral infectious disease data more generally, we have recently developed three new IDO extensions: IDO Virus (VIDO); the Coronavirus Infectious Disease Ontology (CIDO); and an extension of CIDO focusing on COVID-19 (IDO-COVID-19). Reflecting the fact that viruses lack cellular parts, we have introduced into IDO Core the term acellular structure to cover viruses and other acellular entities studied by virologists. We now distinguish between infectious agents – organisms with an infectious disposition – and infectious structures – acellular structures with an infectious disposition. This in turn has led to various updates and refinements of IDO Core’s content. We believe that our work on VIDO, CIDO, and IDO-COVID-19 can serve as a model for yielding greater conformance with ontology building best practices. Conclusions IDO provides a simple recipe for building new pathogen-specific ontologies in a way that allows data about novel diseases to be easily compared, along multiple dimensions, with data represented by existing disease ontologies. The IDO strategy, moreover, supports ontology coordination, providing a powerful method of data integration and sharing that allows physicians, researchers, and public health organizations to respond rapidly and efficiently to current and future public health crises.https://doi.org/10.1186/s13326-021-00245-1CoronavirusCOVID-19Infectious diseaseInfectious disease ontologyOntologyData integration |
| spellingShingle | Shane Babcock John Beverley Lindsay G. Cowell Barry Smith The Infectious Disease Ontology in the age of COVID-19 Journal of Biomedical Semantics Coronavirus COVID-19 Infectious disease Infectious disease ontology Ontology Data integration |
| title | The Infectious Disease Ontology in the age of COVID-19 |
| title_full | The Infectious Disease Ontology in the age of COVID-19 |
| title_fullStr | The Infectious Disease Ontology in the age of COVID-19 |
| title_full_unstemmed | The Infectious Disease Ontology in the age of COVID-19 |
| title_short | The Infectious Disease Ontology in the age of COVID-19 |
| title_sort | infectious disease ontology in the age of covid 19 |
| topic | Coronavirus COVID-19 Infectious disease Infectious disease ontology Ontology Data integration |
| url | https://doi.org/10.1186/s13326-021-00245-1 |
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