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Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework

Luis Marenco, Yuli Li, Maryann E. Martone, Paul W. Sternberg, Gordon M. Shepherd, Perry L. Miller
2008 Neuroinformatics  
This paper describes a pilot query interface that has been constructed to help us explore a "concept-based" approach for searching the Neuroscience Information Framework (NIF).  ...  how the pilot concept-based query interface operates.  ...  Acknowledgments This project has been funded in whole or in part through the NIH Blueprint for Neuroscience Research with Federal funds from the National Institute on Drug Abuse, National Institutes of  ... 
doi:10.1007/s12021-008-9035-9 pmid:18953674 pmcid:PMC2664632 fatcat:rsdcnggvmfavvdnpi4s4xqdciy

The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience

Daniel Gardner, Huda Akil, Giorgio A. Ascoli, Douglas M. Bowden, William Bug, Duncan E. Donohue, David H. Goldberg, Bernice Grafstein, Jeffrey S. Grethe, Amarnath Gupta, Maryam Halavi, David N. Kennedy (+9 others)
2008 Neuroinformatics  
With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience  ...  The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of  ...  Marenco et al. (2008a, b) present two enabling components, the NIF LinkOut Broker and a concept-based query interface.  ... 
doi:10.1007/s12021-008-9024-z pmid:18946742 pmcid:PMC2661130 fatcat:7nx5cbmxd5d3rls544evrknnue

Integration of "omics" Data and Phenotypic Data Within a Unified Extensible Multimodal Framework

Samir Das, Xavier Lecours Boucher, Christine Rogers, Carolina Makowski, François Chouinard-Decorte, Kathleen Oros Klein, Natacha Beck, Pierre Rioux, Shawn T. Brown, Zia Mohaddes, Cole Zweber, Victoria Foing (+6 others)
2018 Frontiers in Neuroinformatics  
and transparent sharing of processing pipelines to improve computational consistency; (v) store results in a queryable web interface; (vi) offer visualization tools to better view the data; and (vii)  ...  In 2015, the Ludmer Centre for Neuroinformatics and Mental Health at McGill University brought together expertise from the Douglas Mental Health University Institute, the Lady Davis Institute and the Montreal  ...  An intuitive interface design leads users through a process of selecting a genomic fileset, targeting ranges of interest on the genome, and then cross-joining these results by subject ID based on a pre-constructed  ... 
doi:10.3389/fninf.2018.00091 pmid:30631270 pmcid:PMC6315165 fatcat:3jzc2twlxvaf7bipvdamnk765y

Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems

Jyl Boline, Michael Hawrylycz, Robert Williams
2007 Nature Precedings  
More specifics for the design of the query tools will also depend on the outcome of the survey of current software tools and practices. • The issue of allowing users to create their own atlas delineations  ...  Linking of Canonical Atlases In order to use digital rodent atlases as the backbone for a neuroinformatics framework they need to be linked in a manner that will allow tools to navigate across different  ... 
doi:10.1038/npre.2007.1046.1 fatcat:5mxnau7o4ngfjdjr2s6c6wo6um

Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems

Jyl Boline, Jyl Boline, Michael Hawrylycz, Robert Williams
2007 Nature Precedings  
More specifics for the design of the query tools will also depend on the outcome of the survey of current software tools and practices. • The issue of allowing users to create their own atlas delineations  ...  Linking of Canonical Atlases In order to use digital rodent atlases as the backbone for a neuroinformatics framework they need to be linked in a manner that will allow tools to navigate across different  ... 
doi:10.1038/npre.2007.1046 fatcat:z24zvfjejbev5ntlyb3sbzds54

AlzPharm: integration of neurodegeneration data using RDF

Hugo YK Lam, Luis Marenco, Tim Clark, Yong Gao, June Kinoshita, Gordon Shepherd, Perry Miller, Elizabeth Wu, Gwendolyn T Wong, Nian Liu, Chiquito Crasto, Thomas Morse (+2 others)
2007 BMC Bioinformatics  
Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in  ...  Results: We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure.  ...  The full contents of the supplement are available online at http://www.biomedcentral.com/ 1471-2105/8?issue=S3.  ... 
doi:10.1186/1471-2105-8-s3-s4 pmid:17493287 pmcid:PMC1892101 fatcat:iot4qgjhnfe4tidgz43b23wkja

Integration of Multidisciplinary Sensory Data: A Pilot Model of the Human Brain Project Approach

P. L. Miller, P. Nadkarni, M. Singer, L. Marenco, M. Hines, G. Shepherd
2001 JAMIA Journal of the American Medical Informatics Association  
data within a single unifying framework. s J Am Med Inform Assoc. 2001;8:34-48.  ...  A b s t r a c t The paper provides an overview of neuroinformatics research at Yale University being performed as part of the national Human Brain Project.  ...  NeuronDB is currently populated with information describing the olfactory mitral cell and a range of neuron types in other brain regions and has been available as a pilot resource for the field for over  ... 
doi:10.1136/jamia.2001.0080034 pmid:11141511 pmcid:PMC134590 fatcat:ameowsyfqvg2tnnzgthkv4ctna

Opportunities at the Intersection of Bioinformatics and Health Informatics: A Case Study

P. L. Miller
2000 JAMIA Journal of the American Medical Informatics Association  
A b s t r a c t This paper provides a "viewpoint discussion" based on a presentation made to the 2000 Symposium of the American College of Medical Informatics.  ...  It discusses potential opportunities for researchers in health informatics to become involved in the rapidly growing field of bioinformatics, using the activities of the Yale Center for Medical Informatics  ...  We believe that this provides a strong pilot proof of concept for the EAV/CR model and also provides a robust, flexible database environment for the further development of these and future HBP databases  ... 
doi:10.1136/jamia.2000.0070431 pmid:10984461 pmcid:PMC79037 fatcat:2xeziv2gffelng4hat53sbezh4

QIS: A Framework for Biomedical Database Federation

Luis Marenco, Tzuu-Yi Wang, Gordon Shepherd, Perry L. Miller, Prakash Nadkarni
2004 JAMIA Journal of the American Medical Informatics Association  
network-based queries in the biosciences.  ...  The QIS framework uses standard technologies and is intended to be deployable by administrators with a moderate level of technological expertise: It comes with various tools, such as interfaces for the  ...  The TAMBIS team uses custom function libraries for each information source, which provide a function-based view of the source.  ... 
doi:10.1197/jamia.m1506 pmid:15298995 pmcid:PMC524633 fatcat:5w3kgpmvhzbj7gpll2mcnc2wyq

Achieving Evolvable Web-Database Bioscience Applications Using the EAV/CR Framework: Recent Advances

Luis Marenco, Nicholas Tosches, Chiquito Crasto, Gordon Shepherd, Perry L. Miller, Prakash M. Nadkarni
2003 JAMIA Journal of the American Medical Informatics Association  
The EAV/CR framework, designed for database support of rapidly evolving scientific domains, utilizes metadata to facilitate schema maintenance and automatic generation of Web-enabled browsing interfaces  ...  EAV/CR is used in SenseLab, a neuroscience database that is part of the national Human Brain Project. This report describes various enhancements to the framework.  ...  To address these issues, the EAV/CR framework allows the user to query the data in terms of the conceptual schema.  ... 
doi:10.1197/jamia.m1303 pmid:12807806 pmcid:PMC212781 fatcat:35mjpsht6feyjkqfxnnqyf7wmy

Action and Language Mechanisms in the Brain: Data, Models and Neuroinformatics

Michael A. Arbib, James J. Bonaiuto, Ina Bornkessel-Schlesewsky, David Kemmerer, Brian MacWhinney, Finn Årup Nielsen, Erhan Oztop
2013 Neuroinformatics  
We assess the challenges of studying action and language mechanisms in the brain, both singly and in relation to each other to provide a novel perspective on neuroinformatics, integrating the development  ...  of databases for encoding -separately or together -neurocomputational models and empirical data that serve systems and cognitive neuroscience.  ...  The existence of diverse neuroinformatics databases opens up numerous possibilities to link and query between them.  ... 
doi:10.1007/s12021-013-9210-5 pmid:24234916 pmcid:PMC4101894 fatcat:j5ddog5unbf6tlbgn6mt4oj334

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research

Tarek Sherif, Pierre Rioux, Marc-Etienne Rousseau, Nicolas Kassis, Natacha Beck, Reza Adalat, Samir Das, Tristan Glatard, Alan C. Evans
2014 Frontiers in Neuroinformatics  
CBRAIN leverages remote computing cycles and facilitates resource-interoperability in a transparent manner for the end-user.  ...  The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research  ...  In addition to the authors, we would like to thank Mathieu Desrosiers for contributing sustained development efforts and site project coordination.  ... 
doi:10.3389/fninf.2014.00054 pmid:24904400 pmcid:PMC4033081 fatcat:67qhzkijujg4hgabntljsewq3m

Cyberinfrastructure for Open Science at the Montreal Neurological Institute

Samir Das, Tristan Glatard, Christine Rogers, John Saigle, Santiago Paiva, Leigh MacIntyre, Mouna Safi-Harab, Marc-Etienne Rousseau, Jordan Stirling, Najmeh Khalili-Mahani, David MacFarlane, Penelope Kostopoulos (+22 others)
2017 Frontiers in Neuroinformatics  
ACKNOWLEDGMENTS The authors thank the following people for their sustained efforts toward building the MNI Open Science cyberinfrastructure: Justin Kat, Nicolas Brossard, Ted Strauss, Stella Lee, Gregory  ...  Scans transferred to the Imagebank server will be loaded through a series of software scripts into LORIS, and automatically made available for download through the Imagebank's web-based browser interface  ...  Imagebank Infrastructure In its pilot phase, the MNI's Imagebank will serve as a central repository of scans primarily collected at the BIC's MRI unit.  ... 
doi:10.3389/fninf.2016.00053 pmid:28111547 pmcid:PMC5216036 fatcat:nefxyg5vfzbxfcfx7qqc7t7j7u

KGRAM Versatile Inference and Query Engine for the Web of Linked Data

Olivier Corby, Alban Gaignard, Catherine Faron Zucker, Johan Montagnat
2012 2012 IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology  
This work describes the design of a versatile query system named KGRAM that supports (i) multiple query languages among which the SPARQL 1.1 standard, (ii) federation of multiple heterogeneous and distributed  ...  KGRAM provides abstractions for both the query language and the data model, thus delivering unifying reasoning mechanisms.  ...  ACKNOWLEDGMENT This work is partly funded by the French National Agency for Research under grant ANR-09-COSI-03 "VIP".  ... 
doi:10.1109/wi-iat.2012.223 dblp:conf/webi/CorbyGFM12 fatcat:l3cki4p6vjfefc653wweejleva

Shanoir: Applying the Software as a Service Distribution Model to Manage Brain Imaging Research Repositories

Christian Barillot, Elise Bannier, Olivier Commowick, Isabelle Corouge, Anthony Baire, Ines Fakhfakh, Justine Guillaumont, Yao Yao, Michael Kain
2016 Frontiers in ICT  
Thanks to a formal model of medical imaging data (an ontology), Shanoir provides an open source neuroinformatics environment designed to structure, manage, archive, visualize, and share neuroimaging data  ...  in the need for cooperation to gather the relevant imaging data.  ...  provided by the French government through the Agence Nationale de la Recherche as part of the Investment in the Future Program under references ANR-10-COHO-002 (for OFSEP) and ANR-11-INBS-006 (for FLI  ... 
doi:10.3389/fict.2016.00025 fatcat:hxqx3ti6f5eqbkbar7p7liuvii
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