Minimum information about a spinal cord injury experiment: MIASCI
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
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 |
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
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 |
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.
Doing experiments is hard work. Ask Cookie Monster.
| grandcookiechallenge.pdf |