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. 2013 Aug 30;7:18.
doi: 10.3389/fninf.2013.00018. eCollection 2013.

NeuroLex.org: An Online Framework for Neuroscience Knowledge

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Free PMC article

NeuroLex.org: An Online Framework for Neuroscience Knowledge

Stephen D Larson et al. Front Neuroinform. .
Free PMC article

Abstract

The ability to transmit, organize, and query information digitally has brought with it the challenge of how to best use this power to facilitate scientific inquiry. Today, few information systems are able to provide detailed answers to complex questions about neuroscience that account for multiple spatial scales, and which cross the boundaries of diverse parts of the nervous system such as molecules, cellular parts, cells, circuits, systems and tissues. As a result, investigators still primarily seek answers to their questions in an increasingly densely populated collection of articles in the literature, each of which must be digested individually. If it were easier to search a knowledge base that was structured to answer neuroscience questions, such a system would enable questions to be answered in seconds that would otherwise require hours of literature review. In this article, we describe NeuroLex.org, a wiki-based website and knowledge management system. Its goal is to bring neurobiological knowledge into a framework that allows neuroscientists to review the concepts of neuroscience, with an emphasis on multiscale descriptions of the parts of nervous systems, aggregate their understanding with that of other scientists, link them to data sources and descriptions of important concepts in neuroscience, and expose parts that are still controversial or missing. To date, the site is tracking ~25,000 unique neuroanatomical parts and concepts in neurobiology spanning experimental techniques, behavioral paradigms, anatomical nomenclature, genes, proteins and molecules. Here we show how the structuring of information about these anatomical parts in the nervous system can be reused to answer multiple neuroscience questions, such as displaying all known GABAergic neurons aggregated in NeuroLex or displaying all brain regions that are known within NeuroLex to send axons into the cerebellar cortex.

Keywords: knowledge management; neuroanatomy; ontology; semantics; wiki.

Figures

Figure 1
Figure 1
Landing page for NeuroLex.org. Several features are highlighted. (A) Login/user management controls. (B) Global site search bar. (C) Quick navigation to neuron or brain region information. (D) NIF Navigator, connecting the Neuroscience Information Framework b's federated resources to each NeuroLex page. (E) Global site search bar. (F) Quick navigation to hierarchies or tables containing detailed information about diverse entities in Neuroscience. (G) Quick creation forms for cells, brain regions, resources, and generic page contents.
Figure 2
Figure 2
Example category page for the concept entry ”Cerebellum” (A) Global site search bar. (B) Wiki controls for this page, including link to a discussion page, page edit history, and edit controls for this page. (C) Basic facts for this entry, including text description, super category and more. Tabbed interface also contains additional advanced facts. (D) Advanced auto-generated report for neurons whose somas or axons are located in the Cerebellum. (E) Advanced auto-generated report of other brain regions that are listed as being a part of the cerebellum. (F) Advanced auto-generated report of outgoing and incoming projections for the cerebellum (G) List of users that have made edits to this page. (H) List of subcategories for this entry, i.e. concepts that are more specific than this current concept. (I) A widget that allows users to share this page with their social networks. (J) A global footer that contains last modified information, as well as site-wide information like recent changes, a list of new pages, special reports, and version information.
Figure 3
Figure 3
The edit form for the Cerebellum granule cell page. The form is invoked by clicking the Edit button, shown in the enlargement in the upper right. Text boxes enable the user to make edits to the fields of information on the page. Fields whose values link to other category pages have an autocomplete feature, which may be further refined through defining a domain restriction. In the example shown here, the “Neurotransmitter receptors” field selects from subclasses of “Molecule” (solid arrowhead). The save button at the bottom of the page makes the edits immediately visible in NeuroLex.
Figure 4
Figure 4
Traffic sources to NeuroLex.org since December 2008. Direct traffic refers to a user typing “neurolex.org” into the browser or following a personal bookmark. Referring sites are visits where a user started at another site and clicked a link to arrive at NeuroLex.org. Search engines refer to any user that came to NeuroLex.org from a web search. Google searches made up 95% of the search engine traffic.
Figure 5
Figure 5
A graph of visits to NeuroLex.org over time since December 2008. Hits in 2010 were depressed by modifications in the presentation of metadata for search engines. This was corrected at the end of 2010, which led to increased traffic seen in 2011. Traffic dipped again briefly at the end of 2011 because of a site configuration error that was corrected early 2012. A trend line is added to show average traffic changes over time.
Figure 6
Figure 6
Overview of key relations. Derived from data that appears on the web at http://neurolex.org/wiki/Special:Properties.
Figure 7
Figure 7
The page for all Glutamatergic neurons. This page is a defined neuron class, which means that it is a collection of neurons that come together as a result of a shared property, the presence of glutamate as its neurotransmitter. The neurons within NeuroLex for which this is true are listed in the Overview section, which starts with the open arrowhead.
Figure 8
Figure 8
The modified overview section of the Glutamatergic neuron page. After having entered Glutamate as the Neurotransmitter released in the Cerebellum granule cell page (Figure 3), this neuron now appears in the list when it did not before (compare with open arrowhead in Figure 7 above).

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