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Related Concept Videos

Taxonomy01:31

Taxonomy

Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics. It uses a hierarchy of increasingly inclusive categories with Latin names. The smallest units of taxonomy, species and genus, are used to assign a formal, taxonomic name to each species in a system. This classification system, referred to as binomial nomenclature, was formalized by Carolus Linnaeus in the 18th century.Hierarchy of TaxonomyThe hierarchy that Carolus Linnaeus first...
¹H NMR Signal Integration: Overview00:58

¹H NMR Signal Integration: Overview

The intensity of a signal, which can be represented by the area under the peak, depends on the number of protons contributing to that signal. The area under each peak is shown as a vertical line called an integral, with the integral value listed under it, as seen in the proton NMR spectrum of benzyl acetate. Each integral value is divided by the smallest integral value to obtain the ratio of the number of protons producing each signal. The ratio reveals the relative number of protons and not...
Schemas01:42

Schemas

A schema is a mental construct consisting of a cluster or collection of related concepts (Bartlett, 1932). There are many different types of schemata, and they all have one thing in common: schemata are a method of organizing information that allows the brain to work more efficiently. When a schema is activated, the brain makes immediate assumptions about the person or object being observed.
Natural and Artificial Concepts01:24

Natural and Artificial Concepts

In psychology, concepts can be divided into two categories: natural and artificial. Natural concepts are formed through direct or indirect experiences. For example, consider the concept of snow. If you live in a place with regular snowfall, such as Essex Junction, Vermont, you know snow through direct experiences. You’ve seen it fall, touched it, shoveled it, and played in it. You recognize its texture, appearance, and even its smell. In contrast, if you live on an island like Saint Vincent in...
Mass Analyzers: Overview01:13

Mass Analyzers: Overview

The mass analyzer is a crucial component of the mass spectrometer. In the ionization chamber, the vaporized sample is bombarded with a high-energy electron beam to generate a radical cation and further fragment into neutral molecules, radicals, and cations. A series of negatively charged accelerator plates accelerate the cations into the mass analyzer. The mass analyzer separates ions according to their mass-to-charge (m/z) ratios and then directs them to the detector. The common types of mass...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Related Experiment Video

Updated: Jun 1, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

Tomasz Adamusiak1, Tony Burdett, Natalja Kurbatova

  • 1European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK. tomasz@ebi.ac.uk

BMC Bioinformatics
|May 31, 2011
PubMed
Summary
This summary is machine-generated.

OntoCAT offers a unified interface to access diverse bioinformatics ontologies, simplifying data mapping and reducing duplicated research efforts. This tool integrates multiple ontology resources for easier use.

Related Experiment Videos

Last Updated: Jun 1, 2026

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
05:34

Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods

Published on: June 6, 2025

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Integration

Background:

  • Ontologies are crucial in bioinformatics, but accessing diverse resources like EBI Ontology Lookup Service (OLS) and NCBO BioPortal is challenging.
  • Disparities in access modes and content across ontology resources hinder data mapping and lead to redundant research efforts.

Purpose of the Study:

  • To develop a unified solution for accessing and querying heterogeneous ontology resources.
  • To simplify the integration of ontology data into research workflows.

Main Methods:

  • OntoCAT provides a programmatic interface using Java, Bioconductor/R, and REST web services.
  • It supports querying remote services (OLS, BioPortal) and local OWL/OBO files.
  • OntoCAT is also available as a stand-alone MOLGENIS database and Google App Engine application.

Main Results:

  • OntoCAT enables seamless querying of multiple ontology resources through a unified interface.
  • It facilitates the reuse and integration of ontology software by abstracting technological variations.
  • The tool supports both remote and locally specified ontology terms.

Conclusions:

  • OntoCAT offers a robust and configurable solution for accessing ontology terms from diverse sources.
  • It has been successfully validated in practical use cases such as ArrayExpress, MOLGENIS, EFO, and Gen2Phen.
  • The tool promotes efficient ontology data integration in bioinformatics research.