NeuroLex
Encyclopedia
NeuroLex is a dynamic lexicon
of neuroscience
concepts. It is a structured as a semantic wiki
, using Semantic MediaWiki
. NeuroLex is supported by the Neuroscience Information Framework
project.
in databases and other resources (http://neurolex.org/wiki/Category:Structured_knowledge_resource) like the literature
(http://neurolex.org/wiki/Category:Literature_corpus). When one uses the same terms to mean different things, one cannot easily ask questions that span across multiple resources. For example, if three databases have information about what gene
s are expressed in cortex
, but they all use different definitions of cerebral cortex
(http://neurolex.org/wiki/Category:Cerebral_cortex), then one cannot compare them easily.
Blueprint for Neuroscience Research, the NIF enables scientists and students to discover global neuroscience web resources that cut across traditional boundaries – from experimental, clinical and translational neuroscience databases, to knowledge bases, atlases, and genetic/genomic resources.
Unlike general search engines, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, search strategies tailored to neuroscience, and access to content that is traditionally “hidden” from web search engine
s. The Framework is a dynamic inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology
(i.e. NeuroLex). NIF supports concept-based queries across multiple scales of biological structure and multiple levels of biological function, making it easier to search for and understand the results.
As part of the NIF, a simple search interface to many different sources of neuroscience information and data is provided. To make this search more effective, the NIF is constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g. stating that a neuron
is a cell
. This helps users to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that are used to describe data, e.g., anatomical terms, techniques, organism
names.
(http://neurolex.org/wiki/Category:Nervous_system), subcellular structures (http://neurolex.org/wiki/Subcellular_Hierarchy), disease
s (http://neurolex.org/wiki/Category:Disease), functions and techniques. NIF is soliciting community input to add more content and correct what is there.
in September 2008:
More information on related publications can be found on the NIF publications page.
Lexicon
In linguistics, the lexicon of a language is its vocabulary, including its words and expressions. A lexicon is also a synonym of the word thesaurus. More formally, it is a language's inventory of lexemes. Coined in English 1603, the word "lexicon" derives from the Greek "λεξικόν" , neut...
of neuroscience
Neuroscience
Neuroscience is the scientific study of the nervous system. Traditionally, neuroscience has been seen as a branch of biology. However, it is currently an interdisciplinary science that collaborates with other fields such as chemistry, computer science, engineering, linguistics, mathematics,...
concepts. It is a structured as a semantic wiki
Semantic Wiki
A semantic wiki is a wiki that has an underlying model of the knowledge described in its pages. Regular, or syntactic, wikis have structured text and untyped hyperlinks...
, using Semantic MediaWiki
Semantic MediaWiki
Semantic MediaWiki is an extension to MediaWiki that allows for annotating semantic data within wiki pages, thus turning a wiki that incorporates the extension into a semantic wiki...
. NeuroLex is supported by the Neuroscience Information Framework
Neuroscience Information Framework
The Neuroscience Information Framework is a repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources.-Description:...
project.
Overview
The NeuroLex is intended to help improve the way that neuroscientists communicate about their data (http://neurolex.org/wiki/Category:Data_object), so that information systems like the NIF can find data more easily and provide more powerful means of integrating data that occur across distributed resources. One of the big roadblocks to data integration in neuroscience is the inconsistent use of terminologyTerminology
Terminology is the study of terms and their use. Terms are words and compound words that in specific contexts are given specific meanings, meanings that may deviate from the meaning the same words have in other contexts and in everyday language. The discipline Terminology studies among other...
in databases and other resources (http://neurolex.org/wiki/Category:Structured_knowledge_resource) like the literature
Literature
Literature is the art of written works, and is not bound to published sources...
(http://neurolex.org/wiki/Category:Literature_corpus). When one uses the same terms to mean different things, one cannot easily ask questions that span across multiple resources. For example, if three databases have information about what gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s are expressed in cortex
Cortex (anatomy)
In anatomy and zoology the cortex is the outermost layer of an organ. Organs with well-defined cortical layers include kidneys, adrenal glands, ovaries, the thymus, and portions of the brain, including the cerebral cortex, the most well-known of all cortices.The cerebellar cortex is the thin gray...
, but they all use different definitions of cerebral cortex
Cerebral cortex
The cerebral cortex is a sheet of neural tissue that is outermost to the cerebrum of the mammalian brain. It plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It is constituted of up to six horizontal layers, each of which has a different...
(http://neurolex.org/wiki/Category:Cerebral_cortex), then one cannot compare them easily.
Utilization within the Neuroscience Information Framework
The NIF enables discovery and access to public research data and tools worldwide through an open source, networked environment. Funded by the NIHNational Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
Blueprint for Neuroscience Research, the NIF enables scientists and students to discover global neuroscience web resources that cut across traditional boundaries – from experimental, clinical and translational neuroscience databases, to knowledge bases, atlases, and genetic/genomic resources.
Unlike general search engines, NIF provides deeper access to a more focused set of resources that are relevant to neuroscience, search strategies tailored to neuroscience, and access to content that is traditionally “hidden” from web search engine
Web search engine
A web search engine is designed to search for information on the World Wide Web and FTP servers. The search results are generally presented in a list of results often referred to as SERPS, or "search engine results pages". The information may consist of web pages, images, information and other...
s. The Framework is a dynamic inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology
Ontology
Ontology is the philosophical study of the nature of being, existence or reality as such, as well as the basic categories of being and their relations...
(i.e. NeuroLex). NIF supports concept-based queries across multiple scales of biological structure and multiple levels of biological function, making it easier to search for and understand the results.
As part of the NIF, a simple search interface to many different sources of neuroscience information and data is provided. To make this search more effective, the NIF is constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g. stating that a neuron
Neuron
A neuron is an electrically excitable cell that processes and transmits information by electrical and chemical signaling. Chemical signaling occurs via synapses, specialized connections with other cells. Neurons connect to each other to form networks. Neurons are the core components of the nervous...
is a cell
Cell (biology)
The cell is the basic structural and functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. The Alberts text discusses how the "cellular building blocks" move to shape developing embryos....
. This helps users to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that are used to describe data, e.g., anatomical terms, techniques, organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
names.
Content
The initial entries in the NeuroLex were built from the NIFSTD ontologies which subsumed an earlier vocabulary BIRNLex. It currently contains concepts that span gross anatomy, cells of the nervous systemNervous system
The nervous system is an organ system containing a network of specialized cells called neurons that coordinate the actions of an animal and transmit signals between different parts of its body. In most animals the nervous system consists of two parts, central and peripheral. The central nervous...
(http://neurolex.org/wiki/Category:Nervous_system), subcellular structures (http://neurolex.org/wiki/Subcellular_Hierarchy), disease
Disease
A disease is an abnormal condition affecting the body of an organism. It is often construed to be a medical condition associated with specific symptoms and signs. It may be caused by external factors, such as infectious disease, or it may be caused by internal dysfunctions, such as autoimmune...
s (http://neurolex.org/wiki/Category:Disease), functions and techniques. NIF is soliciting community input to add more content and correct what is there.
Further reading
NIF was featured in the volume 6 number 3 issue in the journal NeuroinformaticsNeuroinformatics (journal)
Neuroinformatics is a scientific journal published by Springer under the imprint Humana Press. As the title indicates it publishes articles about neuroinformatics....
in September 2008:
More information on related publications can be found on the NIF publications page.