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. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

After motivating a framework for evaluating top-down, middle-out, middle-in, and bottom-up ontology development strategies, we apply our framework to investigate whether infectious disease ontologies - specifically, the Virus Infectious Disease Ontology (VIDO) and the Coronavirus Infectious Disease Ontology (CIDO) - effectively promote semantic interoperability.

Ontology: Tool for Broad Spectrum Knowledge Integration (Foreword to Chinese translation of Building Ontologies with Basic Formal Ontology).

Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-offs between precision (...) and ambiguity that are key to designing effective solutions for generating big data about biodiversity. We focus on the importance of theory-dependence as a source of ambiguity in taxonomic nomenclature and hence a persistent challenge for implementing a single, long-term solution to storing and accessing meaningful sets of biological specimens. We argue that ambiguity does have a positive role to play in scientific progress as a tool for efficiently symbolizing multiple aspects of taxa and mediating between conflicting hypotheses about their nature. Pursuing a deeper understanding of the trade-offs and synthesis of precision and ambiguity as virtues of scientific language and communication systems then offers a productive next step for realizing sound, big biodiversity data services. (shrink)

Psychiatric disorders present distinct clinical challenges which are partly attributable to their multifactorial aetiology and the absence of laboratory tests that can be used to confirm diagnosis or predict risk. Psychiatric disorders are highly heritable, but also polygenic, with genetic risk conferred by interactions between thousands of variants of small effect that can be summarized in a polygenic risk score. We discuss four areas in which the use of polygenic risk scores in psychiatric research and clinical contexts could have ethical (...) implications. First, there is concern that clinical use of polygenic risk scores may exacerbate existing health inequities. Second, research findings regarding polygenic risk could be misinterpreted in stigmatising or discriminatory ways. Third, there are concerns associated with testing minors as well as eugenics concerns elicited by prenatal polygenic risk testing. Fourth, potential challenges that could arise with the feedback and interpretation of high polygenic risk for a psychiatric disorder would require consideration. While there would be extensive overlap with the challenges of feeding back genetic findings in general, the potential clinical use of polygenic risk scoring warrants discussion in its own right, given the recency of this possibility. To this end, we discuss how lay interpretations of risk and genetic information could intersect. Consideration of these factors would be necessary for ensuring effective and constructive communication and interpretation of polygenic risk information which, in turn, could have implications for the uptake of any therapeutic recommendations. Recent advances in polygenic risk scoring have major implications for its clinical potential, however, care should be taken to ensure that communication of polygenic risk does not feed into problematic assumptions regarding mental disorders or support reductive interpretations. (shrink)

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. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

The ambiguities and overspecificities of prescription semantics along with their lack of standardization hinders the adoption of electronic prescriptions in some countries, limit data interoperabil...

Functionally graded materials (FGMs) have been used in many different kinds of applications in recent years and have attracted significant research attention. However, we do not yet have a commonly accepted way of representing the various aspects of FGMs. Lack of standardised vocabulary creates obstacles to the extraction of useful information relating to pertinent aspects of different applications. A standard resource is needed for describing various elements of FGMs, including existing applications, manufacturing techniques, and material characteristics. This motivated the creation (...) of the FGM Ontology (FGMO) in 2016. Here, we present a revised and expanded version of the FGM Ontology, which includes enrichments along four dimensions: (1) documenting recent FGMs applications; (2) reorganising the framework to incorporate an updated representation of types of manufacturing processes; (3) enriching the axioms of the ontology; and (4) importing mid-level ontologies from the Common Core Ontologies (CCO) and Product Life Cycle (PLC) Ontologies. The work is being carried out within the framework of the Industry Ontology Foundry (IOF), and the ontology is conformant to Basic Formal Ontology (BFO). (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability amon...

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update (...) settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is provided to demonstrate the features of Ontobull and BFOConvert. (shrink)

To avoid post-neurosurgical language deficits, intraoperative mapping of the language function in the brain can be complemented with preoperative mapping with functional magnetic resonance imaging. The validity of an fMRI “language localizer” paradigm crucially depends on the choice of an optimal language task and baseline condition. This study presents a new fMRI “language localizer” in Russian using overt sentence completion, a task that comprehensively engages the language function by involving both production and comprehension at the word and sentence level. The (...) paradigm was validated in 18 neurologically healthy volunteers who participated in two scanning sessions, for estimating test–retest reliability. For the first time, two baseline conditions for the sentence completion task were compared. At the group level, the paradigm significantly activated both anterior and posterior language-related regions. Individual-level analysis showed that activation was elicited most consistently in the inferior frontal regions, followed by posterior temporal regions and the angular gyrus. Test–retest reliability of activation location, as measured by Dice coefficients, was moderate and thus comparable to previous studies. Test–retest reliability was higher in the frontal than temporo-parietal region and with the most liberal statistical thresholding compared to two more conservative thresholding methods. Lateralization indices were expectedly left-hemispheric, with greater lateralization in the frontal than temporo-parietal region, and showed moderate test-retest reliability. Finally, the pseudoword baseline elicited more extensive and more reliable activation, although the syllable baseline appears more feasible for future clinical use. Overall, the study demonstrated the validity and reliability of the sentence completion task for mapping the language function in the brain. The paradigm needs further validation in a clinical sample of neurosurgical patients. Additionally, the study contributes to general evidence on test–retest reliability of fMRI. (shrink)

BackgroundSmartphone addiction has become a social problem that affects peoples’ quality of life and is frequently reported to be correlated with alexithymia, avoidant or anxious attachment styles, and subjective well-being. This study aimed to investigate the relationship between SA and alexithymia, attachment style, and subjective well-being.MethodsA meta-analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The following electronic databases were searched: PubMed, Web of Science, Embase, PsycINFO, PsycArticles, China National Knowledge Infrastructure, WANFANG DATA, and Chongqing (...) VIP Information Co., Ltd.. Stata 16.0 was used to analyze the overall effect and test the moderating effect.ResultsOne hundred and ten studies were included, involving a total of 96,680 participants. SA had a significantly high positive correlation with alexithymia, attachment anxiety, and negative emotions, and a low positive correlation with attachment avoidance. In addition, there was a high negative correlation between SA and subjective well-being and a low negative correlation between SA, life satisfaction, and positive emotions. A moderation analysis revealed that age significantly moderated the relationship between SA and positive emotions. The tools for measuring SA significantly moderated the relationship between SA, alexithymia, attachment anxiety, and subjective well-being. Meanwhile, subjective well-being measurement tools significantly moderated the relationships between SA, subjective well-being, and negative emotions.ConclusionSA was closely related to alexithymia, attachment style, and subjective well-being. In the future, longitudinal research can be conducted to better investigate the dynamic changes in the relationship between them.Systematic review registration[www.crd.york.ac.uk/PROSPERO/], identifier [CRD42022334798]. (shrink)

Reuse of elements from existing ontologies in the construction of new ontologies is a foundational principle in ontological design. It offers the benefits, among others, of consistency and interoperability between such knowledge structures as well as sharing resources. Reuse is widely found within important collections of established ontologies, such as BioPortal and the OBO Foundry. However, reuse comes with its own potential problems involving ontological commitment, granularity, and ambiguity. Guidelines are proposed to aid ontology developers and curators in their prospective (...) reuse of content. These guidelines have been gleaned over years of practice in the ontology field. The guidelines are couched in experiential reports on designing and curating particular ontologies (e.g., EXACT and EXACT2) and using generally accepted approaches (e.g., MIREOT) in doing so. Various software tools to assist in ontology reuse are surveyed and discussed. (shrink)

The purpose of this study was to evaluate, revise, and extend the Informed Consent Ontology (ICO) for expressing clinical permissions, including reuse of residual clinical biospecimens and health data. This study followed a formative evaluation design and used a bottom-up modeling approach. Data were collected from the literature on US federal regulations and a study of clinical consent forms. Eleven federal regulations and fifteen permission-sentences from clinical consent forms were iteratively modeled to identify entities and their relationships, followed by community (...) reflection and negotiation based on a series of predetermined evaluation questions. ICO included fifty-two classes and twelve object properties necessary when modeling, demonstrating appropriateness of extending ICO for the clinical domain. Twenty-six additional classes were imported into ICO from other ontologies, and twelve new classes were recommended for development. This work addresses a critical gap in formally representing permissions clinical permissions, including reuse of residual clinical biospecimens and health data. It makes missing content available to the OBO Foundry, enabling use alongside other widely-adopted biomedical ontologies. ICO serves as a machine-interpretable and interoperable tool for responsible reuse of residual clinical biospecimens and health data at scale. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

A direct scalar implicature (DSI) arises when a sentence with a weaker term like sometimes implies the negation of the stronger alternative always (e.g., John sometimes (∼ not always) drinks coffee). A reverse implicature, often referred to as indirect scalar implicature (ISI), arises when the stronger term is under negation and implicates the weaker alternative (e.g., John doesn’t always (∼ sometimes) drink coffee). Recent research suggests that English-speaking adults and children behave differently in interpreting these two types of SI ( (...) Cremers and Chemla, 2014 ; Bill et al., 2016 ). However, little attention has been paid to how these two types of SI are processed in a non-native, or second language (L2). By using a covered box paradigm, this study examines how these two types of SI are computed and suspended in a second language by measuring the visible vs. covered picture selection percentage as well as response times (RTs) taken for the selection. Data collected from 26 native speakers of English to 24 L1-Chinese L2-English learners showed that unlike native speakers, L2 speakers showed asymmetries in their generation and suspension of DSI and ISI. That is, L2 speakers computed DSI more often than ISI, but they suspended ISI more frequently than DSI. Furthermore, our RT data suggested that L2 speakers suspended ISI not only more frequently but also significantly faster than DSI. Regarding the asymmetrical behavior among L2 speakers, we consider the number of alternative meanings involved in DSI vs. ISI suspension and different routes to the suspension of SI. (shrink)

It is known that the aging process entails a cognitive decline in certain processes such as attention, episodic memory, working memory, processing speed and executive functions. In recent years, ef...

Problematic smartphone use in college students has been a major public health concern in modern society, which may also lead to adverse health outcomes. Using a three-wave longitudinal study design, the current study aimed to examine the prevalence and psychosocial factors of PSU in a large sample of Chinese college students. The data used in this study was obtained from an ongoing longitudinal study in Guangdong, China. In the current study, a total of 7,434 freshmen and sophomores who completed the (...) first three surveys were included. Self-administered questionnaires were used to assess PSU, possible social anxiety disorders, depressive symptoms, loneliness, family conflicts, academic stress, and some demographic characteristics. Generalized estimating equation models were performed to determine the risk factors associated with PSU. The results showed that 65.8, 58.1, and 52.8% of college students reported PSU at three waves, with an apparent downward trend. Female students reported higher prevalence rates of PSU than males. Depressive symptoms, possible social anxiety disorders, loneliness, family conflicts, and high academic pressure were important risk factors for PSU. Early intervention and identification of those who show signs of PSU may prevent the development of maladaptive coping responses and addictive behaviors, so as to prevent future negative psychosocial consequences. (shrink)

The promotion of patient welfare is a central goal of medical professionals and serves as a fundamental principle of medical professionalism. Despite its importance, however, it is unclear what is meant by patient welfare. In my dissertation, I explore patient welfare by analyzing the ordinary notion of welfare and applying this analysis to the patient population. I argue that welfare is best understood and expressed in terms of capabilities, which I define using the structure and vocabulary of Basic Formal Ontology. (...) I conclude that patient welfare is a multi-dimensional quality of the human organism corresponding to the degree to which that patient has realized the array of capabilities typical of the human kind. I then identify certain important implications for this view on the practice of medicine. (shrink)