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Article ; Online: Coordinating virus research

John Beverley / Shane Babcock / Gustavo Carvalho / Lindsay G. Cowell / Sebastian Duesing / Yongqun He / Regina Hurley / Eric Merrell / Richard H. Scheuermann / Barry Smith

PLoS ONE, Vol 19, Iss

The Virus Infectious Disease Ontology

2024 Volume 1

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Infectious Disease Ontology in the age of COVID-19.

Babcock, Shane / Beverley, John / Cowell, Lindsay G / Smith, Barry

Journal of biomedical semantics

2021 Volume 12, Issue 1, Page(s) 13

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 ... ...

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.
MeSH term(s)	Biological Ontologies/statistics & numerical data ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Communicable Disease Control/methods ; Communicable Disease Control/statistics & numerical data ; Communicable Diseases/epidemiology ; Communicable Diseases/therapy ; Communicable Diseases/transmission ; Computational Biology/methods ; Computational Biology/statistics & numerical data ; Data Mining/methods ; Data Mining/statistics & numerical data ; Epidemics ; Humans ; Information Dissemination/methods ; Public Health/methods ; Public Health/statistics & numerical data ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/physiology ; Semantics
Language	English
Publishing date	2021-07-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2548651-2
ISSN	2041-1480 ; 2041-1480
ISSN (online)	2041-1480
ISSN	2041-1480
DOI	10.1186/s13326-021-00245-1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Coordinating virus research: The Virus Infectious Disease Ontology.

Beverley, John / Babcock, Shane / Carvalho, Gustavo / Cowell, Lindsay G / Duesing, Sebastian / He, Yongqun / Hurley, Regina / Merrell, Eric / Scheuermann, Richard H / Smith, Barry

PloS one

2024 Volume 19, Issue 1, Page(s) e0285093

Abstract: The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to ... ...

Abstract	The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.
MeSH term(s)	Humans ; Pandemics ; Biological Ontologies ; Vocabulary, Controlled ; Virus Diseases ; Communicable Diseases ; COVID-19/epidemiology
Language	English
Publishing date	2024-01-18
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0285093
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Infectious Disease Ontology in the age of COVID-19

Shane Babcock / John Beverley / Lindsay G. Cowell / Barry Smith

Journal of Biomedical Semantics, Vol 12, Iss 1, Pp 1-

2021 Volume 20

Abstract: 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 ... ...

Abstract	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 ...
Keywords	Coronavirus ; COVID-19 ; Infectious disease ; Infectious disease ontology ; Ontology ; Data integration ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	006 ; 004
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Infectious Disease Ontology in the Age of COVID-19

Babcock, Shane / Cowell, Lindsay G. / Beverley, John / Smith, Barry

2020

Abstract: The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be ... ...

Abstract	The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research.
Keywords	Philosophy ; covid19
Subject code	630
Language	English
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Coordinating Coronavirus Research

Beverley, John / Smith, Barry / Babcock, Shane / Cowell, Lindsay G.

The COVID-19 Infectious Disease Ontology

2020

Abstract: The COVID-19 pandemic prompted immense investigation of the SARS-CoV-2 virus. Rapidly, accurately, and easily interpreting generated data is of fundamental concern. Ontologies – structured, controlled, vocabularies – support interoperability, and prevent ...

Abstract	The COVID-19 pandemic prompted immense investigation of the SARS-CoV-2 virus. Rapidly, accurately, and easily interpreting generated data is of fundamental concern. Ontologies – structured, controlled, vocabularies – support interoperability, and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontology Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases, in turn, extend from IDO Core, such as the Coronavirus Infectious Disease Ontology (CIDO). The growing list of virus specific IDO extensions has motivated construction of a reference ontology covering content common to viral infectious disease investigations: the Virus Infectious Disease Ontology (VIDO). Additionally, the present pandemic has motivated construction of a more specific extension of CIDO, covering terminological content specific to the pandemic: the COVID-19 Infectious Disease Ontology (IDO-COVID-19). We report here the development of VIDO and IDO-COVID-19. More specifically, we examine newly minted terms for each ontology, showcase reuse of terms from existing OBO ontologies, motivate choice-points for ontological decisions based on research from relevant life sciences, apply ontology terms to explicate viral pathogenesis, and discuss the annotating power of virus ontologies for use in machine learning projects.
Keywords	covid19
Publisher	Center for Open Science
Publishing country	us
Document type	Book ; Online
DOI	10.31219/osf.io/5bx8c
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: The Infectious Disease Ontology in the Age of COVID-19

Babcock, Shane / Beverley, John / Cowell, Lindsay G. / Smith, Barry

2020

Abstract: BackgroundEfforts to respond effectively to public health emergencies, such as we are now experiencing with COVID-19, require data sharing across multiple disciplines, and this is hindered by the fact that relevant information is often collected using ... ...

Abstract	BackgroundEfforts to respond effectively to public health emergencies, such as we are now experiencing with COVID-19, require data sharing across multiple disciplines, and this is hindered by the fact that relevant information is often collected using discipline-specific terminologies and coding systems and stored in heterogenous databases. Ontologies provide a powerful data sharing and integration tool. In practice, however, this method is often undermined by uncoordinated ontology development. Following the principles of the Open Biomedical Ontologies Foundry, the Infectious Disease Ontology (IDO) represents one step towards overcoming such silo problems.ResultsIDO is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including: IDO Virus (VIDO); the Coronavirus Infectious Disease Ontology (CIDO); and an extension of CIDO focusing on COVID-19 (IDO-COVID-19). We discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research.ConclusionsAs we face the continued threat of novel pathogens in the future, 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 already curated data from earlier diseases. IDO’s tightly coordinated suite of ontologies modules provides a powerful method of data integration and sharing that will allow physicians, researchers, and public health organizations to respond rapidly and efficiently both to the current and future public health crises.
Keywords	covid19
Publisher	Center for Open Science
Publishing country	us
Document type	Book ; Online
DOI	10.31219/osf.io/az6u5
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Coordinating Coronavirus Research

Beverley, John / Babcock, Shane / Carvalho, Gustavo / Cowell, Lindsay / Duesing, Sebastian / Hurley, Regina / Smith, Barry

The COVID-19 Infectious Disease Ontology

2020

Abstract: Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open ... ...

Abstract	Rapidly, accurately and easily interpreting generated data is of fundamental concern. Ontologies – structured controlled vocabularies – support interoperability and prevent the development of data silos which undermine interoperability. The Open Biological and Biomedical Ontologies (OBO) Foundry serves to ensure ontologies remain interoperable through adherence by its members to core ontology design principles. For example, the Infectious Disease Ontology (IDO) Core includes terminological content common to investigations of all infectious diseases. Ontologies covering more specific infectious diseases in turn extend from IDOCore, such as the Coronavirus Infectious Disease Ontology (CIDO). The growing list of virus-specific IDO extensions has motivated construction of a reference ontology covering content common to viral infectious disease investigations: the Virus Infectious Disease Ontology (VIDO). Additionally the present pandemic has motivated construction of a more specific extension of CIDO covering terminological contents specific to the pandemic: the COVID-19 Infectious Disease Ontology (IDO-COVID-19). We report here the development of VIDO and IDO-COVID-19. More specifically we examine newly minted terms for each ontology, showcase reuse of terms from existing OBO ontologies, motivate choicepoints for ontological decisions based on research from relevant life sciences, apply ontology terms to explicate viral pathogenesis, and discuss the annotating power of virus ontologies for use in machine-learning projects.
Keywords	Philosophy ; covid19
Subject code	004
Language	English
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Behind the mask of method: political orientation and constitutional interpretive preferences.

Furgeson, Joshua R / Babcock, Linda / Shane, Peter M

Law and human behavior

2008 Volume 32, Issue 6, Page(s) 502–510

Abstract: Debate about how to best interpret the Constitution often revolves around interpretive methodologies (e.g., originalism or expansive interpretation). This article examines whether individuals' political orientation influences the methodologies they ... ...

Abstract	Debate about how to best interpret the Constitution often revolves around interpretive methodologies (e.g., originalism or expansive interpretation). This article examines whether individuals' political orientation influences the methodologies they prefer to use to interpret the Constitution. We study this proposed relationship using a survey of federal law clerks and an experimental study with college students. The survey results indicate that, compared to conservatives, liberal clerks prefer the current meaning or the most plausible appealing meaning of the constitutional text, while conservatives prefer the original meaning of the text. Liberal clerks also prefer to interpret the Constitution much more expansively. The second study manipulates the policy implications of expansive interpretation and finds this manipulation differentially affects liberals' and conservatives' expansiveness preferences.
MeSH term(s)	Constitution and Bylaws ; Decision Making ; Government ; Humans ; Judgment ; Law Enforcement ; Politics ; Public Policy ; Regression Analysis ; Students ; United States
Language	English
Publishing date	2008-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2017882-7
ISSN	1573-661X ; 0147-7307
ISSN (online)	1573-661X
ISSN	0147-7307
DOI	10.1007/s10979-007-9112-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Do a law's policy implications affect beliefs about its constitutionality? An experimental test.

Furgeson, Joshua R / Babcock, Linda / Shane, Peter M

Law and human behavior

2008 Volume 32, Issue 3, Page(s) 219–227

Abstract: Although a substantial empirical literature has found associations between judges' political orientation and their judicial decisions, the nature of the relationship between policy preferences and constitutional reasoning remains unclear. In this ... ...

Abstract	Although a substantial empirical literature has found associations between judges' political orientation and their judicial decisions, the nature of the relationship between policy preferences and constitutional reasoning remains unclear. In this experimental study, law students were asked to determine the constitutionality of a hypothetical law, where the policy implications of the law were manipulated while holding all legal evidence constant. The data indicate that, even with an incentive to select the ruling best supported by the legal evidence, liberal participants were more likely to overturn laws that decreased taxes than laws that increased taxes. The opposite pattern held for conservatives. The experimental manipulation significantly affected even those participants who believed their policy preferences had no influence on their constitutional decisions.
MeSH term(s)	Adult ; Attitude ; Constitution and Bylaws ; Culture ; Decision Making, Organizational ; Female ; Humans ; Male ; Public Policy ; Surveys and Questionnaires ; United States
Language	English
Publishing date	2008-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2017882-7
ISSN	1573-661X ; 0147-7307
ISSN (online)	1573-661X
ISSN	0147-7307
DOI	10.1007/s10979-007-9102-z
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