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Providing traceability for neuroimaging analyses

Richard McClatchey, Andrew Branson, Ashiq Anjum, Peter Bloodsworth, Irfan Habib, Kamran Munir, Jetendr Shamdasani, Kamran Soomro
2013 International Journal of Medical Informatics  
With the increasingly digital nature of biomedical data and as the complexity of analyses in medical research increases, the need for accurate information capture, traceability and accessibility has become  ...  For neuroscientific analyses, especially those centred on complex image analysis, traceability of processes and datasets is essential but up to now this has not been captured in a manner that facilitates  ...  Acknowledgements The authors wish to thank their institutes and the European Commission for their support and to  ... 
doi:10.1016/j.ijmedinf.2013.05.005 pmid:23763909 fatcat:c3yyjdxqizgp7hlowa32zfthny

Traceability and Provenance in Big Data Medical Systems

Richard McClatchey, Jetendr Shamdasani, Andrew Branson, Kamran Munir, Zsolt Kovacs, Giovanni Frisoni
2015 2015 IEEE 28th International Symposium on Computer-Based Medical Systems  
Researchers require systems that provide traceability of information through provenance data capture and management to support their clinical analyses.  ...  We present an approach that has been adopted in the neuGRID and N4U projects, which aimed to provide detailed traceability to support research analysis processes in the study of biomarkers for Alzheimers  ...  In N4U, CRISTAL manages data from the Analysis Service, containing the full history of computing task execution; it can also provide this level of traceability for any piece of data in the system, such  ... 
doi:10.1109/cbms.2015.10 dblp:conf/cbms/McClatcheySBMKF15 fatcat:m2y6utkz6jcadetkcktudui3um

Position Paper: Provenance Data Visualisation for Neuroimaging Analysis [article]

Bilal Arshad, Kamran Munir, Richard McClatchey, Saad Liaquat
2015 arXiv   pre-print
neuroimaging analysis.  ...  Systems are required that offer provenance data capture and visualisation support for analyses.  ...  Visualisation of provenance data for the workflow provides means to analyse all the intermediary image sets and results to verify that the results were incorrect.  ... 
arXiv:1502.01556v1 fatcat:t44kjzyiobhond67kn76ezvs7y

Ten simple rules for neuroimaging meta-analysis

Veronika I. Müller, Edna C. Cieslik, Angela R. Laird, Peter T. Fox, Joaquim Radua, David Mataix-Cols, Christopher R. Tench, Tal Yarkoni, Thomas E. Nichols, Peter E. Turkeltaub, Tor D. Wager, Simon B. Eickhoff
2018 Neuroscience and Biobehavioral Reviews  
However, the field lacks specific guidelines for the conduct of such meta-analyses.  ...  In addition, we provide specific guidelines and a checklist that will hopefully improve the transparency, traceability, replicability and reporting of meta-analytical results of neuroimaging data.  ...  First, we provide best-practice recommendations that should be considered carefully when performing neuroimaging meta-analyses and help researchers to make informed and traceable decisions.  ... 
doi:10.1016/j.neubiorev.2017.11.012 pmid:29180258 pmcid:PMC5918306 fatcat:6aksogfarbdhhht5kvw6ltzzdm

BIOMIST: A Platform for Biomedical Data Lifecycle Management of Neuroimaging Cohorts

Marianne Allanic, Pierre-Yves Hervé, Cong-Cuong Pham, Myriam Lekkal, Alexandre Durupt, Thierry Brial, Arthur Grioche, Nada Matta, Philippe Boutinaud, Benoit Eynard, Marc Joliot
2017 Frontiers in ICT  
Overall, the BIOMIST platform is well suited for the management of neuroimaging cohorts, and it is currently used for the management of the BIL&GIN dataset (300 participants) and the ongoing magnetic resonance  ...  Product Lifecycle Management (PLM) systems rely on an object-oriented data model and allow the traceability of data and workflows throughout the life of a product, from its design to its manufacturing,  ...  "Mapping Strategy for Data Import, " "The DIMP Method for Integration of Processing Pipelines, " "Implementation, " and "Application"; C-CP worked on Sections "Querying Strategies" and "Implementation"  ... 
doi:10.3389/fict.2016.00035 fatcat:7riec4yeorbyjlcemjab5idwkq

A Review on the Bioinformatics Tools for Neuroimaging

Mei Yen Man, Mei Sin Ong, Mohd Saberi Mohamad, Safaai Deris, Ghazali Sulong, Jasmy Yunus, Fauzan Khairi Che Harun
2015 Malaysian Journal of Medical Sciences  
Sources, links, and descriptions of the application of each tool are provided in this paper as well.  ...  Neuroimaging data are becoming of more interest among the circle of neuroimaging experts. Therefore, it is necessary to develop a large amount of neuroimaging tools.  ...  AFNI Facilities are provided for several types of statistical analyses of multiple 3D functional data sets.  ... 
pmid:27006633 pmcid:PMC4795522 fatcat:z7hjo67kgvfmzd3rchie3bgwdi

PLM as a strategy for the management of heterogeneous information in bio-medical imaging field

Marianne Allanic, Pierre Yves Hervé, Alexandre Durupt, Marc Joliot, Philippe Boutinaud, Benoît Eynard
2017 International Journal of Information Technology and Management  
Reference to this paper should be made as follows: Allanic, M., Hervé, P-Y., Durupt, A., Joliot, M., Boutinaud, P. and Eynard, B. (2017) 'PLM as a strategy for the management of heterogeneous information  ...  Some data management systems have been developed in neuroimaging field, however they miss to integrate the data provenance all along the research works, from study specifications to scientific publication  ...  ANR-13-CORD-0007) for thematic axis no. 2 of the Contint 2013 Call for Proposal: from content to knowledge and big data.  ... 
doi:10.1504/ijitm.2017.080950 fatcat:ouzk5gymxvbcllaxi4afoqe4uq

PLM as a strategy for the management of heterogeneous information in bio-medical imaging field

Benoît Eynard, Marc Joliot, Philippe Boutinaud, Alexandre Durupt, Marianne Allanic, Pierre Yves Hervé
2017 International Journal of Information Technology and Management  
Reference to this paper should be made as follows: Allanic, M., Hervé, P-Y., Durupt, A., Joliot, M., Boutinaud, P. and Eynard, B. (2017) 'PLM as a strategy for the management of heterogeneous information  ...  Some data management systems have been developed in neuroimaging field, however they miss to integrate the data provenance all along the research works, from study specifications to scientific publication  ...  ANR-13-CORD-0007) for thematic axis no. 2 of the Contint 2013 Call for Proposal: from content to knowledge and big data.  ... 
doi:10.1504/ijitm.2017.10001017 fatcat:7mxoqkraqrd7be2oqh2mbypj3i

Data provenance tracking as the basis for a biomedical virtual research environment [article]

Richard McClatchey
2018 arXiv   pre-print
work of others and to ensure appropriate conditions data have been used for specific analyses.  ...  We have extended the work carried out in the neuGRID and N4U projects in providing a so-called Virtual Laboratory to provide the foundation for a generic VRE in which sets of biomedical data (images, laboratory  ...  highlight the support of their home institutes and acknowledge funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n. 211714 ("neuGRID") and n. 283562 ("neuGRID for  ... 
arXiv:1803.07433v1 fatcat:5pe5trly6fesjb4rmx3npnwbdu

Towards Provenance and Traceability in CRISTAL for HEP

Jetendr Shamdasani, Andrew Branson, Richard McClatchey
2014 Journal of Physics, Conference Series  
This paper discusses the CRISTAL object lifecycle management system and its use in provenance data management and the traceability of system events.  ...  From these examples, applications are drawn for the High Energy Physics domain and some initial ideas for its use in data preservation HEP are outlined in detail in this paper.  ...  Also by providing complete traceability of a clinical analysis provenance information can aid in finding areas where a clinicians work may have failed.  ... 
doi:10.1088/1742-6596/513/3/032091 fatcat:425xcbkhrzbolfycwxkx2t5xee

From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research

Anisha Keshavan, Jean-Baptiste Poline
2019 Frontiers in Neuroinformatics  
Here, we review the landscape of web technologies used in neuroimaging research, and discuss future applications, areas for improvement, and the limitations of using web technology in research.  ...  As the neuroimaging informatics research community amasses large datasets to answer complex neuroscience questions, we find that the web is the best medium to facilitate novel insights by way of improved  ...  The neuroimaging community is just beginning to engage citizen scientists as a resource in our data analyses.  ... 
doi:10.3389/fninf.2019.00003 pmid:30881299 pmcid:PMC6405692 fatcat:k7x2llfff5hfrhr6igrt7hwhu4

Towards Semantic Provenance in CRISTAL

Jetendr Shamdasani, Richard McClatchey, Andrew Branson
2012 Extended Semantic Web Conference  
Traceability is an important feature of workflow based systems, and is a key source of provenance data.  ...  This paper presents CRISTAL, a mature software platform developed and used at CERN for experiment construction at the LHC.  ...  Also by providing complete traceability of a clinical analysis provenance information can aid in finding areas where a clinicians work may have failed.  ... 
dblp:conf/esws/ShamdasaniMB12 fatcat:bqajaiuufnfrdkuutk6escsw6m

Application of PLM for Bio-Medical Imaging in Neuroscience [chapter]

Marianne Allanic, Alexandre Durupt, Marc Joliot, Benoît Eynard, Philippe Boutinaud
2013 IFIP Advances in Information and Communication Technology  
A PLM neuroimaging datamodel that has been designed in collaboration between the GIN laboratory, Roberval laboratory and Cadesis company to meet the needs of the GIN, is described.  ...  The researchers of the GIN (Neuroimaging Functional Group) laboratory study brain maps of anatomical and functional cognitive activation of hundred-subject cohorts, acquired with Magnetic Resonance Imaging  ...  The authors wish to thank in particular the Association Nationale de la Recherche et de la Technologie (ANRT) for its financial support to their work (CIFRE 2012/0420).  ... 
doi:10.1007/978-3-642-41501-2_52 fatcat:4ixoxchndjd5djgwqk7saui7c4

Research Traceability using Provenance Services for Biomedical Analysis [article]

Ashiq Anjum, Peter Bloodsworth, Andrew Branson, Irfan Habib, Richard McClatchey, Tony Solomonides, the neuGRID Consortium
2014 arXiv   pre-print
and execution of workflows in biomedical analyses.  ...  provenance management could emerge for more generic application to the (Health)Grid community.  ...  and to provide traceability of their research data and algorithms.  ... 
arXiv:1403.0230v1 fatcat:xfhuf4mghvakfl4cyhkc5mjxm4

Research Traceability using Provenance Services for Biomedical Analysis [article]

Ashiq Anjum, Peter Bloodsworth, Andrew Branson, Irfan Habib, Richard McClatchey, Tony Solomonides, the neuGRID Consortium
2012 arXiv   pre-print
and execution of workflows in biomedical analyses.  ...  provenance management could emerge for more generic application to the (Health)Grid community.  ...  and to provide traceability of their research data and algorithms.  ... 
arXiv:1202.5517v1 fatcat:zhkhowd2pzccdjwkx56ts6emli
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