The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

User-centered visual analysis using a hybrid reasoning architecture for intensive care units

One problem pertaining to Intensive Care Unit information systems is that, in some cases, a very dense display of data can result. To ensure the overview and readability of the increasing volumes of data, some special features are required (e.g., data prioritization, clustering, and selection mechanisms) with the application of analytical methods (e.g., temporal data abstraction, principal component analysis, and detection of events). This paper addresses the problem of improving the integration of the visual and analytical methods applied to medical monitoring systems. We present a knowledge- and machine learning-based approach to support the knowledge discovery process with appropriate analytical and visual methods. Its potential benefit to the development of user interfaces for intelligent monitors that can assist with the detection and explanation of new, potentially threatening medical events. The proposed hybrid reasoning architecture provides an interactive graphical user interface to adjust the parameters of the analytical methods based on the users' task at hand. The action sequences performed on the graphical user interface by the user are consolidated in a dynamic knowledge base with specific hybrid reasoning that integrates symbolic and connectionist approaches. These sequences of expert knowledge acquisition can be very efficient for making easier knowledge emergence during a similar experience and positively impact the monitoring of critical situations. The provided graphical user interface incorporating a user-centered visual analysis is exploited to facilitate the natural and effective representation of clinical information for patient care

Literacy improves short-term serial recall of spoken verbal but not visuospatial items - Evidence from illiterate and literate adults

© 2019 Elsevier B.V. This manuscript is made available under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence (CC BY-NC-ND 4.0). For further details please see: https://creativecommons.org/licenses/by-nc-nd/4.0/It is widely accepted that specific memory processes, such as serial-order memory, are involved in written language development and predictive of reading and spelling abilities. The reverse question, namely whether orthographic abilities also affect serial-order memory, has hardly been investigated. In the current study, we compared 20 illiterate people with a group of 20 literate matched controls on a verbal and a visuospatial version of the Hebb paradigm, measuring both short- and long-term serial-order memory abilities. We observed better short-term serial-recall performance for the literate compared with the illiterate people. This effect was stronger in the verbal than in the visuospatial modality, suggesting that the improved capacity of the literate group is a consequence of learning orthographic skills. The long-term consolidation of ordered information was comparable across groups, for both stimulus modalities. The implications of these findings for current views regarding the bi-directional interactions between memory and written language development are discussed.Peer reviewe

Capturing Scientific Knowledge on Medical Risk Factors

In this paper, we describe a model for representing scientific knowledge of risk factors in medicine in an explicit format which enables its use for automated reasoning. The resulting model supports linking the conclusions of up-to-date clinical research with data relating to individual patients. This model, which we have implemented as an ontology-based system using Linked Data, enables the capture of risk factor knowledge and serves as a translational research tool to apply that knowledge to assist with patient treatment, lifestyle, and education. Knowledge captured using this model can be disseminated for other intelligent systems to use for a variety of purposes, for example, to explore the state of the available medical knowledge

Embodiment and embodied design

Picture this. A preverbal infant straddles the center of a seesaw. She gently tilts her weight back and forth from one side to the other, sensing as each side tips downward and then back up again. This child cannot articulate her observations in simple words, let alone in scientific jargon. Can she learn anything from this experience? If so, what is she learning, and what role might such learning play in her future interactions in the world? Of course, this is a nonverbal bodily experience, and any learning that occurs must be bodily, physical learning. But does this nonverbal bodily experience have anything to do with the sort of learning that takes place in schools - learning verbal and abstract concepts? In this chapter, we argue that the body has everything to do with learning, even learning of abstract concepts. Take mathematics, for example. Mathematical practice is thought to be about producing and manipulating arbitrary symbolic inscriptions that bear abstract, universal truisms untainted by human corporeality. Mathematics is thought to epitomize our species’ collective historical achievement of transcending and, perhaps, escaping the mundane, material condition of having a body governed by haphazard terrestrial circumstance. Surely mathematics is disembodied

Balancing Access to Data And Privacy. A review of the issues and approaches for the future

Access to sensitive micro data should be provided using remote access data enclaves. These enclaves should be built to facilitate the productive, high-quality usage of microdata. In other words, they should support a collaborative environment that facilitates the development and exchange of knowledge about data among data producers and consumers. The experience of the physical and life sciences has shown that it is possible to develop a research community and a knowledge infrastructure around both research questions and the different types of data necessary to answer policy questions. In sum, establishing a virtual organization approach would provided the research community with the ability to move away from individual, or artisan, science, towards the more generally accepted community based approach. Enclave should include a number of features: metadata documentation capacity so that knowledge about data can be shared; capacity to add data so that the data infrastructure can be augmented; communication capacity, such as wikis, blogs and discussion groups so that knowledge about the data can be deepened and incentives for information sharing so that a community of practice can be built. The opportunity to transform micro-data based research through such a organizational infrastructure could potentially be as far-reaching as the changes that have taken place in the biological and astronomical sciences. It is, however, an open research question how such an organization should be established: whether the approach should be centralized or decentralized. Similarly, it is an open research question as to the appropriate metrics of success, and the best incentives to put in place to achieve success.Methodology for Collecting, Estimating, Organizing Microeconomic Data

Shared understandings of dementia? : An application of the Common Sense Self Regulation Model to a case study

Peer reviewedPostprin

Using ontology in query answering systems: Scenarios, requirements and challenges

Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of such a system, each component being designed to solve some one part of the total problem and at the same time reflect well-defined needs on the prat of our customers. We compare our strategy with the research roadmap proposed by the Question Answering Committee of the National Institute of Standards and Technology (NIST), paying special attention to the role of ontology

Home-based reach-to-grasp training for people after stroke: study protocol for a feasibility randomized controlled trial

BackgroundThis feasibility study is intended to assess the acceptability of home-based task-specific reach-to-grasp (RTG) training for people with stroke, and to gather data to inform recruitment, retention, and sample size for a definitive randomized controlled trial. Methods/designThis is to be a randomized controlled feasibility trial recruiting 50 individuals with upper-limb motor impairment after stroke. Participants will be recruited after discharge from hospital and up to 12 months post-stroke from hospital stroke services and community therapy-provider services. Participants will be assessed at baseline, and then electronically randomized and allocated to group by minimization, based on the time post-stroke and extent of upper-limb impairment. The intervention group will receive 14 training sessions, each 1 hour long, with a physiotherapist over 6 weeks and will be encouraged to practice independently for 1 hour/day to give a total of 56 hours of training time per participant. Participants allocated to the control group will receive arm therapy in accordance with usual care. Participants will be measured at 7 weeks post-randomization, and followed-up at 3 and 6 months post-randomization. Primary outcome measures for assessment of arm function are the Action Research Arm Test (ARAT) and Wolf Motor Function Test (WMFT). Secondary measures are the Motor Activity Log, Stroke Impact Scale, Carer Strain Index, and health and social care resource use. All assessments will be conducted by a trained assessor blinded to treatment allocation. Recruitment, adherence, withdrawals, adverse events (AEs), and completeness of data will be recorded and reported. DiscussionThis study will determine the acceptability of the intervention, the characteristics of the population recruited, recruitment and retention rates, descriptive statistics of outcomes, and incidence of AEs. It will provide the information needed for planning a definitive trial to test home-based RTG training. Trial registrationISRCTN: ISRCTN5671658