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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 Grethe (University of California, San Diego), Anita Bandrowski (University of California, San Diego), Jonathan Cachat (University of California, San Diego), Amarnath Gupta (University of California, San Diego), Fahim Imam (University of California, San Diego), Stephen Larson (University of California, San Diego), Luis Marenco (Yale University), Perry Miller (Yale University), Gordon Shepherd (Yale University), Maryann Martone (University of California, San Diego), NIF Consortium (University of California, San Diego)

The Neuroscience Information Framework (NIF; was launched in 2008 to address the problem of finding and integrating neuroscience-relevant resources through the establishment of a semantically enhanced framework. The NIF discovery portal provides simultaneous search across multiple types of information sources to connect neuroscientists and biomedical researchers to available resources. These sources include the: (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. Search and annotation of resources and resource content is enhanced through the utilization of a comprehensive ontology (NIFSTD) that covers major domains in neuroscience, including diseases, brain anatomy, cell types, subcellular anatomy, small molecules, techniques and resource descriptors. The NIFSTD ontologies are used to refine or expand queries by utilization of the relationships encoded in the ontology.

Over the past year, NIF has continued to grow significantly in content, providing access to over 4800 resources through the Registry, and more than 150 independent databases in the data federation, making NIF the largest source of neuroscience 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 semantically-enhanced discovery portal
*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 linked data and tools for its maintenance
*myNIF and the NIF Digest – personalized services for researchers
Preferred presentation format: Demo
Why demo: The goal of this presentation is to provide hands-on practical experience with the tools and services available through NIF - which can only be accomplished via a demonstration. This demonstration will build on the successful demonstration provided during the INCF Nodes workshop.
Topic: Infrastructural and portal services

Andrew Davison
Andrew Davison says:
May 11, 2012 03:19 PM
This is of course excellent work, but it is very well known by now, and so I don't think it should have a spotlight presentation.