The NeuroLex Neuron curation project: Practical experience aggregating structured information about neurons on a semantic wiki
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1
University of California San Diego, United States
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2
Yale University, United States
The use of structured information, such as information in databases, ontologies and other machine readable forms, is a critical strategy to dealing with the vast number of neurons, brain regions, and details of neuronal morphology present within neuroscience. Unfortunately it is challenging to create structured data in neuroscience that has a degree of authoritativeness due to the significant practical challenges of aggregating knowledge from experts. Past strategies, including sending emails soliciting help and arranging in person workshops have been useful for some knowledge aggregation, but a sustained effort is usually required to coordinate with experts to create a knowledge base of any significant depth.
Since May 2012, we have engaged in a targeted and sustained curation project for neuronal types. We updated a standard form for neuronal type information to streamline it for curator input. The level of modeling chosen was carefully selected to favor broad population of fewer properties rather than deep population across few cells. Using this resource, we can compile useful information about cell types through the native functions of the wiki, including categories like "Cholinergic neuron", "Spiny neuron", "projection neuron".
We recruited 40 experts throughout the field of neuroscience and have aggregated their knowledge about neuronal types into structured information using the wiki platform NeuroLex.org (Grethe, 2009). In collaboration with these experts, we have added ~50 new neuron types and filled in ~1000 new properties (Fig 1), as well as modified and removed existing neuron types that had inaccuracies. The entire contents of the curation project are available at NeuroLex.org and as structured RDF.
We chose to expose this information through the semantic wiki rather than a relational database or journal article because these pages are readily accessible to search engines and are open to community contribution. Because this platform is also used for modeling brain structures, molecules and parts of nerve cells, the representation is already integrated automatically across these different scales. We believe that this platform serves as a model for exposing neuroscience information in a way that facilitates data integration in the neurosciences.
Acknowledgements
The authors wish to thank Dr. Giorgio Ascoli and Dr. Anita Bandrowski for their assistance in the project.
The authors wish to thank the INCF for providing funding to make this project possible.
References
Grethe, J. S. (2009). NeuroLex and the Neuroscience Information Framework: Building comprehensive neuroscience ontologies with and for the community. Frontiers in neuroscience conference abstract: Neuroinformatics 2009. doi:10.3389/conf.neuro.11.2009.08.140
Keywords:
wiki,
Neurons,
neurolex,
semantics,
curation
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Poster
Topic:
General neuroinformatics
Citation:
Larson
SD,
Martone
M and
Shepherd
GM
(2013). The NeuroLex Neuron curation project: Practical experience aggregating structured information about neurons on a semantic wiki.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00033
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Received:
30 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Mr. Stephen D Larson, University of California San Diego, La Jolla, CA, 92093-0446, United States, stephen.larson@gmail.com