NEUROSCIENCE INFORMATION FRAMEWORK: ACCESS TO WEB NEUROSCIENCENIF Consortium: G.A. Ascoli1, D. Gardner2, M.E. Martone3, G.M. Shepherd4, P.W. Sternberg5

1Krasnow Institute, George Mason U, Fairfax, VA; 2Lab of Neuroinformatics, Weill Cornell, NY, NY; 3Neuroscience, UCSD, La Jolla, CA; 4Neurobiology, Yale Medical School, New Haven, CT; 5Biology, Caltech, Pasadena, CA

ACKNOWLEDGEMENTS:

CONCLUSIONS AND PROJECTIONS:

ANEUROSCIENCE INFORMATION FRAMEWORKFOR THE NIH NEUROSCIENCE BLUEPRINT

• The NIFv1 will reduce the costs, and enhance the benefits, of neuroscience data sharing.

• The NIFv1’s inventory and content-aware queries will empower investigators by locating and relating neuroscience data and knowledge.

• NIFv1 design and open code will lower barriers to making available new neuroinformatic resources.

• NIFv1 advanced query methods will enable direct access to an increasing number of new and existing neuroscience databases.

The Neuroscience Information Framework team gratefullyacknowledges the support of:• NIH Neuroscience Blueprint Contract HHSN271200577531C via NIDA• Volunteer consultant-collaborators and friends • The Society for Neuroscience

The Advisory Committee consists of the authors, Huda Akil,Bernice Grafstein, David C. Van Essen, and Robert W. Williams.

We thank our NIDA Program Officer:• Karen Skinner

and the NIH Project Team:• Zohara Cohen, NIBIB• Greg Farber, NCRR• Michael F. Huerta, NIMH• Kathy Mann Koepke, NINR• Yuan Liu, NINDS

Web Resources Aid Neuroscience Research Global neuroscience web resources available and underdevelopment include experimental, clinical, and translationalneurodatabases, knowledge bases, atlases, genetic/genomic andmaterial resources, and tool and modeling sites for processing,analysis, or simulation of brain data. This diversity of sites spansmultiple biological scales, techniques, and data models, servingcommunities of neuroscientists with specific conventions, individualterminologies, and distinct foci.

The Neuroscience Information Framework WillAdvance Web-Based Neuroscience Research andthe Goals of the NIH Neuroscience BlueprintWith support from the NIH Neuroscience Blueprint Institutes andCenters, we report progress developing our new initiative forintegrating access to and use of these resources: the NeuroscienceInformation Framework (NIF).

The rollout of the initial NIF version 1 (NIFv1) is scheduled forMarch 1st, 2008, with development and beta versions accessible vianeurogateway.org and other sites to be announced.

NIFv1 offers the neuroscience community neuroinformatic tools andresources to aid scientific inquiry. It builds upon prior developmentof neuroinformatics by the Human Brain Project and others,including the Society for Neuroscience’s Neuroscience DatabaseGateway, UCSD’s BIRN and CCDB, Caltech’s Textpresso, GeorgeMason’s NeuroMorpho.Org, Cornell’s Neurodatabase.org, andcollaborators’ Braininfo.org, Internet Accessible Tool Resource,SumsDB, and others.

All NIFv1 code and terminologies are Open Source.

NEUROMORPHO.ORG PROVIDES NIF ACCESS TO NEURONAL RECONSTRUCTIONS

NIFV1 WILL OFFER THESE FEATURESUPON RELEASE

NIFV1 WILL PROVIDE INTEGRATED SEARCHES OF NEUROSCIENCE WEBRESOURCES, DATA AND LITERATURE

The NIF Consortium: Synthesizing Neuroscienceand Neuroinformatics Toward a New Resource

CONTENT-BASED QUERIES PROBE THELITERATURE VIA TEXTPRESSO

2. NeuroMorpho.Org: Reconstruction Search andRetrieval by MetadataNeuroMorpho.Org is an inventory of digitally reconstructed neurons,providing the NIF with curated and dense coverage of a specific datatype. A. Drop-down menus illustrating a query based on species andstrain, morphological class and subclasses, and a histological detail,matched by 20 cells. B. Organization of the pop-up results requestedas a summary with images and selected information (cells arehyperlinked and can be selected or deselected).

3. NeuroMorpho.org: Range of Available Data A. An individual neuron page, including download links of the rawand processed data files and information logs, images and options fordynamic displays, and experimental, literature, and morphometricdetails. B. Distribution of the 1160 reconstructions available in version1.1 by major “browse” features.

“What cell types, and in which brain areas, havebeen associated with TRP channels?”Such queries, which span conventional categories in neuroscience, canbe answered by making use of Textpresso’s extensive parsing of theneuroscience literature.

5. Textpresso Finds Papers That Relate theSelected Terms and ConceptsThe full text of the archive’s neuroscience papers is searched bymarked-up categories of terms, here yielding matches in two papers.Results may be further filtered, and viewed with or without abstracts.

4. Textpresso’s Search InterfaceThe query is posed by specifying multiple categories selected fromdrop-down lists in the Textpresso for neuroscience search interface.Selected are: Brain Area, NIF cell types, and TRP channel. For expertusers, a query language is available.

1. Prototype NIFv1 QueryInterface and Search ResultsA neuroscientist’s query for informationrelevant to Purkinje neurons andcerebellum is posed at the upper leftusing NIF keywords. Arrows radiatefrom each of the NIFv1 classes ofinformation, all of which have beenselected by the user:• Neuroscience Web resources• Neuroscience literature• NIF federated databases

The list of neuroscience Web resourcesfound is shown in the upper right, withlinks for the convenience of the user.

Examples of literature reporting Purkinjeneurons is shown center right.

In the center of the figure is the returnedlist of NIF federated databases offeringmore detailed access to data. SenseLabhas been selected, and the NIFv1 links tothe relevant record in SenseLab’sNeuronDB, providing extensive data onthe cerebellar purkinje cell.

The NIF Vocabularies include extensivetrees of neuroscience metadata generatedat a series of NIF-organized workshopsat which invited neuroscientists exploreconcepts and specify clear and currentdescriptive terms.

6. How Textpresso Marks Up Text• Get full text of papers (15000 papers)• Split into sentences (~3 million) and words (~150 million)• Mark up each word or phrase using Textpresso ontology categories. • Index occurrences of labels in text for fast retrieval and store in database

Leadership anddevelopment sites:PI: Daniel Gardner

Weill Cornell Medical Coll.

Project directors:Giorgio Ascoli

George Mason UniversityMaryann Martone

UC San DiegoGordon Shepherd

Yale UniversityPaul Sternberg

Caltech

Collaborators:NIF development is partneredwith the Society forNeuroscience, itsNeuroinformatics Committee,and volunteer consultant-collaborators:Huda Akil Douglas BowdenKristin M. HarrisGwen A. JacobsDavid N. KennedyKen SmithDavid C. Van EssenJohn D. Van HornRobert W. Williams

Team members:Vadim AstakhovWilliam BugEliza ChanFabien CampagneMark EllismanRonit GadagkarBernice GrafsteinJeffrey Grethe Amaranth GuptaAjit Jagdale

Erdem KurulLuis MarencoPerry MillerHans-Michael MüllerThien NguyenXufei QianAdrian RobertRuggero ScorcioniWilly WoongIlya Zaslavsky

NIFv1 Will Include a Unified Portal Interface to:• A dynamic inventory of neuroscience Web resources, including

databases and neuroinformatic or analytic tools. Resources are NIF curated and annotated using NIF terminologies, so users can be directed to relevant sites.

• An expanding Textpresso literature repository for Neuroscience

• Neuromorpho.org as an exemplar database

• The prototype NIF data federation, a selected subset of resources meeting deep interoperability requirements and NIF terminology compatibility, allowing direct access to data using NIFv1 query methods.

• A link-out function relating PubMed and NIFv1 resources

The user interface will accept and aid concept-based queries thatspan resources across multiple levels of biological function toprovide rapid, informative, and clear responses. The public betaversion may include limited functionality.

• Peter Lyster, NIGMS• Michael T. Marron, NCRR• Michael D. Oberdorfer, NEI• Jonathan D. Pollock, NIDA• David Shurtleff, NIDA

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