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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
TLDR
This work describes the OBO Foundry initiative and provides guidelines for those who might wish to become involved and describes an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality.
Diagnostic Criteria for Temporomandibular Disorders (DC/TMD) for Clinical and Research Applications: recommendations of the International RDC/TMD Consortium Network* and Orofacial Pain Special
TLDR
The newly recommended evidence-based new DC/TMD protocol is appropriate for use in both clinical and research settings and 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.
Building Ontologies with Basic Formal Ontology
TLDR
This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use.
Relations in biomedical ontologies
TLDR
A methodology for providing consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation is advanced.
SNAP and SPAN: Towards Dynamic Spatial Ontology
TLDR
It is argued that dynamic spatial ontology must combine these two distinct types of inventory of the entities and relationships in reality, and characterizations of spatiotemporal reasoning in the light of the interconnections between them are provided.
BioPortal: ontologies and integrated data resources at the click of a mouse
TLDR
BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping’ to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.
Biodynamic ontology: applying BFO in the biomedical domain.
We propose a modular formal ontology of the biomedical domain with two components, one for biological objects, corresponding broadly to anatomy, and one for biological processes, corresponding
BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse
TLDR
BioPortal is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies developed in OBO, OWL, Protege frames, and RDF.
Beyond Concepts: Ontology as Reality Representation
TLDR
The thesis that ontologies developed for research in the natural sciences should be understood as having as their subject matter, not concepts, but rather the universals and particulars which exist in reality and are captured in scientific laws is defended.
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