Barry Smith an sich

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński

Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results

OAE: The Ontology of Adverse Events

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data

OAE: The Ontology of Adverse Events

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data

Uberon, an integrative multi-species anatomy ontology

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.or

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis

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

A black art: Ontology, data, and the Tower of Babel problem

Computational ontologies are a new type of emerging scientific media (Smith, 2016) that process large quantities of heterogeneous data about portions of reality. Applied computational ontologies are used for semantically integrating (Heiler, 1995; Pileggi & Fernandez-Llatas, 2012) divergent data to represent reality and in so doing applied computational ontologies alter conceptions of materiality and produce new realities based on levels of informational granularity and abstraction (Floridi, 2011), resulting in a new type of informational ontology (Iliadis, 2013) the critical analysis of which requires new methods and frameworks. Currently, there is a lack of literature addressing the theoretical, social, and critical dimensions of such informational ontologies, applied computational ontologies, and the interdisciplinary communities of practice (Brown & Duguid, 1991; Wenger, 1998) that produce them. This dissertation fills a lacuna in communicative work in an emerging subfield of Science and Technology Studies (Latour & Woolgar, 1979) known as Critical Data Studies (boyd & Crawford, 2012; Dalton & Thatcher, 2014; Kitchin & Lauriault, 2014) by adopting a critical framework to analyze the systems of thought that inform applied computational ontology while offering insight into its realism-based methods and philosophical frameworks to gauge their ethical import. Since the early 1990s, computational ontologies have been used to organize massive amounts of heterogeneous data by individuating reality into computable parts, attributes, and relations. This dissertation provides a theory of computational ontologies as technologies of individuation (Simondon, 2005) that translate disparate data to produce informational cohesion. By technologies of individuation I mean engineered artifacts whose purpose is to partition portions of reality into computable informational objects. I argue that data are metastable entities and that computational ontologies restrain heterogeneous data via a process of translation to produce semantic interoperability. In this way, I show that computational ontologies effectively re-ontologize (Floridi, 2013) and produce reality and thus that have ethical consequences, specifically in terms of their application to social reality and social ontology (Searle, 2006). I use the Basic Formal Ontology (Arp, Smith, & Spear, 2015)—the world’s most widely used upper-level ontology—as a case study and analyze its methods and ensuing ethical issues concerning its social application in the Military Ontology before recommending an ethical framework. “Ontology” is a term that is used in philosophy and computer science in related but different ways—philosophical ontology typically concerns metaphysics while computational ontology typically concerns databases. This dissertation provides a critical history and theory of ontology and the interdisciplinary teams of researchers that came to adopt methods from philosophical ontology to build, persuade, and reason with applied computational ontology. Following a critical communication approach, I define applied computational ontology construction as a solution to a communication problem among scientists who seek to create semantic interoperability among data and argue that applied ontology is philosophical, informational in nature, and communicatively constituted (McPhee & Zaug, 2000). The primary aim is to explain how philosophy informs applied computational ontology while showing how such ontologies became instantiated in material organizations, how to study them, and describe their ethical implications

Perspectives on next steps in classification of oro-facial pain - part 1: role of ontology

The purpose of this study was to review existing principles of oro-facial pain classifications and to specify design recommendations for a new system that would reflect recent insights in biomedical classification systems, terminologies and ontologies. The study was initiated by a symposium organised by the International RDC/TMD Consortium Network in March 2013, to which the present authors contributed. The following areas are addressed: problems with current classification approaches, status of the ontological basis of pain disorders, insufficient diagnostic aids and biomarkers for pain disorders, exploratory nature of current pain terminology and classification systems, and problems with prevailing classification methods from an ontological perspective. Four recommendations for addressing these problems are as follows: (i) develop a hypothesis-driven classification structure built on principles that ensure to our best understanding an accurate description of the relations among all entities involved in oro-facial pain disorders; (ii) take into account the physiology and phenomenology of oro-facial pain disorders to adequately represent both domains including psychosocial entities in a classification system; (iii) plan at the beginning for field-testing at strategic development stages; and (iv) consider how the classification system will be implemented. Implications in relation to the specific domains of psychosocial factors and biomarkers for inclusion into an oro-facial pain classification system are described in two separate papers