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Minimum information about a spinal cord injury experiment: MIASCI

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Insuring that spinal cord injury experiments are interpretable requires that substantial amounts of metadata about the experiments be provided to interested researchers.   An international team of scientists began work in 2012 to develop a reporting standard about Spinal Cord Injury experiments.   As researchers, editors and reviewers begin to use MIASCI, SCI experiments should be more transparent, easier to reproduce and data miners should be able to provide better solutions to exploring the flood of experiments on SCI (over 2800 papers in 2013).  Details about MIASCI can be found at Biosharing and the current version of MIASCI is available a SourceForge.  A paper on MIASCI is out at J Neurotrauma.  This effort is continuing in a new form.  Adam Ferguson and Karim Fouad are leading the charge.  Check out the Open Data Commons - Spinal Cord Injury

J Neurotrauma. 2014 May 28. [Epub ahead of print]
Minimum Information About a Spinal Cord Injury Experiment (MIASCI) - a proposed reporting standard for spinal cord injury experiments.
Lemmon VP, Ferguson AR, Popovich PG, Xu XM, Snow DM, Igarashi M, Beattie CE, Bixby JL, Consortium M, Abeyruwan SW, Beattie MS, Bethea J, Bradke F, Bresnahan JC, Bunge MB, Callahan A, David S, Dunlop SA, Fawcett J, Fehlings M, Fischer I, Giger RJ, Goshima Y, Grimpe B, Hagg T, Hall ED, Harrison BJ, Harvey AR, He C, He Z, Hirata T, Hoke A, Hulsebosch CE, Hurtado A, Jain A, Kadoya K, Kamiguchi H, Kengaku M, Kocsis JD Ph D, Kwon BK, Lee JK, Liebl DJ PhD, Liu SJ, Lowery LA, Mandrekar-Colucci S, Martin JH, Mason CA, McTigue DM, Mokarram N, Moon LD, Muller HW, Nakamura T, Namba T, Nishibe M, Oinuma I, Oudega M, Pleasure DE, Raisman G, Rasband MN, Reier PJ, Santiago-Medina M, Schwab JM, Schwab ME, Shinmyo Y, Silver J, Smith GM, So KF, Sofroniew MV Md PhD, Strittmatter SM, Tuszynski MH, Twiss JL, Visser U, Watkins TA, Wu W, Yoon SO, Yuzaki M, Zheng B, Zhou F, Zou Y.

A piece of advice:  Publishing a paper with 77 co-authors is a fool's errand.

Callahan A, Abeyruwan SW, Al-Ali H, Sakurai K, Ferguson AR, Popovich PG, Shah NH, Visser U, Bixby JL, Lemmon VP. RegenBase: a knowledge base of spinal cord injury biology for translational research. Database (Oxford). 2016 Apr 7;2016. pii: baw040. Print 2016. PMID: 27055827

Callahan A, Anderson KD, Beattie MS, Bixby JL, Ferguson AR, Fouad K, Jakeman LB, Nielson JL, Popovich PG, Schwab JM, Lemmon VP; FAIR Share Workshop Participants. Developing a data sharing community for spinal cord injury research. Exp Neurol. 2017 Sep;295:135-143. doi: 10.1016/j.expneurol.2017.05.012. Epub 2017 May 30. Review. PMID: 28576567

FAIR SCI Ahead: The Evolution of the Open Data Commons for Pre-Clinical Spinal Cord Injury Research. Fouad K, Bixby JL, Callahan A, Grethe JS, Jakeman LB, Lemmon VP, Magnuson DSK, Martone ME, Nielson JL, Schwab JM, Taylor-Burds C, Tetzlaff W, Torres-Espin A, Ferguson AR; FAIR-SCI Ahead Workshop Participants. J Neurotrauma. 2020 Mar 15;37(6):831-838. doi: 10.1089/neu.2019.6674. Epub 2019 Dec 6.PMID: 31608767

LaPlaca MC, Huie JR, Alam HB, Bachstetter AD, Bayir H, Bellgowan PF, Cummings D, Dixon CE, Ferguson AR, Ferland-Beckham C, Floyd CL, Friess SH, Galanopoulou AS, Hall ED, Harris NG, Hawkins BE, Hicks RR, Hulbert LE, Johnson VE, Kabitzke PA, Lafrenaye AD, Lemmon VP, Lifshitz CW, Lifshitz J, Loane DJ, Misquitta L, Nikolian VC, Noble-Haeusslein LJ, Smith DH, Taylor-Burds C, Umoh N, Vovk O, Williams AM, Young M, Zai LJ. Pre-Clinical Common Data Elements for Traumatic Brain Injury Research: Progress and Use Cases.  .J Neurotrauma. 2021 May 15;38(10):1399-1410. doi: 10.1089/neu.2020.7328. Epub 2021 Feb 24. PMID: 33297844


MIASCI.pdf
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A paper related to MIASCI was published in Neural Regeneration Research:
Facilitating transparency in spinal cord injury studies using data standards and ontologies.  Vance P Lemmon, Saminda Abeyruwan, Ubbo Visser, John L Bixby.   Neural Regeneration Research:  9:6-7, 2014
nrr1401.pdf
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Quoting Adam Ferguson at UCSF: "I always tell the story of the grand cookie challenge when people ask me 'what is wrong with CNS disease research - why can't you replicate!?!?'."

Doing experiments is hard work.  Ask Cookie Monster.
grandcookiechallenge.pdf
File Size: 4682 kb
File Type: pdf
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  • Research
    • LemBix News
    • High Content Screening
    • Kinases and regeneration
    • PNS vs CNS Regeneration
    • RNA-Seq
    • Master Nodes
    • Light Sheet Fluorescent Microscopy
    • MIASCI: a reporting standard
    • RegenBase
    • Assay Guidance Manual
    • BioAssay Ontology
  • Bixby
    • John Bixby PubMed Serch
  • Lemmon
    • BLM
    • Xiao-Ming Xu
    • Miami Project SCI Course
    • Vance's Papers
    • Back in the day
    • SBI2
    • Growth Cone Videos
    • Bike Safety
    • Miscellaneous
  • Ali
  • Lab Members
    • Group Photos >
      • PAMM 160728
      • ProjectRock 190524
      • Escape Room 210524
    • Abdiel Badillo-Martinez
    • Yania Martinez, VVC Core >
      • Yania's Monarch
    • Yan Shi, M.S. Imaging and HCA Core
    • Macarena Vergara
    • Former Lab Members >
      • Sam Beckerman, MD/PhD student
      • Julia Brzac
      • Willi Buchser, PhD
      • Nathaniel Cleri
      • Danny Cooper, Ph.D.
      • Danny Cabrera
      • Pingping Chen, MD/PhD, Viral Vector Core
      • Matt Danzi, PhD student
      • Ellie Dawson
      • Roberto E Diaz
      • Kireeti Dulla
      • Laetitia Francelle, Ph.D.
      • Nathan Fox
      • Jared Gans, M.D.
      • Juliana Hemela
      • Pingping Jai, M.S. Viral Vector Core
      • Victor Jann
      • Danny L. John, MS1
      • Ryohei Kurosawa
      • Lyndah Lovell
      • Jeffrey Lowell
      • Nick O'Neill, PhD student
      • Kim Madhwani
      • Kar Men Mah, Ph.D.
      • Dario Motti, PhD
      • Melissa Munoz
      • Maya Murry: Computer Science REU
      • Michael Ortega
      • Marcos Rivas: HHMI SURF
      • Saloni Mehta, PhD student
      • Sevika Singh
      • Tatiana Slepak, M.S.
      • Robin Smith, PhD
      • Moya Tomlin, MS2
      • Enjolie Vadella
      • Eli Weaver, Lab Manager
      • Giulia Zunino, Ph.D.
  • Resources
    • Forms