Related Experiment Video
Updated: Jun 5, 2026
10:41
Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools
Published on: December 16, 2015
Logical development of the cell ontology
Terrence F Meehan1, Anna Maria Masci, Amina Abdulla
1Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA. tmeehan@informatics.jax.org
BMC Bioinformatics
|January 7, 2011
Summary
Computable definitions were created for over 340 hematopoietic cell types in the Cell Ontology (CL). This improves ontology accuracy and supports advanced biological queries and hypothesis generation.
Area of Science:
- Bioinformatics
- Ontology Engineering
- Immunology
Background:
- The Cell Ontology (CL) represents in vivo cell types but faces challenges in complexity and maintenance.
- Making ontology information computable aids error detection and classification using automated reasoners.
- This study focused on generating computable definitions for hematopoietic cell types within the CL.
Purpose of the Study:
- To create computable definitions for hematopoietic cell types in the Cell Ontology.
- To enhance the accuracy and usability of the Cell Ontology through automated reasoning.
- To support advanced biological queries and hypothesis generation related to cell types.
Main Methods:
- Employed a genus-differentia approach to define over 340 Cell Ontology classes.
- Utilized automated reasoners to verify the ontology and identify curation errors.
- Integrated multiple classification axes, including cell surface protein complexes, biological processes, and phenotypic characteristics.
Main Results:
- Generated computable definitions for over 340 hematopoietic cell types.
- Automated reasoners detected errors and identified needs for new cell type classes.
- Inferred new relationships within the CL and between contributing ontologies.
- The restructured ontology aids immune cell identification and sophisticated biological queries.
Conclusions:
- Computable definitions significantly enhance Cell Ontology development.
- This approach improves the interoperability of Open Biological Ontologies (OBO).
- The computable ontology facilitates cell identification, complex queries, and hypothesis generation.
More Related Videos
08:16Isotropic Light-Sheet Microscopy and Automated Cell Lineage Analyses to Catalogue Caenorhabditis elegans Embryogenesis with Subcellular Resolution
Published on: June 6, 2019
07:09A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
Related Concept Videos
01:24Origin of Cellular Life
The origin of life on Earth is a complex and enigmatic event rooted in ancient biochemical processes and geological conditions. Experimental evidence supports the hypothesis that life began with the spontaneous formation of organic molecules such as RNA nucleotides, amino acids, and lipids under early Earth conditions. Factors like volcanic activity, intense UV radiation, and a reducing atmosphere without free oxygen likely facilitated these reactions. Hydrothermal vents on the ocean floor are...
00:57Cellular Differentiation
How does a complex organism such as a human develop from a single cell? It all starts from a single fertilized egg which gives rise to a vast array of cell types, such as nerve cells, muscle cells, and epithelial cells that characterize the adult? Throughout development and adulthood, cellular differentiation leads cells to assume their final morphology and physiology. Differentiation is the process by which unspecialized cells become specialized to carry out distinct functions.
A zygote is a...
A zygote is a...
01:13Cell Diversity
The concept of a cell started with microscopic observations of dead cork tissue by Robert Hooke in 1665. Hooke coined the term "cell" based on the resemblance of the small subdivisions in the cork to the rooms that monks inhabited, called cells. About ten years later, Antonie van Leeuwenhoek became the first person to observe the living and moving cells under a microscope. In the century that followed, the theory that cells represented the basic unit of life developed.
Multicellular organisms...
Multicellular organisms...
00:56What is the Cell Cycle?
The cell cycle refers to the sequence of events occurring throughout a typical cell’s life. In eukaryotic cells, the somatic cell cycle has two stages: the interphase and the mitotic phase. During interphase, the cell grows, performs its basic metabolic functions, copies its DNA, and prepares for mitotic cell division. Then, during mitosis and cytokinesis, the cell divides its nuclear and cytoplasmic materials, respectively. This generates two daughter cells that are identical to the original...
01:04What is the Cell Cycle?
The cell cycle refers to the sequence of events occurring throughout a typical cell’s life. In eukaryotic cells, the somatic cell cycle has two stages: interphase and the mitotic phase. During interphase, the cell grows, performs its basic metabolic functions, copies its DNA, and prepares for mitotic cell division. Then, during mitosis and cytokinesis, the cell divides its nuclear and cytoplasmic materials, respectively. This generates two daughter cells that are identical to the original...
00:56What is the Cell Cycle?
The cell cycle refers to the sequence of events occurring throughout a typical cell’s life. In eukaryotic cells, the somatic cell cycle has two stages: the interphase and the mitotic phase. During interphase, the cell grows, performs its basic metabolic functions, copies its DNA, and prepares for mitotic cell division. Then, during mitosis and cytokinesis, the cell divides its nuclear and cytoplasmic materials, respectively. This generates two daughter cells that are identical to the original...