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Items: 39

1.

Bio-AnswerFinder: a system to find answers to questions from biomedical texts.

Ozyurt IB, Bandrowski A, Grethe JS.

Database (Oxford). 2020 Jan 1;2020. pii: baz137. doi: 10.1093/database/baz137.

PMID:
31925435
2.

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. 2019 Dec 6. doi: 10.1089/neu.2019.6674. [Epub ahead of print]

PMID:
31608767
3.

A data citation roadmap for scholarly data repositories.

Fenner M, Crosas M, Grethe JS, Kennedy D, Hermjakob H, Rocca-Serra P, Durand G, Berjon R, Karcher S, Martone M, Clark T.

Sci Data. 2019 Apr 10;6(1):28. doi: 10.1038/s41597-019-0031-8.

4.

Addendum: The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Jan Aalbersberg I, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, Hoen PAC', Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Jan Velterop, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2019 Mar 19;6(1):6. doi: 10.1038/s41597-019-0009-6. No abstract available.

5.

Everything Matters: The ReproNim Perspective on Reproducible Neuroimaging.

Kennedy DN, Abraham SA, Bates JF, Crowley A, Ghosh S, Gillespie T, Goncalves M, Grethe JS, Halchenko YO, Hanke M, Haselgrove C, Hodge SM, Jarecka D, Kaczmarzyk J, Keator DB, Meyer K, Martone ME, Padhy S, Poline JB, Preuss N, Sincomb T, Travers M.

Front Neuroinform. 2019 Feb 7;13:1. doi: 10.3389/fninf.2019.00001. eCollection 2019.

6.

Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement.

Ozyurt IB, Grethe JS.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay130.

7.

Uniform resolution of compact identifiers for biomedical data.

Wimalaratne SM, Juty N, Kunze J, Janée G, McMurry JA, Beard N, Jimenez R, Grethe JS, Hermjakob H, Martone ME, Clark T.

Sci Data. 2018 May 8;5:180029. doi: 10.1038/sdata.2018.29.

8.

DataMed - an open source discovery index for finding biomedical datasets.

Chen X, Gururaj AE, Ozyurt B, Liu R, Soysal E, Cohen T, Tiryaki F, Li Y, Zong N, Jiang M, Rogith D, Salimi M, Kim HE, Rocca-Serra P, Gonzalez-Beltran A, Farcas C, Johnson T, Margolis R, Alter G, Sansone SA, Fore IM, Ohno-Machado L, Grethe JS, Xu H.

J Am Med Inform Assoc. 2018 Jan 13. doi: 10.1093/jamia/ocx121. [Epub ahead of print]

PMID:
29346583
9.

DATS, the data tag suite to enable discoverability of datasets.

Sansone SA, Gonzalez-Beltran A, Rocca-Serra P, Alter G, Grethe JS, Xu H, Fore IM, Lyle J, Gururaj AE, Chen X, Kim HE, Zong N, Li Y, Liu R, Ozyurt IB, Ohno-Machado L.

Sci Data. 2017 Jun 6;4:170059. doi: 10.1038/sdata.2017.59.

10.

The Resource Identification Initiative: a cultural shift in publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N; RINL Resource Identification Initiative.

Brain Behav. 2015 Dec 8;6(1):e00417. doi: 10.1002/brb3.417. eCollection 2016 Jan.

11.

The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, 't Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B.

Sci Data. 2016 Mar 15;3:160018. doi: 10.1038/sdata.2016.18. Erratum in: Sci Data. 2019 Mar 19;6(1):6.

12.

Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature.

Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE.

PLoS One. 2016 Jan 5;11(1):e0146300. doi: 10.1371/journal.pone.0146300. eCollection 2016.

13.

The Resource Identification Initiative: A Cultural Shift in Publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SC, Washington N, Zudilova-Seinstra E, Vasilevsky N.

J Comp Neurol. 2016 Jan 1;524(1):8-22. doi: 10.1002/cne.23913.

14.

The Resource Identification Initiative: A cultural shift in publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan S, Washington N, Zudilova-Seinstra E, Vasilevsky N; Resource Identification Initiative Members are listed here: https://www.force11.org/node/4463/members.

Version 2. F1000Res. 2015 May 29 [revised 2015 Jan 1];4:134. doi: 10.12688/f1000research.6555.2. eCollection 2015.

15.

The Resource Identification Initiative: A Cultural Shift in Publishing.

Bandrowski A, Brush M, Grethe JS, Haendel MA, Kennedy DN, Hill S, Hof PR, Martone ME, Pols M, Tan SS, Washington N, Zudilova-Seinstra E, Vasilevsky N; RINL Resource Identification Initiative.

Neuroinformatics. 2016 Apr;14(2):169-82. doi: 10.1007/s12021-015-9284-3.

16.

The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases.

Whetzel PL, Grethe JS, Banks DE, Martone ME.

PLoS One. 2015 Sep 22;10(9):e0136206. doi: 10.1371/journal.pone.0136206. eCollection 2015.

17.

Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources.

Marenco LN, Wang R, Bandrowski AE, Grethe JS, Shepherd GM, Miller PL.

Front Neuroinform. 2014 May 28;8:58. doi: 10.3389/fninf.2014.00058. eCollection 2014.

18.

A survey of the neuroscience resource landscape: perspectives from the neuroscience information framework.

Cachat J, Bandrowski A, Grethe JS, Gupta A, Astakhov V, Imam F, Larson SD, Martone ME.

Int Rev Neurobiol. 2012;103:39-68. doi: 10.1016/B978-0-12-388408-4.00003-4. Review.

PMID:
23195120
19.

Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach.

Imam FT, Larson SD, Bandrowski A, Grethe JS, Gupta A, Martone ME.

Front Genet. 2012 Jun 22;3:111. doi: 10.3389/fgene.2012.00111. eCollection 2012.

20.

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework.

Bandrowski AE, Cachat J, Li Y, Müller HM, Sternberg PW, Ciccarese P, Clark T, Marenco L, Wang R, Astakhov V, Grethe JS, Martone ME.

Database (Oxford). 2012 Mar 20;2012:bas005. doi: 10.1093/database/bas005. Print 2012.

21.

Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics.

Astakhov V, Bandrowski A, Gupta A, Kulungowski AW, Grethe JS, Bouwer J, Molina T, Rowley V, Penticoff S, Terada M, Wong W, Hakozaki H, Kwon O, Martone ME, Ellisman M.

Procedia Comput Sci. 2012;9:1595-1603. doi: 10.1016/j.procs.2012.04.175.

22.

XCEDE: an extensible schema for biomedical data.

Gadde S, Aucoin N, Grethe JS, Keator DB, Marcus DS, Pieper S; FBIRN, MBIRN, BIRN-CC.

Neuroinformatics. 2012 Jan;10(1):19-32. doi: 10.1007/s12021-011-9119-9.

23.

Federated web-accessible clinical data management within an extensible neuroimaging database.

Ozyurt IB, Keator DB, Wei D, Fennema-Notestine C, Pease KR, Bockholt J, Grethe JS.

Neuroinformatics. 2010 Dec;8(4):231-49. doi: 10.1007/s12021-010-9078-6.

24.

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

Keator DB, Wei D, Gadde S, Bockholt J, Grethe JS, Marcus D, Aucoin N, Ozyurt IB.

Front Neuroinform. 2009 Sep 7;3:30. doi: 10.3389/neuro.11.030.2009. eCollection 2009.

25.

Mediator infrastructure for information integration and semantic data integration environment for biomedical research.

Grethe JS, Ross E, Little D, Sanders B, Gupta A, Astakhov V.

Methods Mol Biol. 2009;569:33-53. doi: 10.1007/978-1-59745-524-4_3.

PMID:
19623485
26.

Data federation in the Biomedical Informatics Research Network: tools for semantic annotation and query of distributed multiscale brain data.

Bug W, Astahkov V, Boline J, Fennema-Notestine C, Grethe JS, Gupta A, Kennedy DN, Rubin DL, Sanders B, Turner JA, Martone ME.

AMIA Annu Symp Proc. 2008 Nov 6:1220.

PMID:
18999211
27.

The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.

Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA, Martone ME.

Neuroinformatics. 2008 Sep;6(3):175-94. doi: 10.1007/s12021-008-9032-z. Epub 2008 Oct 31.

28.

Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF).

Gupta A, Bug W, Marenco L, Qian X, Condit C, Rangarajan A, Müller HM, Miller PL, Sanders B, Grethe JS, Astakhov V, Shepherd G, Sternberg PW, Martone ME.

Neuroinformatics. 2008 Sep;6(3):205-17. doi: 10.1007/s12021-008-9033-y. Epub 2008 Oct 29.

29.

The neuroscience information framework: a data and knowledge environment for neuroscience.

Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS, Gupta A, Halavi M, Kennedy DN, Marenco L, Martone ME, Miller PL, Müller HM, Robert A, Shepherd GM, Sternberg PW, Van Essen DC, Williams RW.

Neuroinformatics. 2008 Sep;6(3):149-60. doi: 10.1007/s12021-008-9024-z. Epub 2008 Oct 23.

30.

A national human neuroimaging collaboratory enabled by the Biomedical Informatics Research Network (BIRN).

Keator DB, Grethe JS, Marcus D, Ozyurt B, Gadde S, Murphy S, Pieper S, Greve D, Notestine R, Bockholt HJ, Papadopoulos P; BIRN Function; BIRN Morphometry; BIRN-Coordinating.

IEEE Trans Inf Technol Biomed. 2008 Mar;12(2):162-72. doi: 10.1109/TITB.2008.917893.

31.
32.

A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels.

Keator DB, Gadde S, Grethe JS, Taylor DV, Potkin SG; FIRST BIRN.

Neuroinformatics. 2006;4(2):199-212.

PMID:
16845169
33.

Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease.

Grethe JS, Baru C, Gupta A, James M, Ludaescher B, Martone ME, Papadopoulos PM, Peltier ST, Rajasekar A, Santini S, Zaslavsky IN, Ellisman MH.

Stud Health Technol Inform. 2005;112:100-9.

PMID:
15923720
34.

Towards a formalization of disease-specific ontologies for neuroinformatics.

Gupta A, Ludäscher B, Grethe JS, Martone ME.

Neural Netw. 2003 Nov;16(9):1277-92.

PMID:
14622884
35.

The Functional Magnetic Resonance Imaging Data Center (fMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies.

Van Horn JD, Grethe JS, Kostelec P, Woodward JB, Aslam JA, Rus D, Rockmore D, Gazzaniga MS.

Philos Trans R Soc Lond B Biol Sci. 2001 Aug 29;356(1412):1323-39.

36.

Functional anatomy of nonvisual feedback loops during reaching: a positron emission tomography study.

Desmurget M, Gréa H, Grethe JS, Prablanc C, Alexander GE, Grafton ST.

J Neurosci. 2001 Apr 15;21(8):2919-28.

37.

Functional adaptation of reactive saccades in humans: a PET study.

Desmurget M, Pélisson D, Grethe JS, Alexander GE, Urquizar C, Prablanc C, Grafton ST.

Exp Brain Res. 2000 May;132(2):243-59.

PMID:
10853949
38.
39.

Associative learning.

Thompson RF, Bao S, Chen L, Cipriano BD, Grethe JS, Kim JJ, Thompson JK, Tracy JA, Weninger MS, Krupa DJ.

Int Rev Neurobiol. 1997;41:151-89. Review.

PMID:
9378587

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