Linguistic Neuroscience: Extending Perceptual Neuroscience to Language
NEUROSCIENCE INFORMATION FRAMEWORK: ACCESS TO WEB NEUROSCIENCE...
1
NEUROSCIENCE I NFORMATION F RAMEWORK: ACCESS TO WEB NEUROSCIENCE NIF Consortium: G.A. Ascoli 1 , D. Gardner 2 , M.E. Martone 3 , G.M. Shepherd 4 , P.W. Sternberg 5 1 Krasnow Institute, George Mason U, Fairfax, VA; 2 Lab of Neuroinformatics, Weill Cornell, NY, NY; 3 Neuroscience, UCSD, La Jolla, CA; 4 Neurobiology, Yale Medical School, New Haven, CT; 5 Biology, Caltech, Pasadena, CA ACKNOWLEDGEMENTS: CONCLUSIONS AND PROJECTIONS: ANEUROSCIENCE I NFORMATION F RAMEWORK FOR 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 gratefully acknowledges 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 under development include experimental, clinical, and translational neurodatabases, knowledge bases, atlases, genetic/genomic and material resources, and tool and modeling sites for processing, analysis, or simulation of brain data. This diversity of sites spans multiple biological scales, techniques, and data models, serving communities of neuroscientists with specific conventions, individual terminologies, and distinct foci. The Neuroscience Information Framework Will Advance Web-Based Neuroscience Research and the Goals of the NIH Neuroscience Blueprint With support from the NIH Neuroscience Blueprint Institutes and Centers, we report progress developing our new initiative for integrating access to and use of these resources: the Neuroscience Information Framework (NIF). The rollout of the initial NIF version 1 (NIFv1) is scheduled for March 1st, 2008, with development and beta versions accessible via neurogateway.org and other sites to be announced. NIFv1 offers the neuroscience community neuroinformatic tools and resources to aid scientific inquiry. It builds upon prior development of neuroinformatics by the Human Brain Project and others, including the Society for Neuroscience’s Neuroscience Database Gateway, UCSD’s BIRN and CCDB, Caltech’s Textpresso, George Mason’s NeuroMorpho.Org, Cornell’s Neurodatabase.org, and collaborators’ 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 FEATURES UPON RELEASE NIFV1 WILL PROVIDE I NTEGRATED SEARCHES OF NEUROSCIENCE WEB RESOURCES, DATA AND LITERATURE The NIF Consortium: Synthesizing Neuroscience and Neuroinformatics Toward a New Resource CONTENT-BASED QUERIES PROBE THE LITERATURE VIA TEXTPRESSO 2. NeuroMorpho.Org: Reconstruction Search and Retrieval by Metadata NeuroMorpho.Org is an inventory of digitally reconstructed neurons, providing the NIF with curated and dense coverage of a specific data type. A. Drop-down menus illustrating a query based on species and strain, morphological class and subclasses, and a histological detail, matched by 20 cells. B. Organization of the pop-up results requested as a summary with images and selected information (cells are hyperlinked and can be selected or deselected). 3. NeuroMorpho.org: Range of Available Data A. An individual neuron page, including download links of the raw and processed data files and information logs, images and options for dynamic displays, and experimental, literature, and morphometric details. B. Distribution of the 1160 reconstructions available in version 1.1 by major “browse” features. “What cell types, and in which brain areas, have been associated with TRP channels?” Such queries, which span conventional categories in neuroscience, can be answered by making use of Textpresso’s extensive parsing of the neuroscience literature. 5. Textpresso Finds Papers That Relate the Selected Terms and Concepts The full text of the archive’s neuroscience papers is searched by marked-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 Interface The query is posed by specifying multiple categories selected from drop-down lists in the Textpresso for neuroscience search interface. Selected are: Brain Area, NIF cell types, and TRP channel. For expert users, a query language is available. 1. Prototype NIFv1 Query Interface and Search Results A neuroscientist’s query for information relevant to Purkinje neurons and cerebellum is posed at the upper left using NIF keywords. Arrows radiate from each of the NIFv1 classes of information, all of which have been selected by the user: • Neuroscience Web resources • Neuroscience literature • NIF federated databases The list of neuroscience Web resources found is shown in the upper right, with links for the convenience of the user. Examples of literature reporting Purkinje neurons is shown center right. In the center of the figure is the returned list of NIF federated databases offering more detailed access to data. SenseLab has been selected, and the NIFv1 links to the relevant record in SenseLab’s NeuronDB, providing extensive data on the cerebellar purkinje cell. The NIF Vocabularies include extensive trees of neuroscience metadata generated at a series of NIF-organized workshops at which invited neuroscientists explore concepts and specify clear and current descriptive 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 and development sites: PI: Daniel Gardner Weill Cornell Medical Coll. Project directors: Giorgio Ascoli George Mason University Maryann Martone UC San Diego Gordon Shepherd Yale University Paul Sternberg Caltech Collaborators: NIF development is partnered with the Society for Neuroscience, its Neuroinformatics Committee, and volunteer consultant- collaborators: Huda Akil Douglas Bowden Kristin M. Harris Gwen A. Jacobs David N. Kennedy Ken Smith David C. Van Essen John D. Van Horn Robert W. Williams Team members: Vadim Astakhov William Bug Eliza Chan Fabien Campagne Mark Ellisman Ronit Gadagkar Bernice Grafstein Jeffrey Grethe Amaranth Gupta Ajit Jagdale Erdem Kurul Luis Marenco Perry Miller Hans-Michael Müller Thien Nguyen Xufei Qian Adrian Robert Ruggero Scorcioni Willy Woong Ilya 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 that span resources across multiple levels of biological function to provide rapid, informative, and clear responses. The public beta version may include limited functionality. • Peter Lyster, NIGMS • Michael T. Marron, NCRR • Michael D. Oberdorfer, NEI • Jonathan D. Pollock, NIDA • David Shurtleff, NIDA 100.9
Transcript of NEUROSCIENCE INFORMATION FRAMEWORK: ACCESS TO WEB NEUROSCIENCE...
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
100.9
