publication . Article . Other literature type . Preprint . 2016

NIDM‐Results: a Neuroimaging Data Model to share brain mapping statistical results

Camille Maumet; Tibor Auer; Alexander Bowring; Gang Chen; Samir Das; Guillaume Flandin; Satrajit Ghosh; Tristan Glatard; Krzysztof J. Gorgolewski; Karl G. Helmer; ...
Open Access English
  • Published: 06 Dec 2016
  • Publisher: HAL CCSD
Abstract
National Institutes of Health (U.S.) (Grant 1R01EB020740-01A1)
Subjects
free text keywords: [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], QA76, Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, FMRI, REPRODUCIBILITY, METAANALYSIS, TRANSPARENCY, NEUROSCIENCE, EVOLUTION, ONTOLOGY, Article, Medical research, Research data, Statistics, Probability and Uncertainty, Statistics and Probability, Education, Library and Information Sciences, Information Systems, Computer Science Applications
Funded by
NIH| Center for Reproducible Neuroimaging Computation (CRNC)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1P41EB019936-01A1
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING
,
WT| Transforming statistical methodology for neuroimaging meta-analysis.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 100309
  • Funding stream: Cognitive Neuroscience and Mental Health
,
NIH| N-CANDA: Data Analysis Component
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01AA021697-03
  • Funding stream: NATIONAL INSTITUTE ON ALCOHOL ABUSE AND ALCOHOLISM
,
NIH| FUNCTION BIRN
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U24RR021992-04
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
,
NIH| Scientific and Statistical Computing Core
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1ZICMH002888-09
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
Communities
NeuroinformaticsNI Projects: BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER
NeuroinformaticsNI Projects: Fragmented early life environmental and emotional / cognitive vulnerabilities
NeuroinformaticsNI Projects
31 references, page 1 of 3

49. Smith, B. et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251-1255 (2007).

50. Masolo, C. et al. The wonderweb library of fundational ontologies and the dolce ontology. wonderweb deliverable d18, final report (vr. 1.0. 31-12-2003). The WonderWeb Library of Fundational Ontologies and the DOLCE ontology. WonderWeb Deliverable D18, Final Report (vr. 1. 0. 31-12-2003) (2003).

51. Gorgolewski, K. J. et al. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci. Data 3, 160044 (2016).

52. Temal, L., Dojat, M., Kassel, G. & Gibaud, B. Towards an ontology for sharing medical images and regions of interest in neuroimaging. J. Biomed. Inform. 41, 766-778 (2008). [OpenAIRE]

53. Nolan Nichols, B. et al. Building a Web of Linked Data Resources to Advance Neuroscience Research. Preprint at http://dx.doi. org/10.1101/053934 (2016).

54. Glatard, T. et al. Reproducibility of neuroimaging analyses across operating systems. Front. Neuroinform 9, 12 (2015).

55. Carp, J. The secret lives of experiments: methods reporting in the fMRI literature. Neuroimage 63, 289-300 (2012).

56. NIDASH. Google drive Available at https://drive.google.com/drive/folders/0B-BLof5_SOh8ZURQV1RmdU53Z0k. Accessed on 15 June 2016.

57. incf-nidash/nidm. GitHub Available at https://github.com/incf-nidash/nidm. Accessed on 15 June 2016.

58. Statistics Ontology. Available at http://stato-ontology.org. Accessed on 6 January 2016.

59. New term 'residual mean squares' · Issue #35 · ISA-tools/stato. GitHub Available at https://github.com/ISA-tools/stato/issues/35.

60. Larson, S. D. & Martone, M. E. NeuroLex.org: an online framework for neuroscience knowledge. Front. Neuroinform 7, 18-18 (2013).

61. The Neuroscience Lexicon. Available at http://neurolex.org/. Accessed on 15 June 2016.

62. Bandrowski, A. E. & Martone, M. E. RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods. Neuron 90, 434-436 (2016). [OpenAIRE]

63. Resource Identification Portal. Available at https://scicrunch.org/resources. Accessed on 15th June 2016.

31 references, page 1 of 3
Abstract
National Institutes of Health (U.S.) (Grant 1R01EB020740-01A1)
Subjects
free text keywords: [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], QA76, Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, FMRI, REPRODUCIBILITY, METAANALYSIS, TRANSPARENCY, NEUROSCIENCE, EVOLUTION, ONTOLOGY, Article, Medical research, Research data, Statistics, Probability and Uncertainty, Statistics and Probability, Education, Library and Information Sciences, Information Systems, Computer Science Applications
Funded by
NIH| Center for Reproducible Neuroimaging Computation (CRNC)
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1P41EB019936-01A1
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING
,
WT| Transforming statistical methodology for neuroimaging meta-analysis.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 100309
  • Funding stream: Cognitive Neuroscience and Mental Health
,
NIH| N-CANDA: Data Analysis Component
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01AA021697-03
  • Funding stream: NATIONAL INSTITUTE ON ALCOHOL ABUSE AND ALCOHOLISM
,
NIH| FUNCTION BIRN
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U24RR021992-04
  • Funding stream: NATIONAL CENTER FOR RESEARCH RESOURCES
,
NIH| Scientific and Statistical Computing Core
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1ZICMH002888-09
  • Funding stream: NATIONAL INSTITUTE OF MENTAL HEALTH
Communities
NeuroinformaticsNI Projects: BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER
NeuroinformaticsNI Projects: Fragmented early life environmental and emotional / cognitive vulnerabilities
NeuroinformaticsNI Projects
31 references, page 1 of 3

49. Smith, B. et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251-1255 (2007).

50. Masolo, C. et al. The wonderweb library of fundational ontologies and the dolce ontology. wonderweb deliverable d18, final report (vr. 1.0. 31-12-2003). The WonderWeb Library of Fundational Ontologies and the DOLCE ontology. WonderWeb Deliverable D18, Final Report (vr. 1. 0. 31-12-2003) (2003).

51. Gorgolewski, K. J. et al. The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments. Sci. Data 3, 160044 (2016).

52. Temal, L., Dojat, M., Kassel, G. & Gibaud, B. Towards an ontology for sharing medical images and regions of interest in neuroimaging. J. Biomed. Inform. 41, 766-778 (2008). [OpenAIRE]

53. Nolan Nichols, B. et al. Building a Web of Linked Data Resources to Advance Neuroscience Research. Preprint at http://dx.doi. org/10.1101/053934 (2016).

54. Glatard, T. et al. Reproducibility of neuroimaging analyses across operating systems. Front. Neuroinform 9, 12 (2015).

55. Carp, J. The secret lives of experiments: methods reporting in the fMRI literature. Neuroimage 63, 289-300 (2012).

56. NIDASH. Google drive Available at https://drive.google.com/drive/folders/0B-BLof5_SOh8ZURQV1RmdU53Z0k. Accessed on 15 June 2016.

57. incf-nidash/nidm. GitHub Available at https://github.com/incf-nidash/nidm. Accessed on 15 June 2016.

58. Statistics Ontology. Available at http://stato-ontology.org. Accessed on 6 January 2016.

59. New term 'residual mean squares' · Issue #35 · ISA-tools/stato. GitHub Available at https://github.com/ISA-tools/stato/issues/35.

60. Larson, S. D. & Martone, M. E. NeuroLex.org: an online framework for neuroscience knowledge. Front. Neuroinform 7, 18-18 (2013).

61. The Neuroscience Lexicon. Available at http://neurolex.org/. Accessed on 15 June 2016.

62. Bandrowski, A. E. & Martone, M. E. RRIDs: A Simple Step toward Improving Reproducibility through Rigor and Transparency of Experimental Methods. Neuron 90, 434-436 (2016). [OpenAIRE]

63. Resource Identification Portal. Available at https://scicrunch.org/resources. Accessed on 15th June 2016.

31 references, page 1 of 3
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