Scott Edmunds: GigaScience - Big-Data, Data Citation and Future Data Handling
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This document discusses the challenges of handling large-scale genomic and biological data and proposes potential solutions. It notes that data volumes are increasing rapidly due to advances in sequencing technology but dissemination and data handling methods have not kept pace. Several hurdles to data sharing are described including technical issues around data size, heterogeneity and longevity as well as economic and cultural barriers. Potential solutions discussed include providing incentives for data sharing through attribution and citation, adopting data citation practices using Digital Object Identifiers, establishing funding models for long-term curation, and launching new databases and journals focused on publishing and analyzing large-scale datasets.
Scott Edmunds: GigaScience - Big-Data, Data Citation and Future Data Handling
- 1. Scott Edmunds : Big Data, Data Citation and Future Data Handling William Gibson: "Information is the currency of the future world" www.gigasciencejournal.com cc Flickr allan*
- 2. Data Tsunami? Flickr cc: opensourceway
- 4. Rice v Wheat: consequences of publically available genome data. rice wheat 700 600 500 400 300 200 100 0
- 5. Sharing aids everyone… Sharing Detailed Research Data Is Associated with Increased Citation Rate. Piwowar HA, Day RS, Fridsma DB (2007) PLoS ONE 2(3): e308. doi:10.1371/journal.pone.0000308 Every 10 datasets collected contributes to at least 4 papers in the following 3-years. Piwowar, HA, Vision, TJ, & Whitlock, MC (2011). Data archiving is a good investment Nature, 473 (7347), 285-285 DOI: 10.1038/473285a
- 8. Problems? Flickr cc: opensourceway
- 9. Sequencing cost ($ per Mbp) Moore’s Law ~100,000X Sequencing Source: E Lander/Broad
- 10. Sequencing Output Data Moore’s/Kryder s Law
- 11. Sequencing Output Data Dissemination?
- 12. Potential sequencing capacity 1 Illumina HiSeq 2000 (+Truseq upgrade) = 600Gb/run (12 days) X 128 Hiseq = 6Tb/day = >2Pb/year = ~ 2000 Human Genomes/day
- 13. Difficulties keeping up… Flickr cc: opensourceway
- 14. Do we have models for long term funding? Human Gene Mutation Database Kyoto Encyclopedia of Genes and Genomes ? Flickr cc: opensourceway
- 15. Are there now too many hurdles? ?
- 16. Are there now too many hurdles? Technical: too large volumes too heterogeneous no home for many data types too time consuming Economic: too expensive, no long-term funding Cultural: inertia ? no incentives to share unaware of how
- 18. Incentives/credit Credit where credit is overdue: “One option would be to provide researchers who release data to public repositories with a means of accreditation.” “An ability to search the literature for all online papers that used a particular data set would enable appropriate attribution for those who share. “ Nature Biotechnology 27, 579 (2009) Prepublication data sharing (Toronto International Data Release Workshop) “Data producers benefit from creating a citable reference, as it can later be used to reflect impact of the data sets.” Nature 461, 168-170 (2009)
- 19. Datacitation: Datacite and DOIs Digital Object Identifiers (DOIs) offer a solution Mostly widely used identifier for Dataset scientific articles Yancheva et al (2007). Analyses on Researchers, authors, publishers sediment of Lake Maar. PANGAEA. know how to use them doi:10.1594/PANGAEA.587840 Put datasets on the same playing field as articles
- 20. Datacitation: Datacite and DOIs >1 million DOIs since Dec 2009 Central metadata repository to link with WoS/ISI - finally can track and credit use!
- 21. Now taking submissions… Large-Scale Data Journal/Database In conjunction with: Editor-in-Chief: Laurie Goodman, PhD Editor: Scott Edmunds, PhD Assistant Editor: Alexandra Basford, PhD www.gigasciencejournal.com
- 23. Editorial Board: International Stephan Beck, UK Stephen O'Brien, USA Alvis Brazma, UK Hanchuan Peng, USA Ann-Shyn Chiang, Taiwan Russell Poldrack, USA Richard Durbin, UK Ming Qi, China/USA Paul Flicek, UK Susanna-Assunta Sansone, UK Robert Hanner, Canada Michael Schatz, USA Yoshihide Hayashizaki, Japan David Schwartz, USA Henning Hermjakob, UK Fritz Sommer, USA Wolfgang Huber, Germany Lincoln Stein, Canada Gary King, USA Sumio Sugano, Japan Tin-Lap Lee, Hong Kong Thomas Wachtler, Germany Donald Moerman, Canada Jun Wang, China Karen Nelson, USA Alistair Young, New Zealand Francis Ouellette, Canada Zang Yufeng, China Marie Zins, France www.gigasciencejournal.com
- 24. Editorial Board: International Stephan Beck, Epigenomics Stephen O'Brien, Genomics Alvis Brazma, Transcriptomics Hanchuan Peng, Imaging/Neuro Ann-Shyn Chiang, Neuroscience Russell Poldrack, Neuroscience Richard Durbin, Genetics/Genomics Ming Qi, Genetics Paul Flicek, Genomics Susanna-Assunta Sansone, Standards Robert Hanner, DNA Barcoding/Ecology Michael Schatz, Cloud Computing Yoshihide Hayashizaki, Genomics David Schwartz, Optical Mapping Henning Hermjakob, Proteomics Fritz Sommer, Neuroscience Wolfgang Huber, Functional Genomics Lincoln Stein, Cloud Computing Gary King, Medicine Sumio Sugano, Genomics Tin-Lap Lee, Genomics Thomas Wachtler, Neuroscience Donald Moerman, Functional Genomics Jun Wang, Genomics Karen Nelson, Metagenomics Alistair Young, Medical Imaging Francis Ouellette, Genomics Zang Yufeng, Neuroscience Marie Zins, Medicine www.gigasciencejournal.com
- 25. Criteria and Focus of Journal/Database Reproducibility/Reuse Utility/Usability Standards/Searchability/Scale/Sharing Data publishing/DOI www.gigasciencejournal.com
- 26. Use of Data = Importance + Usability subjective? easier to assess www.gigasciencejournal.com
- 27. Reproducibility/Reuse BGI Cloud Computing resources for handling and analyzing large-scale data. Integrated tools to promote more widespread access, viewing, and analysis of data. Encourage and aid use of workflow systems for methods (e.g. submission of Galaxy XML files). www.gigasciencejournal.com
- 28. Special Series/Hub for cloud-based tools Technical notes: test tools in the BGI-Cloud. Tools + Test Data (BGI or user) in one place. Aids reproducibility. Aids reviewers (free) Aids authors: visibility (pubmed, etc.) hosting (included/free offers) –contact us: editorial@gigasciencejournal.com Oledoe flickr cc www.gigasciencejournal.com
- 29. Standards/Searchability/Sharing ISA-Tab compatibility to aid and promote best practice in metadata reporting. All supporting data must be publically available. Ask for MIBBI compliance and use of reporting checklists. Part of the Biosharing network. www.gigasciencejournal.com
- 30. Data publishing/DOI New journal format combines standard manuscript publication with an extensive database to host all associated data. Data hosting will follow standard funding agency and community guidelines. DOI assignment available for submitted data to allow ease of finding and citing datasets, as well as for citation tracking. www.gigasciencejournal.com
- 32. The era of the data consumer?
- 33. The era of the data consumer? ?
- 34. The era of the data consumer? Free access to data – but analysis hubs/nodes for will form around it ?
- 35. GDSAP:Genomic Data Submission and Analytical platform Big data from the Data, Data, Data… “Sequencing Farm” Data Modeling Tin-Lap Lee, CUHK Pipeline design Validation Commercial applications “Apps”
- 38. BGI Datasets Get DOI®s Invertebrate PLANTS Ant Vertebrates Chinese cabbage - Florida carpenter ant Giant panda Macaque Cucumber - Jerdon’s jumping ant - Chinese rhesus Foxtail millet - Leaf-cutter ant - Crab-eating Pigeonpea Roundworm Naked mole rat Potato Silkworm Penguin Sorghum - Emperor penguin Human - Adelie penguin Asian individual (YH) Pigeon, domestic - DNA Methylome Polar bear - Genome Assembly Sheep doi:10.5524/100004 - Transcriptome Tibetan antelope Ancient DNA (coming soon) - Saqqaq Eskimo Microbe - Aboriginal Australian E. Coli O104:H4 TY-2482 Cell-Line Chinese Hamster Ovary
- 39. BGI Datasets Get DOI®s Many unpublished… Invertebrate PLANTS Ant Vertebrates Chinese cabbage - Florida carpenter ant Giant panda Macaque Cucumber - Jerdon’s jumping ant - Chinese rhesus Foxtail millet - Leaf-cutter ant - Crab-eating Pigeonpea Roundworm Naked mole rat Potato Silkworm Penguin Sorghum - Emperor penguin Human - Adelie penguin Asian individual (YH) Pigeon, domestic - DNA Methylome Polar bear - Genome Assembly Sheep doi:10.5524/100004 - Transcriptome Tibetan antelope Ancient DNA (coming soon) - Saqqaq Eskimo Microbe - Aboriginal Australian E. Coli O104:H4 TY-2482 Cell-Line Chinese Hamster Ovary
- 41. Data also submitted to NCBI (including SV data to dbVar) Complemented by citable form, and data-types including: Assemblies of 3 strains Raw Data SNPs InDels CNVs SV
- 42. Our first DOI: To maximize its utility to the research community and aid those fighting the current epidemic, genomic data is released here into the public domain under a CC0 license. Until the publication of research papers on the assembly and whole- genome analysis of this isolate we would ask you to cite this dataset as: Li, D; Xi, F; Zhao, M; Liang, Y; Chen, W; Cao, S; Xu, R; Wang, G; Wang, J; Zhang, Z; Li, Y; Cui, Y; Chang, C; Cui, C; Luo, Y; Qin, J; Li, S; Li, J; Peng, Y; Pu, F; Sun, Y; Chen,Y; Zong, Y; Ma, X; Yang, X; Cen, Z; Zhao, X; Chen, F; Yin, X; Song,Y ; Rohde, H; Li, Y; Wang, J; Wang, J and the Escherichia coli O104:H4 TY-2482 isolate genome sequencing consortium (2011) Genomic data from Escherichia coli O104:H4 isolate TY-2482. BGI Shenzhen. http://dx.doi.org/10.5524/100001 To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to Genomic Data from the 2011 E. coli outbreak. This work is published from: China.
- 45. “The way that the genetic data of the 2011 E. coli strain were disseminated globally suggests a more effective approach for tackling public health problems. Both groups put their sequencing data on the Internet, so scientists the world over could immediately begin their own analysis of the bug's makeup. BGI scientists also are using Twitter to communicate their latest findings.” “German scientists and their colleagues at the Beijing Genomics Institute in China have been working on uncovering secrets of the outbreak. BGI scientists revised their draft genetic sequence of the E. coli strain and have been sharing their data with dozens of scientists around the world as a way to "crowdsource" this data. By publishing their data publicy and freely, these other scientists can have a look at the genetic structure, and try to sort it out for themselves.”
- 47. We want your data! scott@gigasciencejournal.com editorial@gigasciencejournal.com @gigascience facebook.com/GigaScience blogs.openaccesscentral.com/blogs/gigablog/ www.gigasciencejournal.com