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Towards Representing Change in the BFO Open
The Basic Formal Ontology (BFO) is an upper ontology that embraces both continuants and occurrents. Continuants can persist through time while undergoing changes through their participation in processes. Processes are held not to change as…
Semantic Difficulties in FHIR ‘Conditions’ Open
One goal of the Fast Healthcare Interoperability Resources (FHIR) standard is to prevent semantic ambiguities when patient data are electronically exchanged. To assess whether the FHIR specifications live up to this expectation, we examine…
Fiat Surfaces in the Basic Formal Ontology Open
The Basic Formal Ontology (BFO) class continuant fiat boundary and its subclasses, including fiat surface, are not heavily axiomatized; they have elucidations, not definitions; and the meanings of these elucidations are poorly captured by …
Setting the Scene to Link SNOMED CT to Realism-Based Ontologies Open
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 Ba…
Axiomatizing SNOMED CT Disorders: Should There Be Room for Interpretation? Open
SNOMED CT is a large concept-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 O…
An Extendible Realism-Based Ontology for Kinship. Open
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. I…
Challenges in Realism-Based Ontology Design: a Case Study on Creating an Ontology for Motivational Learning Theories. Open
whereas behavioral scientists need to do efforts to make their theories comparable, realism-based ontologies can help them therein only when ontology developers and educators put more effort in making them more accessible without violating…
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† Open
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 t…
Foundations for a Realism-Based Ontology of Protein Aggregates. Open
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 portio…
Expanding Evolutionary Terminology Auditing with Historic Formal and Linguistic Intensions: A Case Study in SNOMED CT Open
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 …
Enhancing the Representational Power of i2b2 through Referent Tracking. Open
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 gene…
Improving the 'Fitness for Purpose' of Common Data Models through Realism Based Ontology. Open
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 b…
The Problems of Realism-Based Ontology Design: a Case Study in Creating Definitions for an Application Ontology for Diabetes Camps. Open
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 …
Analyzing SNOMED CT's Historical Data: Pitfalls and Possibilities. Open
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 …