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 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 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 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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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. (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)

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)

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 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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

Contextual vocabulary acquisition (CVA) is the deliberate acquisition of a meaning for a word in a text by reasoning from context, where “context” includes: (1) the reader’s “internalization” of the surrounding text, i.e., the reader’s “mental model” of the word’s “textual context” (hereafter, “co-text” [3]) integrated with (2) the reader’s prior knowledge (PK), but it excludes (3) external sources such as dictionaries or people. CVA is what you do when you come across an unfamiliar word in your reading, realize that (...) you don’t know what it means, decide that you need to know what it means in order to understand the passage, but there is no one around to ask, and it is not in the dictionary (or you are too lazy to look it up). In such a case, you can try to figure out its meaning “from context”, i.e., from clues in the co-text together with your prior knowledge. Our computational theory of CVA—implemented in a the SNePS knowledge representation and reasoning system [28]—begins with a stored knowledge base containing SNePS representations of relevant PK, inputs SNePS representations of a passage containing an unfamiliar word, and draws inferences from these two (integrated) information sources. When asked to define the word, definition algorithms deductively search the resulting network for information of the sort that might be found in a dictionary definition, outputting a definition frame whose slots are the kinds of features that a definition might contain (e.g., class membership, properties, actions, spatio-temporal information, etc.) and whose slot-fillers contain information gleaned from the network [6–8,20,23,24]. We are investigating ways to make our system more robust, to embed it in a naturallanguage-processing system, and to incorporate morphological information. Our research group, including reading educators, is also applying our methods to the develop-. (shrink)

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)

The notion that there exists a fundamental need to exert control over or to influence one’s environment has enjoyed a long history in psychology (e.g., DeCharms, 1968; Heider, 1958) and has stimulated considerable theoretical work. Such a need has been characterized by theorists at multiple levels of analysis. Control motivation, for example, has been characterized broadly in terms of proactive (White, 1959) or reactive (e.g., Abramson, Seligman, & Teasdale, 1978; Brehm, 1966; Brehm & Brehm, 1981) strivings for control over general (...) or specific (Brehm & Brehm, 1981) and central or peripheral outcomes (Thompson, 1993). Additionally, various types of control strategies used to gain or maintain a sense of personal control have been proposed (e.g., Averill, 1973; Heckhausen & Schulz, 1995; Rothbaum, Weisz, & Snyder, 1982; Thompson, 1981). Modes of control, for instance, have been categorized as either primary or secondary. Primary strategies involve direct action undertaken to produce desirable and avoid undesirable outcomes in the external world, whereas secondary strategies employ primarily cognitive processes undertaken to produce a change within the person. Recently, Heckhausen and Schulz (1995) have further delineated these primary and secondary forms of control according to whether they are based on veridical or illusory causal understandings of the world and whether they are functional or dysfunctional. While most control theorists view primary control as preferable to secondary control, the latter is viewed as critical in the process of adaptation to control failures and in the promotion of future primary control attempts. (shrink)

Eighteenth-century German writers with broad interests in natural history, and in particular, in the kind of ethnographic reports typically included in travel and expedition narratives, had to be able to access and read the original reports or they had to work with translations. The translators of these reports were, moreover, typically forced more than usual into the role of interpreter. This was especially the case when it came to accounts wherein vocabulary did not exist or was at least not settled, (...) and more importantly where scientific understanding was uncertain or altogether lacking, a situation that could only make the creation of semantic categories all the more significant. With this state of affairs in mind, this essay concentrates on Immanuel Kant’s work to develop a specialised racial vocabulary, and does so in a manner that reveals the importance of Buffon’s account of variation as a resource for Kant, even as Kant sought to position the new vocabulary as an improved template for transforming taxonomy or Naturbeschreibung into a genuine historical science or Naturgeschichte. (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)

Control is typically accepted as a necessary condition for moral responsibility. Thus, humans are morally responsible for their actions only if we can realise the right kind of control. Are there good reasons to think that humans can psychologically realise control? This paper is an attempt to address this question by establishing choice and agenthood as separate but interconnected aspects of control. I consider two challenges to the claim that humans can realise the kind of control required for moral responsibility. (...) First, an empirical challenge from cognitive neuroscience provides a familiar way to argue against the realisation of the choice aspect by human psychology. Second, a more formidable conceptual challenge to the aspect of agenthood presents us with scepticism about the kind of explanations that psychology can provide. The second challenge suggests that, in psychological accounts of choice, the agent disappears. Drawing on recent empirical models of cognitive control and philosophical accounts of agency, I conclude that the psychological explanation of choice is consistent with the aspect of agenthood being realised by human psychology. (shrink)

One of the main obstacles to the realization of intentions for future actions and to the successful pursuit of long-term goals is lack of self-control. But, what does it mean to engage in self-controlled behaviour? On a motivational construal of self-control, self-control involves resisting our competing temptations, impulses, and urges in order to do what we deem to be best. The conflict we face is between our better judgments or intentions and “hot” motivational forces that drive or compel us (...) to act in opposing ways. In contrast, on an executive construal of self-control, the emphasis is not on overcoming temptation, but on overriding or inhibiting “cold” automatically triggered routines and habits that are at odds with what we intend to do. Our general aim in this chapter is to contribute to the development of an overarching theory of self-control by exploring ways in which these two apparently competing frameworks can be reconciled. We propose that self-control is best understood as a hybrid set of skills. We draw on recent work on expert motor skill to highlight important ways in which experts differ from novices in the capacities they deploy and the ways in which they deploy them. We consider analogies (and disanalogies) between the domain of sports expertise and the domain of self-control. We end by considering how such a hybrid approach can help us reconcile a motivational and an executive approach to self-control. (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)

This paper empirically raises and examines the question of ‘conceptual control’: To what extent are competent thinkers able to reason properly with new senses of words? This question is crucial for conceptual engineering. This prominently discussed philosophical project seeks to improve our representational devices to help us reason better. It frequently involves giving new senses to familiar words, through normative explanations. Such efforts enhance, rather than reduce, our ability to reason properly, only if competent language users are able to abide (...) by the relevant explanations, in language comprehension and verbal reasoning. This paper examines to what extent we have such ‘conceptual control’ in reasoning with new senses. The paper draws on psycholinguistic findings about polysemy processing to render this question empirically tractable and builds on recent findings from experimental philosophy to address it. The paper identifies a philosophically important gap in thinkers’ control over the key process of stereotypical enrichment and discusses how conceptual engineers can use empirical methods to work around this gap in conceptual control. The paper thus empirically demonstrates the urgency of the question of conceptual control and explains how experimental philosophy can empirically address the question, to render conceptual engineering feasible as an ameliorative enterprise. (shrink)