Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Levels of Organization01:09

Levels of Organization

Biological organization is the classification of biological structures, ranging from atoms at the bottom of the hierarchy to the Earth's biosphere. Each level of the hierarchy represents an increase in complexity that builds upon the previous level.Molecules Are Composed of Atoms, and Biomolecules Are Assembled from Molecules:The most basic levels include atoms, molecules, and biomolecules. Atoms, the smallest unit of ordinary matter, are composed of a nucleus and electrons. Molecules comprise...
Anatomical Terminology01:20

Anatomical Terminology

Knowledge of anatomy is essential to understand human biology and medicine. Anatomists and health care professionals use standard terminology to describe the human body with more precision and no ambiguity. Anatomical terms have mostly Greek and Latin-derived roots. Because these languages are rarely used in conversation, the meaning of words remains the same. Each term is made up of a root in between the prefixes and suffixes. The root of a term often refers to an organ, tissue, or condition,...
Impact of Schemas01:30

Impact of Schemas

Schemas are cognitive structures that provide a framework for interpreting and organizing social information. They help individuals navigate complex environments by offering expectations about people, events, and behaviors. Schemas influence attention, encoding, and retrieval processes, thereby shaping the entire trajectory of information processing in social contexts.Attention and Cognitive LoadDuring initial attention, schemas function as filters that prioritize schema-consistent information,...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Types of Aggregate Grading01:15

Types of Aggregate Grading

Aggregate grading is crucial in economically obtaining a concrete mix with adequate strength, reasonable workability, and minimal segregation. There are four types of aggregate gradation: well-graded, uniformly (or one-sized) graded, gap-graded, and open-graded.
Well-graded aggregates include a complete range of necessary size fractions that fit together to create a dense matrix with minimal voids, represented by a smooth, continuous gradation curve. This type of grading ensures good...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

The economic impact of a physician-introduced web portal on lower back pain: results from a cluster-randomized trial.

Cost effectiveness and resource allocation : C/E·2026
Same author

Towards an Event-Condition-Action (ECA)-Based Formalization of Clinical Guidelines.

Studies in health technology and informatics·2026
Same author

Effectiveness of Guideline-Based Clinical Decision Support Systems: Protocol for a Systematic Review.

JMIR research protocols·2026
Same author

An Event-Condition-Action (ECA)-Based Formalization of Clinical Guidelines.

Studies in health technology and informatics·2026
Same author

Language Models for Automatic Clinical Coding in Veterinary Texts: Experimental Results.

Studies in health technology and informatics·2026
Same author

Standardized Information Model for Clinical Texts: The MII Core Data Set Module Document.

Studies in health technology and informatics·2026

Related Experiment Video

Updated: Jun 24, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Granularity issues in the alignment of upper ontologies.

Stefan Schulz1, Martin Boeker, Holger Stenzhorn

  • 1Universitätsklinikum, Institut für Medizinische Biometrie und Medizinische Informatik, Stefan-Meier-Strasse 26, 79104 Freiburg, Germany. stschulz@uni-freiburg.de

Methods of Information in Medicine
|March 14, 2009
PubMed
Summary
This summary is machine-generated.

Integrating the Basic Formal Ontology (BFO) with the BioTop ontology revealed logical inconsistencies related to granularity. The study suggests modifications for improved interoperability between domain ontologies.

Related Experiment Videos

Last Updated: Jun 24, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
09:34

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Area of Science:

  • Biomedical informatics
  • Ontology engineering
  • Knowledge representation

Background:

  • Upper ontologies are crucial for interoperability between diverse domain ontologies.
  • BioTop aims to align specialized biomolecular and biomedical ontologies.
  • Basic Formal Ontology (BFO) is a foundational upper ontology.

Purpose of the Study:

  • To integrate BioTop with the Basic Formal Ontology (BFO).
  • To assess the compatibility and consistency of this integration.
  • To enhance data sharing and interoperability in biomedical research.

Main Methods:

  • Manual integration of BFO into BioTop, aligning definitions.
  • Utilizing BioTop classes as children of BFO classes.
  • Employing a description logic reasoner for logical consistency checks.
  • Domain adequacy validation by subject matter experts.

Main Results:

  • Logical inconsistencies were identified by the reasoner concerning BFO classes for fiat and aggregated objects.
  • These inconsistencies stemmed from BFO's reliance on physical connectedness.
  • A specific BFO subbranch was recommended for exclusion to facilitate cross-granularity integration.

Conclusions:

  • Addressing granularity issues is essential for robust ontology integration.
  • The study advocates for granularity-independent upper ontologies.
  • Demonstrates embedding granularity-dependent domain ontologies within BioTop-BFO framework.