Fiat Surfaces in the Basic Formal Ontology.

The Basic Formal Ontology (BFO) class and its subclasses, including , are not heavily axiomatized; they have elucidations, not definitions; and the meanings of these elucidations are poorly captured by the relevant BFO axioms. This paper is an effort to make progress in these respects for . We identify a range of desiderata for a BFO-conformant view of , argue that the GitHub does not satisfy them, argue that the view of fiat surfaces in Arp et al.

Setting the Scene to Link SNOMED CT to Realism-Based Ontologies.

In a proof of concept study, we assessed the feasibility of designing a first-order logic (FOL) framework capable of translating SNOMED CT's terminological view on patient data as referencing concepts, into the realism-based view of the Basic Formal Ontology and the Ontology for General Medical Science according to which patient data represent instances of types. Because within the subject domain of this study, SNOMED CT's terminological coverage was excellent, and its EL++ axioms can be automatically translated into FOL as well as the antecedent part of bridging axioms between SNOMED CT and realism-based ontologies, we conclude that this is an area of R&D that deserves further attention and that may lead to new ways of federating terminologies with ontologies.

An Extendible Realism-Based Ontology for Kinship.

Adequately representing kinship relations is crucial for a variety of medical and biomedical applications. Several kinship ontologies have been proposed but none of them have been designed thus far in line with the Basic Formal Ontology. In this paper, we propose a novel kinship ontology that exhibits the following characteristics: (1) it is fully axiomatized in First Order Logic following the rules governing predicate formation as proposed in BFO2020-FOL, (2) it is modularized in 6 separate files written in the Common Logic Interface Format (CLIF) each one of which can be imported based on specific needs, (3) it provides bridging axioms to and from SNOMED CT, and (4) it contains an extra module with axioms which would not be literally true when phrased naively but are crafted in such a way that they highlight the unusual kinship relations they represent and can be used to generate alerts on possible data entry mistakes.

Axiomatizing SNOMED CT Disorders: Should There Be Room for Interpretation?

SNOMED CT is a large -based terminology designed according to epistemic, semantic and pragmatic principles relevant to clinicians. Its goal is structured clinical reporting in electronic healthcare records (EHRs). The Basic Formal Ontology (BFO) is an ontology designed on the basis of claimed to exist in reality based on a domain-independent ontological theory.

Foundations for a Realism-Based Ontology of Protein Aggregates.

The objective of this paper is to propose formal definitions for the terms 'protein aggregate' and 'protein-containing complex' such that the descriptions and usages of these terms in biomedical literature are unified and that those portions of reality are correctly represented. To this end, we surveyed the literature to assess the need for a distinction between these entities, then compared the features of usages and definitions found in the literature to the definitions for those terms found in Bioportal ontologies. Based on the results of this comparison, we propose updated definitions for the terms 'protein aggregate' and 'protein-containing complex'.

Challenges in Realism-Based Ontology Design: a Case Study on Creating an Ontology for Motivational Learning Theories.

Objective: to identify on the basis of a use case major problem types novices in realism-based ontology design face when attempting to construct an ontology intended to explain differences and commonalities between competing scientific theories.

Methodology: an ontology student was tasked (1) to extract manually from a paper about five distinct motivational learning theories the scientific terms used to explain the theories, (2) to map these terms where possible to type-terms from existing realism-based ontologies or create new ones otherwise, (3) to indicate for new type-terms their immediate subsumer, and (4) to document at every step issues that were encountered.

Results: where term extraction and type-term assignment were handled satisfactorily, correct classification in function of the BFO was a major challenge.

Expanding Evolutionary Terminology Auditing with Historic Formal and Linguistic Intensions: A Case Study in SNOMED CT.

A method is described to use SNOMED CT's history mechanism as a means to compute how the formal and linguistic intensions of its concepts change over versions. As a result of this, it is demonstrated that the intended principle of concept permanence is not always adhered to. It is shown that the evolution of formal intensions can be monitored fully automatically and that the proposed procedure includes a method to suggest missing subsumers in a concept's transitive closure set by identifying mistakes that have been made in the past.

Enhancing the Representational Power of i2b2 through Referent Tracking.

The Informatics for Integrating Biology and the Bedside (i2b2) software platform has proven successful in leveraging clinical enterprise data for the identification of cohorts of patients satisfying certain demographic, phenotypic and genetic criteria in support of further studies. An unanswered question thus far is whether i2b2 search criteria could include characteristics of assertions themselves, e.g.

Caveats for the Use of the Active Problem List as Ground Truth for Decision Support.

Diagnoses recorded on the problem list are increasingly being used for decision support applications. To obtain insight in the adequacy of the clinical user interface to capture what the clinician has in mind, and to reconstruct the clinical reality of the patient, we analyzed in the database of an EHR system the transactions that resulted from managing the problem list. Our findings indicate (1) that caution is required when using the evolution of the problem list for determining comorbidity or ongoing disease, and (2) that similarities or differences in problem list annotation sequences do not always correspond with similarities resp.

The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps.

A requirement of realism-based ontology design is that classes denote exclusively entities that exist objectively in reality and that their definitions adhere to strict criteria to ensure that the classes are re-usable in other ontologies while preserving their ontological commitment. Building realism-based ontologies is therefore quite challenging and time-consuming, demanding considerable training. Although the top-level in the form of the Basic Formal Ontology (BFO) is worked out very well, and also the upper levels of certain domains, there is still a disconnect with the bottom- up or middle-out approach which is typical, and more practical, for application ontologies.

Improving the 'Fitness for Purpose' of Common Data Models through Realism Based Ontology.

Common data models are designed and built based on requirements that are aimed towards fitness for purpose. But when common data models are used as lenses through which reality is observed from the perspective according to which they are built, then they exhibit restrictions that distort such view. Realism-based ontology design, when done properly, does not have these limitations as its fitness for purpose is only determined by the degree to which reality is represented the way it is.

On Defining Bruxism.

In a series of recent publications, orofacial researchers have debated the question of how 'bruxism' should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology.

Mismatches between major subhierarchies and semantic tags in SNOMED CT.

The fully specified name of a concept in SNOMED CT is formed by a term to which in the typical case is added a semantic tag. The latter is meant to disambiguate homonymous terms and to indicate in which major subhierarchy of SNOMED CT that concept fits. We have developed a method to determine whether a concept's tag correctly identifies its place in the hierarchy, and applied this method to an analysis of all active concepts in every SNOMED CT release from January 2003 to January 2017.

A Realism-Based View on Counts in OMOP's Common Data Model.

Correctly counting entities is a requirement for analytics tools to function appropriately. The Observational Medical Outcomes Partnership's (OMOP) Common Data Model (CDM) specifications were examined to assess the extent to which counting in OMOP CDM compatible data repositories would work as expected. To that end, constructs (tables, fields and attributes) defined in the OMOP CDM as well as cardinality constraints and other business rules found in its documentation and related literature were compared to the types of entities and axioms proposed in realism-based ontologies.

Ontological Realism for the Research Domain Criteria for Mental Disorders.

At the heart of the Research Domain Criteria for Mental Disorders is a matrix in which functional aspects of behavior are related to genotypic and (endo-)phenotypic research findings, and the various techniques through which they can been observed. The matrix is work in progress. As such it currently suffers from several shortcomings, the resolution of which, we contend, are essential to success of NIMH's goal of fostering translational science on mental disorders.

Business Rules to Improve Secondary Data Use of Electronic Healthcare Systems.

The 'fit for purpose' paradigm used for data quality assessment in electronic healthcare record (EHR) systems is not so fit when assessed in the light of secondary data use. An analysis of the difficulties encountered in trying to use existing EHR data for cohort identification for prospective clinical trials and retrograde data analytics, revealed the root causes to fall in three categories: (1) issues in workflow and data registration, (2) preventable inadequacies in software configuration and personalization and (3) software development issues on the side of the vendor. By reviewing secondary data use requirements and formulating value adding business rules, development and data collection practices can be steered towards greater value in secondary data consumption.

Analyzing SNOMED CT's Historical Data: Pitfalls and Possibilities.

SNOMED CT's Release Format 2 (RF2) has been announced as an improvement over its predecessor, for instance because of its more consistent and almost formal approach towards describing changes in components over different versions, as well as changes in the structure of SNOMED CT itself. We explore two sorts of changes that are only partially formalized in RF2: the relationships between associative relations and reasons for inactivations as expressed in Association Reference Sets and Attribute Value Reference Sets on the one hand, and the various patterns according to which semantic tags appearing in fully specified names change over subsequent versions with or without being related to inactivations. We propose a data conversion methodology that combines assertions about SNOMED CT components into history profiles and use elements of these profiles to build Formal Concept Analysis contexts to discover valid implications that can render implicit assumptions hidden in SNOMED CT's structure explicit.

A preliminary study of a novel emergency department nursing triage simulation for research applications.

Background: Studying the effect on functioning of the emergency department of disasters with a potential impact on staff members themselves usually involves table top and simulated patient exercises. Computerized virtual reality simulations have the potential to configure a variety of scenarios to determine likely staff responses and how to address them without intensive utilization of resources. To decide whether such studies are justified, we determined whether a novel computer simulation has the potential to serve as a valid and reliable model of on essential function in a busy ED.

Diagnosis, misdiagnosis, lucky guess, hearsay, and more: an ontological analysis.

Background: Disease and diagnosis have been the subject of much ontological inquiry. However, the insights gained therein have not yet been well enough applied to the study, management, and improvement of data quality in electronic health records (EHR) and administrative systems. Data in these systems suffer from workarounds clinicians are forced to apply due to limitations in the current state-of-the art in system design which ignore the various types of entities that diagnoses as information content entities can be and are about.

Ontological Foundations for Tracking Data Quality through the Internet of Things.

Amongst the positive outcomes expected from the Internet of Things for Health are longitudinal patient records that are more complete and less erroneous by complementing manual data entry with automatic data feeds from sensors. Unfortunately, devices are fallible too. Quality control procedures such as inspection, testing and maintenance can prevent devices from producing errors.

Biomarkers in the ontology for general medical science.

A great deal of recent work has been devoted to the topic of biomarkers as aids to diagnosis, prognosis and treatment evaluation. Basing our work on the Ontology for General Medical Science (OGMS) and on the specifications provided by the Institute of Medicine (IOM), we propose definitions for biomarkers of various types. These definitions provide a formal representation of what biomarkers are in a way that allows us to remove certain ambiguities and inconsistencies in the documentation provided by the IOM.

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†.

Aims: The 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.

Applying ontological realism to medically unexplained syndromes.

The past decade has witnessed an increased interest in what are called "medically unexplained syndromes" (MUS). We address the question of whether structuring the domain knowledge for MUS can be achieved by applying the principles of Ontological Realism in light of criticisms about their usefulness in areas where science has not yet led to insights univocally endorsed by the relevant communities. We analyzed whether the different perspectives held by MUS researchers can be represented without taking any particular stance and whether existing ontologies based on Ontological Realism can be further built upon.

An information artifact ontology perspective on data collections and associated representational artifacts.

Biomedical data collections are typically compiled on the basis of assessment instruments and associated terminologies and their data structure explained by means of data dictionaries. The Information Artifact Ontology (IAO) is an attempt to give a realism-based account of the essence of information entities and how components of such entities relate to each other and to that what they are information about. Changes in the taxonomy and the definitions of the IAO, most importantly the addition of the terms 'representational artifact' and 'representational unit', are proposed to make the IAO a useful tool to clarify formally the distinctions and commonalities between data collections and associated artifacts that are compiled independently from each other, yet cover the same domain.

SNOMED CT revisions and coded data repositories: when to upgrade?

SNOMED CT is gaining momentum in its acceptance and operational application as a reference terminology in electronic health systems. Because it is revised every six months, organizations using SNOMED CT might feel a need to ensure that their systems are synchronized with these revisions. It has been shown that for certain sorts of applications migration to a new version is a labor-intensive process.