Filters








31 Hits in 2.3 sec

XCEDE: An Extensible Schema for Biomedical Data

Syam Gadde, Nicole Aucoin, Jeffrey S. Grethe, David B. Keator, Daniel S. Marcus, Steve Pieper
2011 Neuroinformatics  
The XCEDE (XML-based Clinical and Experimental Data Exchange) XML schema, developed by members of the BIRN (Biomedical Informatics Research Network), provides an extensive metadata hierarchy for storing  ...  Currently at version 2.0, the XCEDE schema serves as a specification for the exchange of scientific data between databases, analysis tools, and web services.  ...  Many thanks to NITRC for hosting development sandboxes for XCEDE and supporting tools.  ... 
doi:10.1007/s12021-011-9119-9 pmid:21479735 pmcid:PMC3836560 fatcat:unuoxb4rcfgxdk3ph4ymd7krxe

Towards structured sharing of raw and derived neuroimaging data across existing resources

D.B. Keator, K. Helmer, J. Steffener, J.A. Turner, T.G.M. Van Erp, S. Gadde, N. Ashish, G.A. Burns, B.N. Nichols
2013 NeuroImage  
In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating  ...  Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary  ...  The International Neuroinformatics Coordinating Facility provided financial support for some of the work reported in this article (to Satrajit Ghosh).  ... 
doi:10.1016/j.neuroimage.2013.05.094 pmid:23727024 pmcid:PMC4028152 fatcat:enap2ihyhzfdfpz3gmtzqlqgna

Extending XNAT Platform with an Incremental Semantic Framework

Santiago Timón, Mariano Rincón, Rafael Martínez-Tomás
2017 Frontiers in Neuroinformatics  
With the aim of improving the application of semantic models in biobanking systems, an incremental semantic framework that takes advantage of the latest advances in biomedical ontologies and the XNAT platform  ...  Research data archiving solutions are evolving rapidly to address these necessities, however, distributed data integration is still difficult because of the need of explicit agreements for disparate data  ...  To integrate XCEDE import/export processes properly, we have implemented an XNAT service extension following the same principles as its native REST API to serve study data in XCEDE format.  ... 
doi:10.3389/fninf.2017.00057 pmid:28912709 pmcid:PMC5583223 fatcat:nkkveq3lh5akrie3mihpu54dca

Towards structured sharing of raw and derived neuroimaging data across existing resources [article]

D. B. Keator, K. Helmer, J. Steffener, J. A. Turner, T. G. M. Van Erp, S. Gadde, N. Ashish, G. A. Burns, B. N. Nichols, S. S. Ghosh
2013 arXiv   pre-print
In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating  ...  Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary  ...  The International Neuroinformatics Coordinating Facility provided financial support for some of the work reported in this article (to Satrajit Ghosh).  ... 
arXiv:1209.5922v3 fatcat:pcebf7inybfstkgkf6pfwrny7y

Derived Data Storage and Exchange Workflow for Large-Scale Neuroimaging Analyses on the BIRN Grid

David B. Keator
2009 Frontiers in Neuroinformatics  
This manuscript will present a case study of using the XML-Based Clinical Experiment Data Exchange (XCEDE) schema and the Human Imaging Database (HID) in the Biomedical Informatics Research Network's (  ...  The discussion includes an overview of the data structures used in both the XML and the database representations, insight into the design considerations, and the extensibility of the design to support  ...  presented here, and the FBIRN consortium members for the data collection and support of the scientists and engineers involved in the project.  ... 
doi:10.3389/neuro.11.030.2009 pmid:19826494 pmcid:PMC2759340 fatcat:cynqiogpbngihl7c36fmykl7p4

An integrated object model and method framework for subject-centric e-Research applications

Jason M. Lohrey
2009 Frontiers in Neuroinformatics  
A framework that integrates an object model, research methods (workfl ows), the capture of experimental data sets and the provenance of those data sets for subject-centric research is presented.  ...  In this paper, we describe a framework that defi nes an object model to explicitly represent research methods and the resulting acquired and derivative data for subject-centric research.  ...  ACKNOWLEDGEMENTS We thank Gavan McCarthy, Steve Melnikoff, Anna Shadbolt, Lyle Winton, Wilson Liu and Wee Siong-Soh for discussions and development that have helped us to validate and refi ne this work  ... 
doi:10.3389/neuro.11.019.2009 pmid:19636389 pmcid:PMC2715266 fatcat:v4brh7yoenghnkf7mj53okfr6i

A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience

Luca Corradi, Ivan Porro, Andrea Schenone, Parastoo Momeni, Raffaele Ferrari, Flavio Nobili, Michela Ferrara, Gabriele Arnulfo, Marco M Fato
2012 BMC Medical Informatics and Decision Making  
Robust, extensible and distributed databases integrating clinical, imaging and molecular data represent a substantial challenge for modern neuroscience.  ...  There is an increasing request from the neuroscience community for software tools addressing technical challenges about: (i) supporting researchers in the medical field to carry out data analysis using  ...  XCEDE (XML-based Clinical and Experimental Data Exchange) [4] is a widespread data model providing an extensive metadata hierarchy for describing and docu-http://www.biomedcentral.com/1472-6947/12/115  ... 
doi:10.1186/1472-6947-12-115 pmid:23043673 pmcid:PMC3560115 fatcat:b2fdeetjpvdinmdmxwo5kdii2e

Neuroscience Data Integration through Mediation: An (F)BIRN Case Study

Naveen Ashish, José Luis Ambite, Maria Muslea, Jessica A. Turner
2010 Frontiers in Neuroinformatics  
We describe an application of the BIRN mediator to the integration of neuroscience experimental data sources.  ...  The BIRN mediator is a general purpose solution to the problem of providing integrated, semantically-consistent access to biomedical data from multiple, distributed, heterogeneous data sources.  ...  Note that while both data sources have to some extent followed the recommendations of XCEDE , which is a data modeling and definition recommendation for the biomedical experimental informatics domain.  ... 
doi:10.3389/fninf.2010.00118 pmid:21228907 pmcid:PMC3017358 fatcat:vlccr2ronvej3ne7s5r566ruam

Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV)

Gully A.P.C. Burns, Jessica A. Turner
2013 NeuroImage  
OoEVV is designed to be compatible with the XCEDE neuroimaging data standard for data collection terminology, and with the Cognitive Paradigm Ontology (CogPO) for specific reasoning elements of neuroimaging  ...  This is designed to provide a lightweight framework to capture mathematical properties of data, with appropriate 'hooks' to permit linkage to other ontology-driven projects (such as the Ontology of Biomedical  ...  BIRN provides a staged monitoring and classification process for biomedical informatics software development.  ... 
doi:10.1016/j.neuroimage.2013.05.024 pmid:23684873 pmcid:PMC4474486 fatcat:t7seoiv4krhrxoomdq555dimjm

A digital repository with an extensible data model for biobanking and genomic analysis management

Massimiliano Izzo, Francesco Mortola, Gabriele Arnulfo, Marco M Fato, Luigi Varesio
2014 BMC Genomics  
Motivation: Molecular biology laboratories require extensive metadata to improve data collection and analysis.  ...  Single standardization is not feasible and it becomes crucial to develop digital repositories with flexible and extensible data models, as in the case of modern integrated biobanks management.  ...  The XML-based Clinical and Experimental Data Exchange (XCEDE) schema provides an extensive metadata hierarchy for storing, describing and documenting data generated by scientific studies [13] .  ... 
doi:10.1186/1471-2164-15-s3-s3 pmid:25077808 pmcid:PMC4083403 fatcat:fqftjr4uezhjhc3xhbdrqbufnq

Sharing brain mapping statistical results with the neuroimaging data model [article]

Camille Maumet, Tibor Auer, Alexander Bowring, Gang Chen, Samir Das, Guillaume Flandin, Satrajit Ghosh, Tristan Glatard, Krzysztof J. Gorgolewski, Karl G. Helmer, Mark Jenkinson, David Keator (+6 others)
2016 bioRxiv   pre-print
Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community.  ...  In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment.  ...  CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research. Front. Neuroinform. 8, 54 (2014). 27. Gadde, S. et al. XCEDE: an extensible schema for biomedical data.  ... 
doi:10.1101/041798 fatcat:b377pfynmzdj3al3kss6xpclsu

Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database

I. Burak Ozyurt, David B. Keator, Dingying Wei, Christine Fennema-Notestine, Karen R. Pease, Jeremy Bockholt, Jeffrey S. Grethe
2010 Neuroinformatics  
In this paper, an extensible data management system for clinical neuroimaging studies is introduced: The Human Clinical Imaging Database (HID) and Toolkit.  ...  The database schema is constructed to support the storage of new data types without changes to the underlying schema.  ...  The authors thank Syam Gadde at the Duke University for XCEDE Schema and HID application testing, Raul de La Garza at the MIND Institute, New Mexico for HID testing, Gregory G.  ... 
doi:10.1007/s12021-010-9078-6 pmid:20567938 pmcid:PMC2974931 fatcat:tpy7px3etfdnnpd7nder22hgne

Metadata and annotations for multi-scale electrophysiological data

M.R. Bower, M. Stead, B.H. Brinkmann, K. Dufendach, G.A. Worrell
2009 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
An example of a graphical utility for generating and evaluating metadata and annotations for "big data" files is presented.  ...  for analysis place differing demands on data structures and algorithms.  ...  In the context of neuroimaging studies, the XML-based Clinical Data Exchange (XCEDE) schema was developed by the Biomedical Informatics Research Network (BIRN [11]) to document research and clinical studies  ... 
doi:10.1109/iembs.2009.5333570 pmid:19964266 pmcid:PMC2841502 fatcat:sy4gex3555gmjplxvvfgedftxi

Provenance in neuroimaging

Allan J. MacKenzie-Graham, John D. Van Horn, Roger P. Woods, Karen L. Crawford, Arthur W. Toga
2008 NeuroImage  
Knowledge about the origin and history of an image is crucial for establishing data and results quality; detailed information about how it was processed, including the specific software routines and operating  ...  We have drafted a mechanism for describing provenance in a simple and easy to use environment, alleviating the burden of documentation from the user while still providing a rich description of an image's  ...  Within the neuroimaging community, the XCEDE (XML-based Clinical Experiment Data Exchange) schema (Keator et al., 2006) also provides for the storage of data provenance information.  ... 
doi:10.1016/j.neuroimage.2008.04.186 pmid:18519166 pmcid:PMC2664747 fatcat:ue56gsjx7bgqnk7dx4lfiky444

Data sharing in neuroimaging research

Jean-Baptiste Poline, Janis L. Breeze, Satrajit Ghosh, Krzysztof Gorgolewski, Yaroslav O. Halchenko, Michael Hanke, Christian Haselgrove, Karl G. Helmer, David B. Keator, Daniel S. Marcus, Russell A. Poldrack, Yannick Schwartz (+2 others)
2012 Frontiers in Neuroinformatics  
The use of electronic data capture (EDC) methods for neuroimaging greatly simplifies the task of data collection and has the potential to help standardize many aspects of data sharing.  ...  We review here the motivations for sharing neuroimaging data, the current data sharing landscape, and the sociological or technical barriers that still need to be addressed.  ...  within the XCEDE schema and to create a vocabulary for neuroimaging that can be used to annotate data.  ... 
doi:10.3389/fninf.2012.00009 pmid:22493576 pmcid:PMC3319918 fatcat:f4cgaldeuraavmcnxqrsisdebe
« Previous Showing results 1 — 15 out of 31 results