The Neuroscience Information Framework (NIF): practical experience with large scale integration of federated neuroscience data
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1
University of California, San Diego, Department of Neurosciences, United States
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2
Yale Univ, Washington Univ, California Institute of Technology, San Diego, CA, United States
The Neuroscience Information Framework (NIF; http://neuinfo.org) 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 portal provides simultaneous search across multiple information sources to connect neuroscientists to available resources. including : (1) NIF Registry: A human-curated registry of neuroscience-relevant resources annotated with the NIF vocabulary; (2) NIF Web: A web index built using the Nutch indexing system from the NIF registry; (3) NIF Literature: A full text indexed corpus derived from major neuroscience journals, open access literature and specialized bibliographic databases indexed using the Textpresso text retrieval tool; (4) NIF Database Federation: A federation of independent databases registered to the NIF, allowing for direct query of database content. NIF has continued to grow significantly in content, currently accessing over 2800 resources through the Registry, 1 million web pages in the Web Index, and 22 million database records contained within 53 independent databases in the data federation, making NIF one of the largest source of neuroscience resources on the web. Search through the NIF portal is enhanced through a comprehensive ontology (NIFSTD) expressed in OWL-DL, covering major domains in neuroscience, e.g., diseases, brain anatomy, cell types, subcellular anatomy, small molecules, techniques and resource descriptors. NIFSTD is used for annotation of resources and to refine or expand queries by utilization of the relationships encoded in the ontology. They are served through Ontoquest, a database customized for storing and serving OWL ontologies. The NIF search interface autocompletes search strings with concepts in the NIF ontologies and automatically expands to synonyms. In NIF 2.5, we have incorporated more automated expansions to provide concept-based searches over classes defined through logical restrictions in the NIFSTD. For example, concepts like GABAergic neuron are automatically expanded to include children of these classes, i.e., types of GABAergic neurons. When such logical restrictions are present, Ontoquest materializes the inferred hierarchy and auto expands the query to include these classes. As the scope and depth of the NIF data federation grows, NIF has been working to create more unified views across multiple databases that export similar information. For example, NIF has registered several databases that provide mapping of gene expression to brain regions or provide connectivity information among brain structures. For these sources, NIF standardizes the database view based on common data elements and column headers. In performing this type of integration across resources, NIF has had to confront the different terminologies utilized by different resources. While we don’t change the content of the database, we do provide some mappings to the NIF annotation standards for recognized entities such as brain regions and cell types. We have also started to provide a set of standards for annotating quantitative values such as age and gene expression level. To do this, NIF has defined age ranges for adulthood in common laboratory species such as the mouse and a standard set of categories for expression levels. The latest release of NIF lays the foundation for enhanced semantic services in future releases. In NIF2.5, entities contained within the NIFSTD are highlighted within the NIF search results display. For anatomical and cell entities, we have introduced the NIF Cards. NIF cards are specialized search applets that draw upon NIFSTD and the NIF data federation to display additional information about an entity and provide customized search options depending upon the domain. As the NIF Cards evolve, they will provide the basis for linking NIF results into a larger ecosystem of linked data.
Multiple authors in the NIF consortium have contributed to this work: http://www.neuinfo.org/about/people.shtm Yale Univ, Washington Univ, California Institute of Technology, San Diego, CA, United States
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Oral Presentation
Topic:
General neuroinformatics
Citation:
Martone
M and
Multiple The NIF Consortium
A
(1900). The Neuroscience Information Framework (NIF): practical experience with large scale integration of federated neuroscience data.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00071
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Received:
01 Jan 1900;
Published Online:
01 Jan 1900.
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Correspondence:
Maryann Martone, University of California, San Diego, Department of Neurosciences, San Diego, United States, mmartone@ucsd.edu