Related Experiment Video
Updated: Jun 20, 2026
06:38
Pattern-based Search of Epigenomic Data Using GeNemo
Published on: October 8, 2017
Entrez Neuron RDFa: a pragmatic semantic web application for data integration in neuroscience research.
Matthias Samwald1, Ernest Lim, Peter Masiar
1Digital Enterprise Research Institute, National University of Ireland Galway, IDA Business Park, Lower Dangan, Galway, Ireland. samwald@gmx.at
Studies in Health Technology and Informatics
|September 12, 2009
Summary
Entrez Neuron offers a user-friendly interface for querying biomedical data using Semantic Web technologies. This neuron-centric system integrates diverse data types, organizing results hierarchically for easier access.
Area of Science:
- Biomedical Informatics
- Semantic Web Technologies
- Neuroscience Data Management
Background:
- Growing volume of biomedical data in Semantic Web formats.
- Lack of user-friendly interfaces for querying these machine-readable datasets.
- Need for integrated access to diverse neuronal data.
Purpose of the Study:
- Introduce Entrez Neuron, a pilot neuron-centric interface.
- Enable keyword-based queries against curated OWL ontologies.
- Demonstrate Semantic Web for information integration in neuroscience.
Main Methods:
- Developed a neuron-centric web interface (Entrez Neuron).
- Utilized OWL ontologies for neuronal structures, physiology, models, and images.
- Integrated entities from Open Biomedical Ontologies (OBO) and HCLS knowledgebase.
- Employed RDFa for embedding semantic annotations in HTML.
Main Results:
- Hierarchical organization of query results based on brain architecture.
- Successful information integration within and between curated repositories.
- Demonstrated client-side information integration via RDFa markup.
Conclusions:
- Entrez Neuron facilitates access to complex biomedical data.
- Semantic Web technologies are effective for neuroscience data integration.
- RDFa enables practical, client-side semantic data sharing.
Related Concept Videos
01:22Neurons as Communicators of the Brain
Neurons, the fundamental units of the brain and nervous system, function as the primary transmitters of information throughout the body. Their ability to communicate through electrical and chemical signals is vital for every bodily function, from regulating the heartbeat to processing complex thoughts. Each neuron has three main components: the cell body (soma), dendrites, and an axon, each specialized to facilitate swift and efficient neural communication.
Cell Body
The cell body, also known...
Cell Body
The cell body, also known...
01:28Integration of Synaptic Events
Synaptic integration mainly includes the summation of graded potentials. Graded potentials, regardless of their type, cause subtle alterations in membrane voltage, resulting in either depolarization or hyperpolarization. These incremental changes, when combined or summed, can propel the neuron toward its threshold. Consider, for example, a membrane experiencing a +15 mV shift, causing it to depolarize from -70 mV to -55 mV. In this scenario, graded potentials govern the membrane's ability to...
01:21Neurons: The Axon
Axons are long, cytoplasmic processes of nerve cells capable of propagating electrical impulses known as action potentials. The cytoplasm or axoplasm of an axon contains neurofibrils, neurotubules, small vesicles, lysosomes, mitochondria, and various enzymes, all encased within the axolemma, the plasma membrane of the axon.
The axon attaches to the cell body at a cone-shaped elevation called the axon hillock. The initial part of the axon, closest to the hillock, is known as the initial segment.
The axon attaches to the cell body at a cone-shaped elevation called the axon hillock. The initial part of the axon, closest to the hillock, is known as the initial segment.
01:28Neuronal Communication
Neurons, the fundamental units of the brain and nervous system, communicate through complex electrochemical signals that underpin all cognitive and bodily functions. This communication is primarily facilitated by a process involving the generation and propagation of an action potential along the axon of the neuron. When the internal electrical charge of a neuron surpasses a certain threshold, an action potential is triggered. This rapid change in voltage travels swiftly along the axon to the...
01:25Applications Of NMR In Biology
Nuclear magnetic resonance (NMR) spectroscopy is a very valuable analytical technique for researchers. It has been used for more than 50 years as an analytical tool. F. Bloch and E. Purcell formulated NMR in 1946 and won the 1952 Nobel Prize in Physics for their work. Biological macromolecules such as proteins, nucleic acids, lipids, and organic molecules including pharmaceutical compounds, can be studied using this versatile tool that exploits the magnetic properties of certain nuclei.
The...
The...
01:09Synaptic Signaling
Neurons communicate at synapses, or junctions, to excite or inhibit the activity of other neurons or target cells, such as muscles. Synapses may be chemical or electrical.
Most synapses are chemical, meaning an electrical impulse or action potential spurs the release of chemical messengers called neurotransmitters. The neuron sending the signal is called the presynaptic neuron, and the neuron receiving the signal is the postsynaptic neuron.
The presynaptic neuron fires an action potential that...
Most synapses are chemical, meaning an electrical impulse or action potential spurs the release of chemical messengers called neurotransmitters. The neuron sending the signal is called the presynaptic neuron, and the neuron receiving the signal is the postsynaptic neuron.
The presynaptic neuron fires an action potential that...