The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring (...) the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...) information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (shrink)

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: We present (...) computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

In a development that has still been hardly noticed by philosophers, a conception of ontology has been advanced in recent years in a series of extra-philosophical disciplines as researchers in linguistics, psychology, geography and anthropology have sought to elicit the ontological commitments (‘ontologies’, in the plural) of different cultures or disciplines. Exploiting the terminology of Quine, researchers in psychology and anthropology have sought to establish what individual human subjects, or entire human cultures, are committed to, ontologically, in their everyday cognition, (...) in much the same way in which philosophers of science have attempted to elicit the ontological commitments of the natural sciences. Thus they have engaged in inquiries designed to establish how folk ontologies (or folk biologies, folk theories of physics, folk psychologies, and so on) develop through infancy and childhood, or to establish the degree to which given elements of folk ontologies reflect universal features of the human cognitive system. In a parallel development, researchers in biomedicine developed what they called 'ontologies' as controlled vocabularies to ensure interoperability of the way in which, for example, genomic data is described in different biological disciplines. We describe in what follows some of the relations between these efforts and the more traditional concerns of philosophers. (shrink)

This paper addresses the rift between the teacher’s sense of self as a causal agent and the experience of being in lack of control in the classroom, by way of Hans Vaihinger’s philosophy of ‘as if.’ It is argued that understanding agential control in terms of a valuable educational fiction—a practical (ethical) fiction in Vaihinger’s vocabulary—can offer a way of bridging this rift and can help teachers make sense of the tension between their felt need to strive for control (...) and their experience of suffering from lack of control. A fiction, it is argued, is different from an illusion in that fictions can be affirmed without being believed. Unlike illusions, valuable fictions can be recognized as fictions and still retain some of their affective power over us, thereby allowing us to act ‘as if.’ In education, this is helpful as it means that we can make use of valuable fictions without assuming that these have to be protected from the critical gaze of non-believers. In fact, we can openly acknowledge that we rely on fictions as this is part and parcel of being a human being with a limited cognitive ability. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods (...) and formal ontological principles as a first step towards finding answers to this question. (shrink)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the (...) kinds of entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (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)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to (...) the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In (...) the naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It provides a controlled vocabulary, built out of terms (...) that are designed to be maximally comprehensible to all groups of stakeholders and across all the sub-fields of the quantum domain. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of (...) SNOMED CT classes with respect to these principles. Our major results are: 31% of these classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with the phenomenon of multiple inheritance. The advantages and limitations of our approach are also discussed. (shrink)

As available intelligence data and information expand in both quantity and variety, new techniques must be deployed for search and analytics. One technique involves the semantic enhancement of data through the creation of what are called ‘ontologies’ or ‘controlled vocabularies.’ When multiple different bodies of heterogeneous data are tagged by means of terms from common ontologies, then these data become linked together in ways which allow more effective retrieval and integration. We describe a simple case study to show how (...) these benefits are being achieved, and we describe our strategy for developing a suite of ontologies to serve the needs of the war-fighter in the ever more complex battlespace environments of the future. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. 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 virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus (...) Infectious Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development (...) and some of its anticipated uses. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic (...) annotation of large amounts of ncRNA biological and clinical data. (shrink)

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at (...) the level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary (...) for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary (...) for the domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

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)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and (...) metadata registries, thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality (...) through both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology (...) that provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has (...) been expanded to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. (...) Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe (...) the VSO will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

Increasingly, the high throughput technologies used by biomedical researchers are bringing about a situation in which large bodies of data are being described using controlled structured vocabularies—also known as ontologies—in order to support the integration and analysis of this data. Annotation of data by means of ontologies is already contributing in significant ways to the cumulation of scientific knowledge and, prospectively, to the applicability of cross-domain algorithmic reasoning in support of scientific advance. This very success, however, has led to (...) a proliferation of ontologies of varying scope and quality. We define one strategy for achieving quality assurance of ontologies—a plan of action already adopted by a large community of collaborating ontologists—which consists in subjecting ontologies to a process of peer review analogous to that which is applied to scientific journal articles. (shrink)

Freud uses paradoxical and conflictual rhetoric to create an unstable and conflictual picture of the mind. Thus he diverges from both dominant traditions of thought in the West: the Judeo-Christian way of filling all gaps in meaning by putting a single omnipotent divinity in charge of them, and the Enlightenment quest for a final, causal language to describe reality. By both suggesting and displacing a plurality of perspectives on the unconscious, Freud’s text mirrors what it claims happens in our minds, (...) in which unconscious impulses undermine the pretense of total rational self-control. Though Freud suggests that a mechanistic description of the mind may bring us nearer to the reality of the unconscious, he also explains that this reality will remain dark. He not only develops an ostensibly mechanistic vocabulary for unconscious mental processes, but also clarifies that his terminology is most fictional precisely when it seems most scientific. Hence, Freud’s science of the unconscious cannot be assimilated to an empiricist position; its philosophical underpinnings are both Kantian and Nietzschean, with metaphors and analogies playing a crucial role. Two dramatic images, in which the mind appears as a domain of warring gods and a realm of political conflict, demonstrate that Freud did not regard the unconscious as some kind of true inner self. He depicts the mind in general and the unconscious in particular as a pagan, conflictual universe over which no god or goddess can gain exclusive control and where no rigid dictatorship is possible. (shrink)

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its (...) construction and maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

Digital Literacy (DL) is defined as the ability to use information and communication technology to communicate with cognitive and technical skills. One of the Digital Literacy is Mobile-Assisted Language Learning (MALL) or mobile phones-based language learning. Merits of this study are worthy of helping learners easier understand the language learning materials presented by either guided face to face in the classroom or self-learning out of the school. The study used experimental and control classes to compare the results that the significance (...) of Mobile-Assisted Language Learning in learning language could be prescribed. Refer to the initial students’ ability, this study designed pre and post-test for the experiment. Furthermore, participants were 40 students of second-year students at the English Education Department. Same topics were taught for experiment and control class in alter methods. The results claimed that the using post-test of MALL had merits on improving experimental group more than control group performance. The results declared that using MALL would encourage students learning activities such as self-language learning, enriching vocabulary, promoting teacher’s pedagogic, student’s cognitive, writing skill, reading comprehension, speaking, grammar and listening skill. Lastly, this paper implied MALL as a reference for future curriculum and material development. (shrink)

Deliberate contextual vocabulary acquisition (CVA) is a reader’s ability to figure out a (not the) meaning for an unknown word from its “context”, without external sources of help such as dictionaries or people. The appropriate context for such CVA is the “belief-revised integration” of the reader’s prior knowledge with the reader’s “internalization” of the text. We discuss unwarranted assumptions behind some classic objections to CVA, and present and defend a computational theory of CVA that we have adapted to a (...) new classroom curriculum designed to help students use CVA to improve their reading comprehension. (shrink)

The extensive involvement of nonconscious processes in human behaviour has led some to suggest that consciousness is much less important for the control of action than we might think. In this article I push against this trend, developing an understanding of conscious control that is sensitive to our best models of overt action control. Further, I assess the cogency of various zombie challenges—challenges that seek to demote the importance of conscious control for human agency. I argue that though nonconscious contributions (...) to action control are evidently robust, these challenges are overblown. (shrink)

We discuss a research project that develops and applies algorithms for computational contextual vocabulary acquisition (CVA): learning the meaning of unknown words from context. We try to unify a disparate literature on the topic of CVA from psychology, first- and secondlanguage acquisition, and reading science, in order to help develop these algorithms: We use the knowledge gained from the computational CVA system to build an educational curriculum for enhancing students’ abilities to use CVA strategies in their reading of science (...) texts at the middle-school and college undergraduate levels. The knowledge gained from case studies of students using our CVA techniques feeds back into further development of our computational theory. Keywords: artificial intelligence, knowledge representation, reading, reasoning, science education, vocabulary acquisition. (shrink)

Self-control is integral to successful human agency. Without it we cannot extend our agency across time and secure central social, moral, and personal goods. But self-control is not a unitary capacity. In the first part of this paper we provide a taxonomy of self-control and trace its connections to agency and the self. In part two, we turn our attention to the external conditions that support successful agency and the exercise of self-control. We argue that what we call moral security (...) is a critical foundation for agency. Parts three and four explore what happens to agency when moral security is lacking, as in the case of those subject to racism, and those living in poverty. The disadvantages suffered by those who are poor, in a racial minority or other oppressed group, or suffering mental illness or addiction, are often attributed to a lack of individual self-control or personal responsibility. In particular, members of these groups are often seen as irresponsibly focused on short-term pleasures over long-term good, a view underwritten by particular psychological theories of self-control. We explore how narratives about racism and poverty undermine moral security, and limit and distort the possibility of synchronic and diachronic self-control. Where moral security is undermined, the connection between self-control and diachronic goods often fails to obtain and agency contracts accordingly. We close with some preliminary reflections on the implications for responsibility. (shrink)

The English language is immensely rich in terms of vocabulary. When learning vocabulary, successful students employ specific strategies. Several studies have been conducted to explore the vocabulary learning strategies (VLS) English language learners employ. However, there is a lack of empirical research on the topic in Afghanistan. Therefore, the aims of this study were to 1) explore the VLS undergraduate English learners employ; 2) examine the correlation between VLS and gender; 3) examine the correlation between VLS and (...) students’ year of studies; and 4) examine the correlation between VLS and students’ English proficiency level. The study used a descriptive-quantitative research design. The study discovered that metacognitive and memory strategies were the most frequently used, while social strategies were the least frequently used. Moreover, the correlation results revealed that metacognitive strategies were more prevalent among males, while memory strategies were more popular among females. (shrink)

This paper examines Aristotle’s vocabulary of pain, that is the differences and relations of the concepts of pain expressed by synonyms in the same semantic field. It investigates what is particularly Aristotelian in the selection of the pain-words in comparison with earlier authors and specifies the special semantic scope of each word-cluster. The result not only aims to pin down the exact way these terms converge with and diverge from each other, but also serves as a basis for further (...) understanding Aristotle’s philosophical conception of pain. (shrink)

Living organisms act as integrated wholes to maintain themselves. Individual actions can each be explained by characterizing the mechanisms that perform the activity. But these alone do not explain how various activities are coordinated and performed versatilely. We argue that this depends on a specific type of mechanism, a control mechanism. We develop an account of control by examining several extensively studied control mechanisms operative in the bacterium E. coli. On our analysis, what distinguishes a control mechanism from other mechanisms (...) is that it relies on measuring one or more variables, which results in setting constraints in the control mechanism that determine its action on flexible constraints in other mechanisms. In the most basic arrangement, the measurement process directly determines the action of the control mechanism, but in more complex arrangements signals mediate between measurements and effectors. This opens the possibility of multiple responses to the same measurement and responses based on multiple measurements. It also allows crosstalk, resulting in networks of control mechanisms. Such networks integrate the behaviors of the organism but also present a challenge in tailoring responses to particular measurements. We discuss how integrated activity can still result in differential, versatile, responses. (shrink)

Recent work in cognitive modelling has found that most of the data that has been cited as evidence for the dual-process theory (DPT) of reasoning is best explained by non-linear, “monotonic” one-process models (Stephens et al., 2018, 2019). In this paper, I consider an important caveat of this research: it uses models that are committed to unrealistic assumptions about how effectively task conditions can isolate Type-1 and Type-2 reasoning. To avoid this caveat, I develop a coordinated theoretical, experimental, and modelling (...) strategy to better test DPT. First, I propose that Type-1 and Type-2 reasoning are defined as reasoning that precedes and follows metacognitive control, respectively. Second, I argue that reasoning that precedes and follows metacognitive control can be effectively isolated using debiasing paradigms that manipulate metacognitive heuristics (e.g., processing fluency) to prevent or trigger metacognitive control, respectively. Third, I argue that monotonic modelling can allow us to decisively test DPT only when we use them to analyse data from this particular kind of debiasing paradigm. (shrink)

Judgments of blame for others are typically sensitive to what an agent knows and desires. However, when people act negligently, they do not know what they are doing and do not desire the outcomes of their negligence. How, then, do people attribute blame for negligent wrongdoing? We propose that people attribute blame for negligent wrongdoing based on perceived mental control, or the degree to which an agent guides their thoughts and attention over time. To acquire information about others’ mental control, (...) people self-project their own perceived mental control to anchor third-personal judgments about mental control and concomitant responsibility for negligent wrongdoing. In four experiments (N = 841), we tested whether perceptions of mental control drive third-personal judgments of blame for negligent wrongdoing. Study 1 showed that the ease with which people can counterfactually imagine an individual being non-negligent mediated the relationship between judgments of control and blame. Studies 2a and 2b indicated that perceived mental control has a strong effect on judgments of blame for negligent wrongdoing and that first-personal judgments of mental control are moderately correlated with third-personal judgments of blame for negligent wrongdoing. Finally, we used an autobiographical memory manipulation in Study 3 to make personal episodes of forgetfulness salient. Participants for whom past personal episodes of forgetfulness were made salient judged negligent wrongdoers less harshly compared to a control group for whom past episodes of negligence were not salient. Collectively, these findings suggest that first-personal judgments of mental control drive third-personal judgments of blame for negligent wrongdoing and indicate a novel role for counterfactual thinking in the attribution of responsibility. (shrink)

It is tempting to think (though many deny) that epistemic agents exercise a distinctive kind of control over their belief‐like attitudes. My aim here is to sketch a “bottom‐up” model of epistemic agency, one that draws on an analogous model of practical agency, according to which an agent's conditional beliefs are reasons‐responsive planning states that initiate and sustain mental behavior so as to render controlled.

It seems that we can be directly accountable for our reasons-responsive attitudes—e.g., our beliefs, desires, and intentions. Yet, we rarely, if ever, have volitional control over such attitudes, volitional control being the sort of control that we exert over our intentional actions. This presents a trilemma: (Horn 1) deny that we can be directly accountable for our reasons-responsive attitudes, (Horn 2) deny that φ’s being under our control is necessary for our being directly accountable for φ-ing, or (Horn 3) deny (...) that the relevant sort of control is volitional control. This paper argues that we should take Horn 3. (shrink)

Control consciousness is the awareness or experience of seeming to be in control of one’s actions. One view, which I will be arguing against in the present paper, is that control consciousness is a form of sensory consciousness. In such a view, control consciousness is exhausted by sensory elements such as tactile and proprioceptive information. An opposing view, which I will be arguing for, is that sensory elements cannot be the whole story and must be supplemented by direct contributions of (...) nonsensory, motor elements. More specifically, I will be arguing for the view that the neural basis of control consciousness is constituted by states of recurrent activation in relatively intermediate levels of the motor hierarchy. (shrink)

It has been argued that the explanation of self-control requires positing special motivational powers. Some think that we need will-power as an irreducible mental faculty; others that we need to think of the active self as a dedicated and depletable pool of psychic energy or – in today more respectable terminology – mental resources; finally, there is the idea that self-control requires postulating a deep division between reason and passion – a deliberative and an emotional motivational system. This essay argues (...) that no such special motivational powers are necessary. Yet, at the same time, self-control does powerfully illustrate the importance of a feature of the mind. What it illustrates, I argue, is the importance of the mental activity of attention in the control of all action. It is by appeal to this mental activity that we can dispense with special motivational powers. If we think of Humeanism as the view that there is fundamentally only one kind of motivational system and that all action is based in that system, then this essay contributes to a defense of Humeanism. On the other hand, the essay also shows that any model of agency in terms of only beliefs and desires, motivational and representational states, or preferences and credences is incomplete. A different conception of Humeanism as the view that every mental state is either motivational, representational, or a combination of them, is false. (shrink)

This paper discusses the idea that the concept of privacy should be understood in terms of control. Three different attempts to spell out this idea will be critically discussed. The conclusion will be that the Source Control View on privacy is the most promising version of the idea that privacy is to be understood in terms of control.