The Neuroscience Information Framework (NIF): a neuroscience-centered portal for searching and accessing diverse resources
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1
UCSD, Department of Neuroscience, Faculty of Health,Medicine and Life Sciences, United States
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2
ITB-CNR, Italy
Although a plethora of resources (tools, databases, materials) for neuroscientists is now available through the web, finding these resources among the billions of possible web pages continues to be a challenge. The lack of discoverability is particularly acute for on-line databases, whose dynamic content is largely opaque to web search engines such as Google. The Neuroscience Information Framework (NIF; http://neuinfo.org) was launched in 2008 to address the problem of finding neuroscience-relevant resources. It provides simultaneous search across multiple information sources to connect neuroscientists to available resources. These sources include: (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 resources described in the NIF registry; (3) NIF Literature: A full text indexed corpus derived from major neuroscience journals 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.
Search through the NIF portal is enhanced through the utilization of a comprehensive ontology (NIFSTD). NIFSTD is expressed in OWL-DL and covers major domains in neuroscience, including diseases, brain anatomy, cell types, subcellular anatomy, small molecules, techniques and resource descriptors. NIFSTD was constructed through the synthesis of existing terminologies covering these areas and refactoring them to comply with the Basic Formal Ontology (BFO), an upper level ontology that provides a high level and consistent organization for ontologies in science (Smith et al., Nat Biotechnol. Nov;25(11):1251-5). The NIF uses a combination of strategies for employing NIFSTD in search. For the NIF Registry, we use the NIFSTD as a controlled vocabulary for annotating catalog entries. For the NIF databases, we use the ontology to map individual table names, field and values in order to unify search across independent resources with custom terminology. For other resources, we utilize NIFSTD to expand searches to include related terms such as synonyms, parents, children and other relationships.
NIF underwent a significant upgrade in 2009 with the release of NIF 1.5. Major improvements on the front end include expanded content and a greatly improved user interface. On the backend, we redesigned the NIF Registry, and have implemented additional tools for integration of resources into the NIF data federation. These tools include the DISCO suite developed by Marenco and colleagues (Marenco et al., Neuroinformatics, submitted), that provide a means for searching content of unstructured and semi-structured web sites through an XML protocol embedded in the host website. NIF has also developed a more community based portal, taking advantage of tools such as blogs and wikis to provide the neuroscience community an opportunity to participate in the development of the NIF. For example, we established the Neurolex Wiki, using the NIFSTD vocabularies to create a series of wiki pages through which the community can edit and add to the NIF ontologies. We will be using the NIF site as a means to provide current information and perspectives relevant to neuroinformatics, e.g., best practices for database interoperability.
Conference:
Neuroinformatics 2009, Pilsen, Czechia, 6 Sep - 8 Sep, 2009.
Presentation Type:
Poster Presentation
Topic:
Infrastructural and portal services
Citation:
Martone
M,
Mosca
E,
Alfieri
R,
Viti
F,
Merelli
I and
Milanesi
L
(2019). The Neuroscience Information Framework (NIF): a neuroscience-centered portal for searching and accessing diverse resources.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2009.
doi: 10.3389/conf.neuro.11.2009.08.073
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Received:
22 May 2009;
Published Online:
09 May 2019.
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Correspondence:
Maryann Martone, UCSD, Department of Neuroscience, Faculty of Health,Medicine and Life Sciences, San Diego, United States, mmartone@ucsd.edu