GigaDB: Promoting data dissemination and reproducibility

Database

Volumn 2014, Issue , 2014, Pages

  Sneddon, Tam P ^a   Xiao, Sizhe ^b   Edmunds, Scott C ^b   Li, Peter ^b   Goodman, Laurie ^b   Hunter, Christopher I ^b  

^a STANFORD UNIVERSITY   (United States)

^b GigaScience Beijing Genomics Institute Hong Kong (BGIHK) Research Institute   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC DATABASE; INFORMATION DISSEMINATION; PUBLICATION; REPRODUCIBILITY; WRITING;

AUTHORSHIP; DATABASES, GENETIC; INFORMATION DISSEMINATION; PUBLICATIONS; REPRODUCIBILITY OF RESULTS;

EID: 84906561393     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bau018     Document Type: Article

References (28)

1. Liu, L., Li, Y., Li, S. et al. (2012) Comparison of next-generation sequencing systems. J. Biomed. Biotechnol., 2012, 251364. doi: 10.1155/2012/251364.
2. Wasinger, V.C., Zeng, M. and Yau, Y. (2013) Current status and advances in quantitative proteomic mass spectrometry. Int. J. Proteomics, 2013, 180605. doi: 10.1155/2013/180605.
3. Putri, S.P., Yamamoto, S., Tsugawa, H. and Fukusaki, E. (2013) Current metabolomics: technological advances. J. Biosci. Bioeng., 116, 9-16. doi: 10.1016/j.jbiosc.2013.01.004.
4. Gonzalez, A., King, A., Robeson, M.S. III et al. (2012) Characterizing microbial communities through space and time. Curr. Opin. Biotechnol., 23, 431-436. doi: 10.1016/j.copbio.2011.11.017.
5. Haider, S. and Pal, R. (2013) Integrated analysis of transcriptomic and proteomic data. Curr. Genomics, 14, 91-110.
6. Alsheikh-Ali, A.A., Qureshi, W., Al-Mallah, M.H. and Ioannidis, J.P.A. (2011) Public availability of published research data in high-impact journals. PLoS One, 6, e24357. doi: 10.1371/journal.pone.0024357.
7. Stodden, V., Guo, P. and Ma, Z. (2013) Toward reproducible computational research: an empirical analysis of data and code policy adoption by journals. PLoS One, 8, e67111. doi: 10.1371/journal.pone.0067111.
8. Editorial, (2009) Credit where credit is overdue. Nat. Biotechnol., 27, 579. http://dx.doi.org/10.1038/nbt0709-579.
9. Rosenthal, D.S.H. and Vargas, D.L. (2013) Distributed digital preservation in the cloud. Int. J. Digit. Curation, 8, 107-119. doi: 10.2218/ijdc.v8i1.248.
10. Goodman, L., Edmunds, S.C. and Basford, A.T. (2012) Large and linked in scientific publishing. Gigascience, 1, 1. doi: 10.1186/2047-217X-1-1.
11. Sneddon, T.P., Li, P. and Edmunds, S.C. (2012) GigaDB: announcing the GigaScience database. Gigascience, 1, 11. doi: 10.1186/2047-217X-1-11.
12. Piwowar, H.A., Day, R.S. and Fridsma, D.B. (2007) Sharing detailed research data is associated with increased citation rate. PloS One, 2, e308. doi: 10.1371/journal.pone.0000308.
13. Li, D., Xi, F., Zhao, M. et al. (2011) Genomic data from Escherichia coli O104:H4 isolate TY-2482. Gigascience, 365, 718-724. http://dx.doi.org/10.5524/100001.
14. Rohde, H., Qin, J., Cui, Y. et al. (2011) Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N. Engl. J. Med, 365, 718-724. doi: 10.1056/NEJMoa1107643.
15. Hrynaszkiewicz, I., Busch, S. and Cockerill, M.J. (2013) Licensing the future: report on BioMed Central's public consultation on open data in peer-reviewed journals. BMC Res. Notes, 6, 318. doi: 10.1186/1756-0500-6-318.
16. Ball, A. and Duke, M. (2012) How to Cite Datasets and Link to Publications. DCC How-to Guides. Digital Curation Centre, Edinburgh. http://www.dcc.ac.uk/resources/how-guides.
17. Edmunds, S.C., Pollard, T.J., Hole, B. and Basford, A.T. (2012) Adventures in data citation: sorghum genome data exemplifies the new gold standard. BMC Res. Notes, 2, 223. doi: 10.1186/1756-0500-5-223.
18. Luo, R., Liu, B., Xie, Y. et al. (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience, 1, 18. doi:10.1186/2047-217X-1-18.
19. Kan, Z., Zheng, H., Liu, X. et al. (2012) Hepatocellular carcinoma genomic data from the Asian Cancer Research Group. Gigascience, 44, 765-769. http://dx.doi.org/10.5524/100034.
20. Yilmaz, P., Kottmann, R., Field, D. et al. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat. Biotechnol., 29, 415-420. doi: 10.1038/nbt.1823.
21. Sansone, S.A., Rocca-Serra, P., Field, D. et al. (2012) Toward interoperable bioscience data. Nat. Genet., 44, 121-126. doi: 10.1038/ng.1054.
22. Haug, K., Salek, R.M., Conesa, P. et al. (2013) MetaboLights - an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res., 41, D781-D786. doi: 10.1093/nar/gks1004.
23. HoSui, S.J., Begley, K., Reilly, D. et al. (2011) The stem cell discovery engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res., 40, D984-D991.
24. Stoev, P., Komerički, A., Akkari, N. et al. (2013) Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data. Biodivers. Data J, 1, e1013. doi: 10.3897/BDJ.
25. Stoev, P., Komerički, A., Akkari, N. et al. (2013) Transcriptomic, DNA barcoding, and micro-CT imaging data from an advanced taxonomic description of a novel centipede species (Eupolybothrus cavernicolus Komerički & Stoev, spn.). Gigascience, 1, e1013. http://dx.doi.org/10.5524/100063.
26. Goecks, J., Nekrutenko, A., Taylor, J. and the Galaxy Team. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86. doi: 10.1186/gb-2010-11-8-r86.
27. Luo, R., Liu, B., Xie, Y. et al. (2012) Software and supporting material for 'SOAPdenovo2: an empirically improved memory-efficient short read de novo assembly'. Gigascience Database, 1, 18. http://dx.doi.org/10.5524/100044.
28. Bedoya-Reina, O., Ratan, A., Burhans, R. et al. (2013) Galaxy tools to study genome diversity. Gigascience, 2, 17. http://dx.doi.org/10.1186/2047-217X-2-17.