Louis J. Goldberg

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 is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are 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 and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved.

Diagnostic Criteria for Temporomandibular Disorders (DC/TMD) for Clinical and Research Applications: Recommendations of the International RDC/TMD Consortium Network and Orofacial Pain Special Interest Group

AIMSnThe original Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) Axis I diagnostic algorithms have been demonstrated to be reliable. However, the Validation Project determined that the RDC/TMD Axis I validity was below the target sensitivity of ≥ 0.70 and specificity of ≥ 0.95. Consequently, these empirical results supported the development of revised RDC/TMD Axis I diagnostic algorithms that were subsequently demonstrated to be valid for the most common pain-related TMD and for one temporomandibular joint (TMJ) intra-articular disorder. The original RDC/TMD Axis II instruments were shown to be both reliable and valid. Working from these findings and revisions, two international consensus workshops were convened, from which recommendations were obtained for the finalization of new Axis I diagnostic algorithms and new Axis II instruments.nnnMETHODSnThrough a series of workshops and symposia, a panel of clinical and basic science pain experts modified the revised RDC/TMD Axis I algorithms by using comprehensive searches of published TMD diagnostic literature followed by review and consensus via a formal structured process. The panels recommendations for further revision of the Axis I diagnostic algorithms were assessed for validity by using the Validation Projects data set, and for reliability by using newly collected data from the ongoing TMJ Impact Project-the follow-up study to the Validation Project. New Axis II instruments were identified through a comprehensive search of the literature providing valid instruments that, relative to the RDC/TMD, are shorter in length, are available in the public domain, and currently are being used in medical settings.nnnRESULTSnThe newly recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for detecting any pain-related TMD as well as valid diagnostic criteria for differentiating the most common pain-related TMD (sensitivity ≥ 0.86, specificity ≥ 0.98) and for one intra-articular disorder (sensitivity of 0.80 and specificity of 0.97). Diagnostic criteria for other common intra-articular disorders lack adequate validity for clinical diagnoses but can be used for screening purposes. Inter-examiner reliability for the clinical assessment associated with the validated DC/TMD criteria for pain-related TMD is excellent (kappa ≥ 0.85). Finally, a comprehensive classification system that includes both the common and less common TMD is also presented. The Axis II protocol retains selected original RDC/TMD screening instruments augmented with new instruments to assess jaw function as well as behavioral and additional psychosocial factors. The Axis II protocol is divided into screening and comprehensive self report instrument sets. The screening instruments 41 questions assess pain intensity, pain-related disability, psychological distress, jaw functional limitations, and parafunctional behaviors, and a pain drawing is used to assess locations of pain. The comprehensive instruments, composed of 81 questions, assess in further detail jaw functional limitations and psychological distress as well as additional constructs of anxiety and presence of comorbid pain conditions.nnnCONCLUSIONnThe recommended evidence-based new DC/TMD protocol is appropriate for use in both clinical and research settings. More comprehensive instruments augment short and simple screening instruments for Axis I and Axis II. These validated instruments allow for identification of patients with a range of simple to complex TMD presentations.

Biosymbols: Symbols in Life and Mind

The strong continuity thesis postulates that the properties of mind are an enriched version of the properties of life, and thus that life and mind differ in degree and not kind. A philosophical problem for this view is the ostensive discontinuity between humans and other animals in virtue of our use of symbols—particularly the presumption that the symbolic nature of human cognition bears no relation to the basic properties of life. In this paper, we make the case that a genuine account of strong continuity requires the identification of some sort of correlate of symbol-use in basic life properties. Our strategy is three-fold: 1) we argue that examples of proto-symbolism in simple living systems would be consistent with an evolutionary trajectory that ultimately produced symbolic cognition in humans; 2) we introduce Gordon Tomkins’ biological notion of ‘symbol’ as something that represents to the organism a feature of its environment that is significant to its survival; and 3) we employ this biological understanding of symbol-use to suggest that the symbolic nature of human cognition can be understood as an enriched version of the basic symbolic properties of life, thus preserving life-mind continuity in this context.

How Is Meaning Grounded in the Organism

In this paper we address the interrelated questions of why and how certain features of an organism’s environment become meaningful to it. We make the case that knowing the biology is essential to understanding the foundation of meaning-making in organisms. We employ Miguel Nicolelis et al’s seminal research on the mammalian somatosensory system to enrich our own concept of brain-objects as the neurobiological intermediary between the environment and the consequent organismic behavior. In the final section, we explain how brain-objects advance the ongoing discussion of what constitutes a biosemiotic system. In general, this paper acknowledges Marcello Barbieri’s call for biology to make room for meaning, and makes a contribution to that end.

The challenges of defining oral cancer: analysis of an ontological approach.

An important inconsistency currently exists in the literature on oral cancer. Reviewing this literature, one finds that the term oral cancer is defined and described with great variation. In a search in PubMed, at least 17 different terms were found for titles of papers reporting data on oral cancer. The variability of the terms used for designating anatomic regions and type of malignant neoplasms for reporting oral cancer has hampered the ability of researchers to effectively retrieve information concerning oral cancer. Therefore, it is sometimes extremely difficult to provide meaningful comparisons among various studies of oral cancer. Recently, a new ontological strategy that is rooted in consensus-based controlled vocabularies has been proposed to improve the consistency of data in dental research (Smith et al. in J Am Dent Assoc 141:1173–1175, 2010). In this paper, we analyzed the terminology dilemma on oral cancer and explained the current situation. We proposed a possible solution to the dilemma using an ontology-based approach. The advantages for applying this strategy are also discussed.

The qualitative and time-dependent character of spatial relations in biomedical ontologies

MOTIVATIONnThe formal representation of mereological aspects of canonical anatomy (parthood relations) is relatively well understood. The formal representation of other aspects of canonical anatomy, such as connectedness and adjacency relations between anatomical parts, their shape and size as well as the spatial arrangement of anatomical parts within larger anatomical structures are, however, much less well understood and represented in existing computational anatomical and bio-medical ontologies only insufficiently.nnnRESULTSnIn this article, we provide a methodology of how to incorporate this kind of information into anatomical and bio-medical ontologies by applying techniques of representing qualitative spatial information from Artificial Intelligence. In particular, we focus on how to explicitly take into account the qualitative and time-dependent character of these relations. As a running example, we use the human temporomandibular joint (TMJ).nnnAVAILABILITYnUsing the presented methodology, a formal ontology was developed which is accessible on http://www.ifomis.org/bfo/fol. This ontology may help to improve the logical and ontological rigor of bio-medical ontologies such as the OBO relation ontology.

More than a Set of Teeth: Assessing and Enhancing Dental Students' Perceptions of Older Adults

Abstract Dental professionals play a key role in maintaining the well-being of older adults by identifying problems that disturb systemic health. A 3-part instrument was used to assess dental students knowledge of aging, comfort with patient diversity and patient care strategies (Years 1-4; N= 321). Collaborative education and services were developed by the Schools of Dental Medicine and Social Work. Results indicate that dental students knowledge ofaging was low (Palmores FAQ 1 Range = 58%-64%), comfort with geriatric issues improved after the first year of intervention, and strategies for patient care changed with experience. Group differences suggest the importance of utilizing educational “turning points” as teachable moments.

Modeling Principles and Methodologies - Spatial Representation and Reasoning

Spatial relations include mereological relations such as parthood and overlap, topological relations such as connectedness and one-pieceness, as well as location relations. The location and the arrangement of an anatomical structure within the human body can be further specified by means of relations that express spatial orderings in a qualitative way, e.g. superior, anterior, lateral, etc. In this chapter we give an overview of the various kinds of spatial relations and their properties. We particularly focus on properties of spatial relations that can be exploited for automated reasoning. We also discuss the distinction between so-called individual-level and type-level spatial relations.

Coexistent concerns: assessing the social and health needs of dental clinic patients.

Abstract University dental clinic professionals identified increasing numbers of patients with complex problems and generated 2 research questions: (1) Are there significant health and social concerns within the dental clinic population that indicate the need for high-risk screening and social work services?; and (2) How do age, gender, and income influence health and social concerns in this population? This exploratory descriptive cross-sectional study employed a brief self-report survey in a clinic waiting area. Logistic regression was used to understand the influence of age, gender and income on the existence of specific concerns. Results indicate that caregiving, finances and health are issues for 1/3 of the participants and that 44% endorsed 2 or more concerns. These findings were used to develop a routine high-risk screening tool for dental clinic patients and social work services within the clinic; they suggest that community clinics with dental services are an important place for identifying complex unmet needs.

On the Genetic and Epigenetic Bases of Primate Signal Processing

Four sequential, sub-processes are identified as the fundamental steps in the processing of signals by big-brained animals. These are, Detection of the signal, its Representation in correlated sensory brain structure, the Interpretation of the signal in another part of the brain and the Expression of the receiver’s response. We label this four-step spatiotemporal process DRIE. We support the view that when the context within which such signals are produced and received is relatively constant, the DRIE process can be ultimately assimilated into the genome, with the Interpretation sub-phase is markedly decreased in duration as speed and efficiency are maximized. With frequent repetition and learning, an analogous result can be attained epigenetically as exemplified in human word and text recognition, allowing tasks critical to primate social function to be accomplished with rapidity and accuracy.