NeuroLex.org - A semantic wiki for neuroinformatics based on the NIF Standard Ontology

• ¹ UCSD, Department of Neuroscience, Faculty of Health,Medicine and Life Sciences, United States

The neuroscience community needs its basic domain concepts organized into a coherent framework. Ontologies provide an important medium for reconciling knowledge into a portable and machine readable form. 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 projects (http://neuinfo.org). 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). The list of topics it covers includes behavioral activity, behavioral paradigms, brain regions, cells, diseases, molecules, nervous system function, subcellular components, information resources, resource types, and qualities.

One of the largest roadblocks that we encountered was the lack of tools for domain experts to view, edit, and contribute their knowledge to the NIFSTD ontology. Existing editing tools were difficult to use or required expert knowledge to employ. By combining several open source technologies related to semantic wikis and NIFSTD, we have created NeuroLex.org, the first semantic wiki for neuroscience.

NeuroLex.org is built on top of the open source Semantic Mediawiki platform (http://semantic-mediawiki.org). Semantic Mediawiki makes querying the concepts in the ontology via properties or class hierarchy very straightforward. In addition, we have incorporated tools such as Semantic Forms, which allow the ontology classes to be edited as a form rather than as a wiki page with special text mark-up. Some of the fields in the form support autocomplete which allows users to populate those fields with other classes from the ontology.

NeuroLex.org has evolved into a powerful platform for collaboratively maintaining and extending the NIFSTD ontology. We have been able to incorporate user feedback and create custom views of the ontology content with very rapid turnaround. Table 1 shows some key metrics that we have collected on its usage. The content contributed to the Neurolex 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.

We conclude that the Semantic Mediawiki 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.