Scott Edmunds: Data Dissemination: Difficulties, Data Citation, DOI's (and GigaSciece)
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Scott Edmunds: Data Dissemination: Difficulties, Data Citation, DOI's (and GigaSciece)

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Scott Edmunds talk at the first EMP meeting introducing BGI and BMC's new GigaScience journal.

Scott Edmunds talk at the first EMP meeting introducing BGI and BMC's new GigaScience journal.

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Scott Edmunds: Data Dissemination: Difficulties, Data Citation, DOI's (and GigaSciece) Scott Edmunds: Data Dissemination: Difficulties, Data Citation, DOI's (and GigaSciece) Presentation Transcript

  • Scott Edmunds
    Data Dissemination:
    Difficulties, Data Citation, DOIs and,
    (“Mo Data Mo Problems”)
  • The Ecoresponsive Genome of Daphnia pulexColbourne et al., Science4 February 2011:
    200Mb Genome, 30,907 genes
    Duplicated genes most responsive to ecological challenges
  • Daphnia Genome Consortium
    wFleabase: Mar 2006
    Genome release: July 2007
    Genome Published: Feb 2011
    >58 companion papers
    https://daphnia.cgb.indiana.edu/Publications
  • Difficulties
    Flickr cc: opensourceway
  • Sequencing cost($ per Mbp)
    Moore’s Law
    ~100,000X
    Sequencing
    Source: E Lander/Broad
  • Sequencing Output
    Data
    Storage
    Moore’s/Kryders Law
  • Sequencing Output
    Data
    Publication
    Dissemination?
  • Potential sequencing capacity
    1 IlluminaHiSeq 2000 (+Truseq upgrade)
    = 600Gb/run (12 days)
    X 128 Hiseq= 6Tb/day = >2Pb/year
    = ~ 2000 Human Genomes/day
  • SRA Closure
  • 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.”
    Nature461, 168-170 (2009)
  • Datacitation: Datacite and DOIs
    Digital Object Identifiers (DOIs) offer a solution
    • Mostly widely used identifier for scientific articles
    • Researchers, authors, publishers know how to use them
    • Put datasets on the same playing field as articles

    Dataset
    Yancheva et al (2007). Analyses on sediment of Lake Maar. PANGAEA.
    doi:10.1594/PANGAEA.587840
  • Datacitation: Datacite and DOIs
    >1 million DOIs since Dec 2009
    Central metadata repository to link with WoS/ISI
    - finally can track and credit use!
  • Coming soon…
    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
  • Criteria and Focus of Journal/Database
    • Reproducibility/Reuse
    • Utility/Usability
    • Standards/Searchability/Scale/Sharing
    • Data publishing/DOI
    www.gigasciencejournal.com
  • Use of Data = Importance + Usability
    easier to assess
    subjective?
    www.gigasciencejournal.com
  • 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
  • Standards/Searchability/Sharing
    • ISA-Tab compatibility to aid and promote best practice in metadata reporting.
    • Allsupporting data must be publically available.
    • Ask for MIBBI compliance and use of reporting checklists.
    • Part of the Biosharing network.
    www.gigasciencejournal.com
  • 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 findingand citing datasets, as well as for citation tracking.
    www.gigasciencejournal.com
  • 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. doi:10.5524/100001 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.
  • E. Coli #crowdsourcing: the first tweenome?
  • Questions?
    scott.edmunds@genomics.org.cn
    editorial@gigasciencejournal.com
    @gigascience
    www.gigasciencejournal.com