A multi-scale parts list for the brain: community-based ontology curation for neuroinformatics with NeuroLex.org

Abstract

Event Abstract Back to Event A multi-scale parts list for the brain: community-based ontology curation for neuroinformatics with NeuroLex.org Stephen Larson1*, Fahim Imam1, Rembrandt Bakker2, Luan Pham1 and Maryann Martone1 1 University of California, San Diego, Center for Research of Biological Systems, United States 2 Radboud UMC Nijmegen, Donders Institute for Brain, Cognition and Behaviour, Netherlands What makes up the nervous system? What are the inhibitory neurons? What brain regions are they in? What ion channels do they express? Do their dendrites have spines? What fiber bundles do they participate in? These questions and many more could be answered by a multi-scale parts list for the brain, where each part was uniquely indexed and unambiguously defined. Unfortunately, no such standard list has come into widespread use by the neuroscience community. Our effort to address this challenge has resulted in the instantiation of a semantic wiki, NeuroLex.org. For many years we have been building community ontologies for neuroscience, first through the Biomedical Informatics Research Network and now through the Neuroscience Information Framework (http://neuinfo.org) projects. These projects resulted in the construction of a large modular ontology, constructed by importing existing ontologies where possible, called the NIF Standard Ontology (NIFSTD; Bug et al, 2008). It covers behavioral activity, behavioral paradigms, brain regions, cells, diseases, molecules, nervous system function, subcellular components, information resources, resource types, and qualities. NeuroLex.org was originally populated with the NIFSTD in an effort to improve the process of editing and maintaining it. The initial update processes created one wiki page from each ontological "class", which refers to an entity relevant to neuroscience. Content that is added or updated in NeuroLex.org is contributed back to the NIFSTD. This content is not directly added to NIFSTD, but is incorporated into the NIFSTD OWL file by a knowledge engineer after curation by the NIF ontology group. NeuroLex.org's structuring of knowledge allows classes to be rendered using tables, trees, and lists which combine the asserted content of the class with queried content derived from other classes. For example, the page for "Cerebellum" displays a dynamic tree that lists the brain region classes that have been asserted as "part-of" the Cerebellum. This page also lists the neuron classes that have been asserted as "located-in" the Cerebellum. Neither of these property assertions are made on the Cerebellum page itself; rather they are displayed via dynamic queries that find classes related to the Cerebellum throughout the wiki. NeuroLex.org has served as a test bed for a rallying point for the efforts of the Program of Ontologies of Neural System (PONS), an activity of the International Neuroinformatics Coordinating Facility (INCF). In the last year, content and edits have been contributed by several members of the task forces in this activity. In addition, NeuroLex.org has incorporated a lightweight web application for digital atlasing called the Scalable Brain Atlas (http://scalablebrainatlas.incf.org), which generates atlas plate images that highlight a given brain region, in order to more clearly define it. NeuroLex.org has been online since October 2008 and has evolved into a powerful platform for collaboratively maintaining and extending the NIFSTD ontology. It has received 110,000 edits and has 104 registered users. It regularly receives 225 hits per day on average, 80% of which come directly from search engine hit results. NeuroLex.org is built on top of the open source Semantic Mediawiki platform (http://semantic-mediawiki.org) and incorporates several open source extensions such as Semantic Forms and the Halo Extension. We conclude that NeuroLex.org is a good starting point for the collaborative maintenance of ontologies. Other groups are also using a similar approach, e.g., BioMedGT (http://biomedgt.nci.nih.gov). While we are still working through some issues, e.g., synchronizing the NIFSTD with the content on NeuroLex, exporting and importing OWL, and bulk uploading concepts, we believe that semantic wikis are a good tool for providing community contribution and feedback to projects like NIF.