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. (shrink)

Objectives“Attachment difficulties” is an umbrella term often used to describe various forms of non-secure attachment. Differentiating “attachment difficulties” from autism spectrum disorder and attention deficit hyperactivity disorder has been characterized as challenging. Few studies have explored how this happens in practice, from the perspective of professionals.DesignQualitative study.MethodsWe conducted in-depth semi-structured interviews with healthcare professionals from five NHS Foundation Trusts in the United Kingdom. Participants were recruited using a combination of snowballing, convenience and purposive sampling. Data were analyzed using a thematic (...) approach.ResultsWe identified six interrelated themes that might reflect difficulties with differential conceptualization. These include: a clinical lexicon of attachment; approaching attachment with caution; contextual factors; perceived characteristic behaviors; assessing attachment and adjacent supports; spotlighting intervention and dual conceptualization.ConclusionOur results indicate some of the ways suspicions around attachment are raised in practice. We advocate for more dialogue between research and practice communities on issues of differential conceptualization. We call for collaboration between a panel of experts consisting of attachment and neurodevelopmental orientated practitioners and researchers, to clarify issues around differentiating between attachment difficulties, ASD, and ADHD. (shrink)

We conducted focus groups with 47 potential jurors who were presented with diferent scenarios in a hypothetical malpractice case involving failure to order a PSA test. Better documentation that a patient made an informed decision to decline a PSA test appeared to provide more medical-legal protection for physicians, especially with the use of a decision aid.

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Screening for prostate cancer with the prostate-specific antigen blood test is controversial, as evidence to date has not demonstrated such screening does more good than harm. While the potential benefit of PSA screening on reducing prostate cancer mortality has not been documented in randomized trials, many risks of PSA screening have been well documented. These risks include a substantially higher risk of a prostate cancer diagnosis over a screenee’s lifetime, false-positive and false-negative test results, possible complications from biopsies done in (...) response to suspicious test results, and substantial risks of side effects from subsequent prostate cancer treatments. Nevertheless, PSA screening is widespread in the United States, and many physicians in a national survey reported supporting routine PSA screening as well as getting PSA tests themselves, despite the lack of evidence. (shrink)

ABSTRACTDifficulties with inhibiting fear have been associated with the emergence of anxiety problems and poor response to cognitive–behavioural treatment. Fear inhibition problems measured using experimental paradigms involving aversive stimuli may be inappropriate for vulnerable samples and may not capture fear inhibition problems evident in everyday life. We present the Fear Inhibition Questionnaire, a self-report measure of fear inhibition abilities. We assess the FIQ’s factor structure across two cultures and how well it correlates with fear inhibition indices derived experimentally. Adolescent participants (...) from Hong Kong and England completed the FIQ, with the English participants also completing a conditioning and extinction task to assess fear inhibition problems. Across both cultures, the FIQ showed a single factor structure and low FIQ scores, or worse fear inhibition problems, were associated with self-reports of heightened anxiety. Correlation of FIQ scores with experimental indices, whi... (shrink)

The objective of this study is to evaluate if use of a patient decision aid, when choosing between a repeat cesarean or a trial of labor after a cesarean, reduces medical liability exposure. The authors conclude that use of a PDA conferred liability protection when potential jurors were presented with a hypothetical malpractice claim against an obstetrician following a TOLAC.

Theoretical models propose that attentional biases might account for the maintenance of social anxiety symptoms. However, previous eye-tracking studies have yielded mixed results. One explanation i...

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

The meaning of the term “ethnophilosophy” has evolved in both a significant and controversial variety of ways since it was first introduced by Paulin Hountondji in 1970. It was first challenged by the Kenyan philosopher, H. Odera Oruka, as based upon Hountondji’s unfair appreciation of Africa’s indigenous cultural heritage. Barry Hallen and J. Olubi Sodipo, using a form of analytic philosophy as foundational, thereafter argued that Yoruba ordinary language discourse also served to undermine Hountondji’s critique. The later work of (...) the Ghanaian philosopher, Kwame Gyekye, and the Kenyan D. A. Masolo have further legitimized the epistemological status of elements of African culture that once would have been labeled as of no genuine philosophical significance because they were ‘ethnophilosophical’ in character. The end result of this debate seems to be that both the form and content of philosophy in culture generally must be relativized. The most significant consequence of this would be that African and non-Westernphilosophy generally would finally be culturally liberated from the oppressive influence, indeed dominance, of what has conventionally come to be known as ‘mainstream’ philosophy. (shrink)

The meaning of the term “ethnophilosophy” has evolved in both a significant and controversial variety of ways since it was first introduced by Paulin Hountondji in 1970. It was first challenged by the Kenyan philosopher, H. Odera Oruka, as based upon Hountondji’s unfair appreciation of Africa’s indigenous cultural heritage. Barry Hallen and J. Olubi Sodipo, using a form of analytic philosophy as foundational, thereafter argued that Yoruba ordinary language discourse also served to undermine Hountondji’s critique. The later work of (...) the Ghanaian philosopher, Kwame Gyekye, and the Kenyan D. A. Masolo have further legitimized the epistemological status of elements of African culture that once would have been labeled as of no genuine philosophical significance because they were ‘ethnophilosophical’ in character. The end result of this debate seems to be that both the form and content of philosophy in culture generally must be relativized.The most significant consequence of this would be that African and non-Western philosophy generally would finally be culturally liberated from the oppressive influence, indeed dominance, of what has conventionally come to be known as ‘mainstream’ (Western) philosophy. (shrink)

Frankena, W. K. Morality and moral philosophy.--Soltis, J. F. Men, machines and morality.--Chazan, B. I. The moral situation.--Phenix, P. H. Ethics and the will of God.--Moore, G. E. The indefinability of good.--Morgenbesser, S. Approaches to ethical objectivity.--Sartre, J. P. Existentialism and ethics.--Hare, R. M. Decisions of principle.--Singer, M. G. Moral rules and principles.--Hare, R. M. Adolescents into adults.--Wilson, J. Assessing the morally educated person.--Kohlberg, L. The child as a moral philosopher.--Frankena, W. K. Toward a philosophy of moral education.--Archambault, R. D. (...) Criteria for success in moral instruction.--Raths, L., Harmin, M., and Simon, S. Teaching for value clarity.--Bibliography (p. 188-192). (shrink)

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms serve the current capacities of their containing system. The new proposal unifies the key notions of both kinds of theories, but goes beyond them by explaining how functions in an organism can exist as factors with autonomous causal efficacy. The goal-directedness and normativity (...) of functions exist in this strict sense as well. The theory depends on an internal physiological or neural process that mimics an organism’s fitness, and modulates the organism’s variability accordingly. The structure of the internal process can be subdivided into subprocesses that monitor specific functions in an organism. The theory matches well with each intuition on a previously published list of intuited ideas about biological functions, including intuitions that have posed difficulties for other theories. (shrink)

Researchers from diverse disciplines, including organismal and cellular physiology, sports science, human nutrition, evolution and ecology, have sought to understand the causes and consequences of the surprising variation in metabolic rate found among and within individual animals of the same species. Research in this area has been hampered by differences in approach, terminology and methodology, and the context in which measurements are made. Recent advances provide important opportunities to identify and address the key questions in the field. By bringing together (...) researchers from different areas of biology and biomedicine, we describe and evaluate these developments and the insights they could yield, highlighting the need for more standardisation across disciplines. We conclude with a list of important questions that can now be addressed by developing a common conceptual and methodological toolkit for studies on metabolic variation in animals. (shrink)

A recently developed computational and neurobiological theory of phenomenal consciousness is applied to a series of persistent philosophical problems of consciousness (in recent formulations by Tye, Searle, and Chalmers). Each problem has a clear solution according to this theory, as is briefly explained here. A slightly modified version of this paper can be found as Chapter 16 ('Philosophical problems of consciousness') in my book 'The estimator theory of life and mind: how agency and consciousness can emerge', see VANTET-8 at philpapers (...) . (shrink)

First published in 2002. Routledge is an imprint of Taylor & Francis, an informa company.