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The NIF Components

The current NIF system is built from open source components including GWT, Nutch, Lucene, Flex and Postgres. Current NIF tools include the following:

  1. The NIF Registry:  Central to the NIF resources is the NIF registry, a human-curated Postgres database of neuroscience-relevant resources available through the web.  The NIF registry is assembled by neuroscientists who vet each resource for its content and relevance and annotate it using the NIF vocabularies according to their type, coverage and general content. 
  2. NIF Literature:  Comprised of PubMed and PubMed Central journal articles, NIF Literature searches the full text of the Open Access literature.  The archive may be searched by neuroscience-specific concepts; results may be filtered by year, author, and publication; and results are based on relevance.
  3. NIF Data Federation: NIF provides the ability to directly query databases containing neuroscience-related data, e.g., images, activation loci, that are independently created and maintained.  This type of search provides individual records in the databases directly, and these data are not normally available to search engines.  In order to be accessed by this search, database providers must register their database with the NIF data federation. See NIF Interoperation.
  4. NIFSTD Vocabulary: NIF encourages the use and re-use of the vocabularies. For this reason, it was developed with and adheres to the general pirnciples of the OBO foundry standards.
  5. NeuroLex: Wiki-based interface for community to help build and refine the NIF ontologies.
  6. Ontoquest: A system that provides powerful yet easy-to-use query and reasoning utilities.
  7. NIF Search Tools: NIF's search includes many features to help find what you are looking for including: auto-complete, a concept-based query, advanced search options (to include parts, related concepts, or subclasses of searched terms), and the ability to add to or replace a search.
  8. NIF Services: Programmatic access to NIF tools through Web services.
  9. NIF Registration Tools:
    1. NIF Registry Registration Tool- The "Resource" branch of the NeuroLex Wiki       (Separate from the NIF Vocabularies) is used for cataloging Web resources in the NIF Registry and for assigning specified metadata elements. This tool allows for community participation, attribution, curation, and a variety of other benefits that come with using a Semantic MediaWiki.
    2. Sitemap Registration Tool  - Also available through the "Resource" branch of the NeuroLex Wiki, access to the Sitemap tool is dependent on first Registering your Resource and curation. Once curated, owners of the resource may refer to the "For Resource Owners" section of their entry to generate their sitemap.
    3. Data Federation Registration Tools - Participation makes use of the DISCO protocol, a tool which any Web resource can send automatic, or manual, data updates to the NIF system. For more information refer to NIF Interoperation.
      1. Concept Mapping Tool - To aid in the discovery and interoperability of resources, this tool is used to semi-automate the data annotation process. For more information, visit NIF Annotation Standards.

NIF Statistics



NIF Version: 5.0

Ontology Version: 2.5

Level 2.5/3.0 Resources: 889

Registry Entries: 6,339

Total Records: 356,197,652





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