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The Neuroscience Information Framework (NIF): A Unified Semantic Framework and Associated Tools for Discovery, Integration, and Utilization of Biomedical Data and Resources on the Web

Jeffrey S. Grethe1*, Anita Bandrowski1, Davis Banks1, Jonathan Cachat1, Jing Chen1, Christopher Condit1, Amarnath Gupta2, Fahim Imam1, Stephen D. Larson1, Yueling Li1, Ibrahim B. Ozyurt1, Andrea M. Stagg1, Luis Marenco3, Perry Miller3, Rixin Wang3, Gordon M. Shepherd4, Giorgio Ascoli5 and Maryann E. Martone1
  • 1 University of California, San Diego, Center for Research in Biological Systems, School of Medicine, United States
  • 2 San Diego Supercomputer Center, United States
  • 3 Yale University School of Medicine, Center for Medical Informatics, United States
  • 4 Yale University, Department of Neurobiology, United States
  • 5 George Mason University, Krasnow Institute for Advanced Study, United States

The Neuroscience Information Framework (NIF; http://neuinfo.org) has recently launched a completely re-designed discovery portal for finding and integrating neuroscience-relevant resources, data, and literature. The new portal provides users with new tools to visualize data content (e.g. through analytics that provide a landscape analysis of where data can be found for topics of interest) to more personalized services via myNIF (e.g. the saving of favorite searches). The portal searches across 3 primary collections: (1) NIF Registry: A human-curated registry of neuroscience-relevant resources annotated with the NIF vocabulary; (2) NIF Literature: A full text indexed corpus derived from the PubMed Open Access subset as well as an entire index of PubMed; (3) NIF Database Federation: A federation of independent databases that enables discovery and access to public research data, contained in databases and structured web resources (e.g. queryable web services) that are sometimes referred to as the deep or hidden web.

To further enable the utilization of this vast collection of information, the NIF is applying semantic web technologies to its holdings. By defining a set of standards and best practices for describing and representing data such semantic web and linked data technologies eliminate the barriers between database silos and foster the evolution of the Web into a Web of data. Such technologies are being successfully applied as integration engines for linking biological elements in many domains. Exposing NIF’s content as Linked Open Data will enable further integration with the growing amount of information available from the linked open data cloud – thereby providing much richer resources for the neuroscientist. The publication of this content relies on NIF’s comprehensive ontology (NIFSTD) that covers major domains in neuroscience, including diseases, brain anatomy, cell types, subcellular anatomy, small molecules, techniques and resource descriptors.

Over the past year, NIF has continued to grow significantly in content, providing access to over 6,000 resources through the Registry, and more than 200 independent data resources in the data federation, making NIF the largest source of biomedical information on the web. NIF’s tools help people find and utilize neuroscience related resources - provides a consistent and easy to implement framework for those who are providing such resources, e.g., data, and those looking to utilize these data and resources.

In this demonstration we will provide a tour of NIF’s suite of services, tools, and data:
* Search through NIF’s newly re-designed semantically-enhanced discovery portal
* Working with NIF’s linked data (e.g. nervous system connectivity) via SPARQL
* Services and tools that provide access to the NIF data federation - the largest collection of Neuroscience relevant information on the web
* Contributing to the NeuroLex – a community resource for neuroscience terminology built on a semantic media-wiki platform
* Curation and normalization of data utilizing NIF’s Google Refine services
* NIF’s semantically enhanced data and tools for its maintenance
* myNIF and the NIF Digest – personalized services for researchers

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Acknowledgements

NIH Neuroscience Blueprint HHSN271200800035C via NIDA

Keywords: Data Federation, big data, linked data, Search Engine, Registry, data integration, Neuroscience, ontology

Conference: Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.

Presentation Type: Demo

Topic: Infrastructural and portal services

Citation: Grethe JS, Bandrowski A, Banks D, Cachat J, Chen J, Condit C, Gupta A, Imam F, Larson SD, Li Y, Ozyurt IB, Stagg AM, Marenco L, Miller P, Wang R, Shepherd GM, Ascoli G and Martone ME (2013). The Neuroscience Information Framework (NIF): A Unified Semantic Framework and Associated Tools for Discovery, Integration, and Utilization of Biomedical Data and Resources on the Web. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. doi: 10.3389/conf.fninf.2013.09.00073

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Received: 29 Apr 2013; Published Online: 11 Jul 2013.

* Correspondence: Dr. Jeffrey S Grethe, University of California, San Diego, Center for Research in Biological Systems, School of Medicine, La Jolla, CA, 92093-0446, United States, jgrethe@ucsd.edu