Scott Edmunds

*As part of the FAIRsharing Community Network (see [previous
blog](http://gigasciencejournal.com/blog/presenting-the-fairsharing-community-network/))
and [joint Force11 and Research Data Alliance (RDA) FAIRsharing Working
Group](https://www.force11.org/group/biosharingwg) we have been involved
in efforts to develop a shared, cross-publisher list of recommended data
deposition repositories. The first fruits of these are a
[preprint](https://osf.io/m2bce/) from the working group and
[DataCite](https://datacite.org/) (of which we are also members)
summarising what we feel should be the key criteria for selection. Being
a (FAIR) sharing and caring community we are now seeking wider feedback
on these, and the many publishers involved have published a guest post
here explaining this work on data repository selection and providing a
forum for wider community input.*

**FAIRsharing Needs You** 
![FAIRsharing feedback on Data Repository
Selection](http://gigasciencejournal.com/blog/wp-content/uploads/2019/11/Screenshot-2019-11-29-at-12.09.15-PM-300x300.png){.alignright
.wp-image-3123 .size-medium fetchpriority="high" decoding="async"
width="300" height="300"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2019/11/Screenshot-2019-11-29-at-12.09.15-PM-300x300.png 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/11/Screenshot-2019-11-29-at-12.09.15-PM-150x150.png 150w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/11/Screenshot-2019-11-29-at-12.09.15-PM-768x768.png 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/11/Screenshot-2019-11-29-at-12.09.15-PM-1024x1024.png 1024w, http://gigasciencejournal.com/blog/wp-content/uploads/2019/11/Screenshot-2019-11-29-at-12.09.15-PM.png 1618w"
sizes="(max-width: 300px) 100vw, 300px"}Publishers and journals are
developing data policies to ensure that datasets, as well as other
digital products associated with articles, are deposited and made
accessible via appropriate repositories, also in line with the [FAIR
Principles](https://doi.org/10.1038/sdata.2016.18).  With thousands of
options available, however, the lists of deposition repositories
recommended by publishers are
[often](https://datascience.codata.org/article/10.5334/dsj-2017-042/)
[different](https://fairsharing.org/recommendations/)  and consequently
the guidance provided to authors may vary from journal to journal (see
the [*GigaScience* Editorial Policies & Reporting Standards
page](https://academic.oup.com/gigascience/pages/editorial_policies_and_reporting_standards)
and [FAIRsharing recommendation
page](https://fairsharing.org/recommendation/GigaScience) collecting
these together for examples). This is due to a lack of common criteria
used to select the data repositories, but also to the fact that there is
still no consensus of what constitutes a good data repository.

To tackle this, [FAIRsharing](https://fairsharing.org/) and
[DataCite](https://datacite.org/) have joined forces with a group of
publisher representatives (see the list of participants listed below)
who are actively implementing data policies and recommending data
repositories to researchers. The result of our work is a set of proposed
criteria that journals and publishers believe are important for the
identification and selection of data repositories, which can be
recommended to researchers when they are preparing to publish the data
underlying their findings.

Our work intends to

- reduce complexity for researchers when preparing their submissions to
 journals,
- increase efficiency for data repositories that currently have to work
 with all individual publishers, and
- simplify the process of recommending data repositories for publishers.

Our work will make the implementation of research data policies more
efficient and consistent, which may help to improve approaches to data
sharing by promoting the use of reliable data repositories.

Although we recognize that researchers and other stakeholders play a
role in the research data life cycle, in this first instance the target
audience for our work are other journals and publishers, repository
developers and maintainers, certification and other evaluation
initiatives, and other policy makers.

This ***proposed criteria*** are intended to:

- *guide* journals and publishers in providing authors with consistent
 recommendations and guidance on data deposition, and improve authors'
 data sharing practices;
- *reduce potential for confusion of researchers and support staff, and
 reduce duplication of effort by different publishers and data
 repositories*
- *inform* data repository developers and managers of the features
 believed to be important by journals and publishers;
- *apprise* certification and other evaluation initiatives, serving as a
 reference and perspective from journals and publishers;
- *drive* the curation of the description of the data repository in
 [FAIRsharing](https://fairsharing.org/), which will enable display,
 filter and search based on these criteria.

We invite you to [**read the pre-print article**](https://osf.io/m2bce/)
that describes the work, its motivation, relations to other initiatives,
and **provide us with feedback** via [this
form](https://tinyurl.com/RepoCriteriaFeedback).

**FAIRsharing Registry: connecting data policies, standards & databases
Working Group:** 
Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra
(FAIRsharing) Helena Cousijn2 (DataCite), Matthew Cannon, Nicholas
Everitt (Taylor & Francis), Wei Mun Chan (eLife), Ilaria Carnevale,
Marina Soares E Silva (Elsevier), Imogen Cranston, Hollydawn Murray,
Jonathan Threlfall (F1000), Scott Edmunds (*GigaScience*), Emma Ganley,
Iain Hrynaszkiewicz (PLOS), Chris Graf, Kathryn Sharples (Wiley), Varsha
K. Khodiyar (Springer Nature), Thomas Lemberger (EMBO Press), Catriona
J. MacCallum (Hindawi), Kiera McNeice (Cambridge University Press)

::: {.col-md-8}
::: {.blog-post}
**Further Reading 
**Sansone SA et al., Data Repository Selection: Criteria That Matter,
v2. *OSF Preprints* (2019) <https://osf.io/m2bce/>

Sansone SA et al., FAIRsharing, a cohesive community approach to the
growth in standards, repositories and policies. *Nature Biotechnology*
**37**, p358--367 (2019)
doi:[10.1038/s41587-019-0080-8](https://doi.org/10.1038/s41587-019-0080-8)
:::
:::

The post [FAIRsharing Guestpost: What Criteria Matters with Data
Repository
Selection?](http://gigasciencejournal.com/blog/fairsharing-data-repository-selection/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.

As part of the FAIRsharing Community Network (see previous blog) and joint Force11 and Research Data Alliance (RDA) FAIRsharing Working Group we have been involved in efforts to develop a shared, cross-publisher list of recommended data deposition repositories. The first fruits of these are a preprint from the working group and DataCite (of which we are also members) summarising what we feel should be the key criteria for selection.

FAIRsharing Guestpost: What Criteria Matters with Data Repository Selection?

**Policies and Standards for Reproducible Research: from theory to
practice**

This month
[*GigaScience*](http://www.gigasciencejournal.com "GigaScience homepage"){target="_blank"
rel="noopener"} co-hosted a
[session](http://gensc.org/gc_wiki/index.php/GSC_13#15:30-17:30_Policies_and_Standards_for_Reproducible_Research:_from_Theory_to_Practice "GSC reproducible research program"){target="_blank"
rel="noopener"} at the [Genomic Standards Consortium
meeting](http://gensc.org/gc_wiki/index.php/GSC_13 "GSC13 wiki"){target="_blank"
rel="noopener"} in Shenzhen on "Policies and Standards for Reproducible
Research: from theory to practice. The session brought together a
diverse group of speakers with different roles in the production,
dissemination and use of data, to discuss all of the issues surrounding
the role of policies and standards enabling reproducible research and
data sharing. Co-chaired by our Editorial Board member [Susanna-Assunta
Sansone](http://www.oerc.ox.ac.uk/people/susanna-assunta-sansone "Susanna Sansone homepage"){target="_blank"
rel="noopener"}, a diverse panel was assembled representing the
different stakeholders involved in the data-production cycle, including
those able enforce data policies such as research funders and journal
editors, users and managers of databases, data producers, and
facilitators of all of these processes.

Susanna opened proceedings and set the scene with an overview of
[BioSharing](http://www.biosharing.org/ "Biosharing homepage"){target="_blank"
rel="noopener"}, of which *BioMed Central* and *GigaScience* are both
[members](http://blogs.biomedcentral.com/bmcblog/2012/03/bmc_research_notes_and_biosharing "BMC and Biosharing"){target="_blank"
rel="noopener"} (slides
[here](http://www.slideshare.net/GigaScience/susannaassunta-sansone-an-overview-of-the-evolving-portfolio-of-data-sharing-enablers-biosharing "Susanna Slides"){target="_blank"
rel="noopener"}). Giving an overview of the evolving portfolio of data
sharing enablers, this was very relevant forum as BioSharing aims to
strengthen collaborations between exactly the groups present in this
session, and to discourage redundant (accidental) competition between
standards-generating groups![Scott Edmunds at
GSC13](http://gigasciencejournal.com/blog/wp-content/uploads/2012/03/6832666364_f0183f1515_c-300x200.jpg){.alignright
.size-medium .wp-image-5441 decoding="async" width="300" height="200"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2012/03/6832666364_f0183f1515_c-300x200.jpg 300w, http://gigasciencejournal.com/blog/wp-content/uploads/2012/03/6832666364_f0183f1515_c-768x512.jpg 768w, http://gigasciencejournal.com/blog/wp-content/uploads/2012/03/6832666364_f0183f1515_c.jpg 799w"
sizes="(max-width: 300px) 100vw, 300px"}

The second scene-setting talk was from our editor Scott Edmunds,
covering the issues and additional incentives needed to enable and
encourage data dissemination (see the
[slides](http://www.slideshare.net/GigaScience/scott-edmunds-revolutionizing-data-dissemination-gigascience "Scott Edmunds GigaScience slides"){target="_blank"
rel="noopener"} below and video
[here](http://youtu.be/J4c2p3vSQkc "Scott GgaScience GSC talk"){target="_blank"
rel="noopener"}). Covering work that *GigaScience* and the BGI has done
to release datasets with citable DOIs, the utility of releasing genomes
pre-publication was nicely shown by the resulting
[crowd-sourcing](http://www.nejm.org/doi/full/10.1056/NEJMoa1107643? "NEJM homepage"){target="_blank"
rel="noopener"} of the the deadly 2011 *E. coli* O104:H4 outbreak genome
sequenced by the BGI (and partners in Hamburg and Birmingham) and
[released by
us](http://blogs.biomedcentral.com/gigablog/2012/03/notes_from_an_e_coli "Notes from a tweenome"){target="_blank"
rel="noopener"} in this manner. A further recent development relating to
this is a [new
study](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033637 "PLoS One E. coli bactericide"){target="_blank"
rel="noopener"} in *PLoS One* that used draft unassembled genome
sequence data to directly develop a targeted bactericidal agent to kill
O104-positive *E. coli*. To enable data-citation to be a recognized form
of credit and viable incentive to  encourage faster data dissemination
in this manner, journals need to allow data to be cited in the
references in the same way as articles. Scott then presented many of the
[recent](http://blogs.biomedcentral.com/gigablog/2012/03/data_citation_enters_the_year "Data Citation December"){target="_blank"
rel="noopener"}
[examples](http://blogs.biomedcentral.com/gigablog/2012/03/data_supporting_rna_editing_study "Transcriptome DOIs in Nature Biotech"){target="_blank"
rel="noopener"} highlighted in [this
blog](http://blogs.biomedcentral.com/gigablog// "GigaBlog"){target="_blank"
rel="noopener"} of journals including *Genome Biology* and *Nature
Biotechnology* (both represented at this meeting) now carrying this out

Being key gatekeepers able to enforce and influence data policies and
standards the perspective of funders was then covered, with Paula
Olsiewski representing the [Alfred P Sloan
Foundation](http://www.sloan.org/ "Sloan Foundation homepage"){target="_blank"
rel="noopener"}, and [Professor Rita
Colwell](http://en.wikipedia.org/wiki/Rita_R._Colwell "Rita Colwell"){target="_blank"
rel="noopener"} providing her wealth of experience as former director of
the NSF, and highlighting the elephants in the room that needed solving.
A group of talks then covered "Breaching the Bio-Domain, providing a
more hands-on point of view from data-producers, curators and database
managers. [Philippe
Rocca-Serra](http://www.oerc.ox.ac.uk/people/philippe-rocca-serra "Philippe Rocca-Serra"){target="_blank"
rel="noopener"} brought a 'data commoning'  perspective and presented on
the
[ISA-Commons](http://www.isacommons.org/ "ISA-commons page"){target="_blank"
rel="noopener"} system, of which we have recently
[collaborated](http://blogs.biomedcentral.com/gigablog/2012/03/gigascience_journal_part_of_global "GigaScience and ISA-Tab"){target="_blank"
rel="noopener"} on a
[publication](http://www.nature.com/ng/journal/v44/n2/full/ng.1054.html "ISA-commons commentary"){target="_blank"
rel="noopener"}. [Folker
Meyer](http://www.mcs.anl.gov/%7Efolker/ "Folker Meyer"){target="_blank"
rel="noopener"} talked of his experience running 
[MG-RAST](http://metagenomics.anl.gov/ "MG-RAST"){target="_blank"
rel="noopener"}, highlighting that of the 41,000 datasets in the
database only a minority were publicly accessible, and appealing for
funders to insist more on this.  Srikrishna Submanian (Institute of
Microbial Technology, India) gave a similarly open-data talk giving
examples and a structural genomics perspective for data  sharing (for an
example see [TOPSAN](http://www.topsan.org/ "TOPSAN"){target="_blank"
rel="noopener"}). Yong Zhang gave a final "data-producer" and BGI
perspective outlining the scale of the challenges ahead, and giving a 
preview of some of the work underway to build biobanks and datacenters
that hope to become the China National Genebank.

The session ended with final perspectives from journal editors, with
*[Genome
Biology](http://genomebiology.com/ "Genome Biology"){target="_blank"
rel="noopener"}* editor Clare Garvey and Craig Mak from *Nature
Biotechnology* giving  overviews of their journal policies and examples
of both of their publishers schemes encouraging aiding data sharing and
standardization.

On top of this session, the meeting was well attended and covered on
twitter and
[google+](https://plus.google.com/u/0/s/%23gsc13 "#gsc13 on g+"){target="_blank"
rel="noopener"} (a first for us), and for a genomics-focussed meeting
participants were remarkably restrained in dropping any "[genomics
bingo](https://docs.google.com/spreadsheet/ccc?key=0AkNPpmDaw5GhdFUyRFJ5TDd2b2l6Wlg3TnJKTl9ySGc#gid=0 "Genomics Bingo"){target="_blank"
rel="noopener"}" buzzwords. The organizers hope to be posting slides on
the conference
[wiki](http://gensc.org/gc_wiki/index.php/GSC_13 "GSC13 wiki"){target="_blank"
rel="noopener"}, and we have also archived some (such as the [opening
address](http://www.slideshare.net/GigaScience/dawn-field "Dawn Field slides"){target="_blank"
rel="noopener"} from GSC president Dawn Field) on our
[slideshare](http://www.slideshare.net/gigascience "GigaScience on Slideshare"){target="_blank"
rel="noopener"} account. There is further
[coverage](http://en.genomics.cn/navigation/show_news.action?newsContent.id=8996 "GSC BGI write-up"){target="_blank"
rel="noopener"} on the BGI news page, pictures on their
[Flickr](http://www.flickr.com/photos/bgievent/sets/72157629580987267/ "GSC13 Flickr"){target="_blank"
rel="noopener"} page, and videos are currently being posted on the [BGI
Youtube](http://www.youtube.com/user/BGIshenzhen "BGI youtube channel"){target="_blank"
rel="noopener"} and [GSC
Scivee](http://www.scivee.tv/node/46384 "GSC13 Scivee"){target="_blank"
rel="noopener"} pages.

**GSC13 special series: call for papers highlighting best practice in
genomics research**

As mentioned in a [previous
posting](http://blogs.biomedcentral.com/gigablog/2012/03/gigascience_at_the_genomic_standards "GigaScience special series"){target="_blank"
rel="noopener"}, to tie in with the meeting we are launching a call for
submissions to a thematic series of discussion and research
[](../../gigablog/entry/gigascience_at_the_genomic_standards#_msocom_1){#_anchor_1
.msocomanchor}from the conference and wider community highlighting best
practice in genomics research, and we are currently reviewing a number
of candidate submissions. BGI is  generously
[covering](../../gigablog/entry/papers_papers_papers "papers, papers, papers"){target="_blank"
rel="noopener"} the open-access [article-processing
charges](http://www.biomedcentral.com/about/apcfaq "APC FAQ"){target="_blank"
rel="noopener"} for the journal's first year, so please contact us at
<editorial@gigasciencejournal.com> if you have related work you would
like to submit to this series or journal, or submit a manuscript
[here](http://www.gigasciencejournal.com/manuscript "submission system"){target="_blank"
rel="noopener"}.

**References** 
[1](http://www.nejm.org/doi/full/10.1056/NEJMoa1107643? "NEJM homepage"){target="_blank"
rel="noopener"}. Rohde, H. *et al.* Open-source genomic analysis of
Shiga-toxin-producing *E. coli* O104:H4. ***N Engl J Med.***
**365**(8):718-24. (2011)

[2](http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0033637 "PLoS One E. coli bactericide"){target="_blank"
rel="noopener"}.  Scholl, D. *et al.*  Genome Sequence of *E. coli*
O104:H4 Leads to Rapid Development of a Targeted Antimicrobial Agent
against This Emerging Pathogen. ***PLoS ONE*** 7(3): e33637. (2012)

[3](http://www.nature.com/ng/journal/v44/n2/full/ng.1054.html "ISA-commons commentary"){target="_blank"
rel="noopener"}. Sansone, S-A. *et al*. Toward interoperable bioscience
data. ***Nature Genetics*** **44**, 2 (2012).

**[Scott Edmunds: Revolutionizing Data Dissemination: GigaScience
Slides](http://www.slideshare.net/GigaScience/scott-edmunds-revolutionizing-data-dissemination-gigascience "Scott Edmunds: Revolutionizing Data Dissemination: GigaScience"){target="_blank"
rel="noopener"}** 
View more
[PowerPoint](http://www.slideshare.net/thecroaker/death-by-powerpoint){target="_blank"
rel="noopener"} from [GigaScience, BGI
Shenzhen](http://www.slideshare.net/GigaScience){target="_blank"
rel="noopener"}

The post [Genomic Standards Community Go Shenzhen: GigaScience session
overview from
\#GSC13](http://gigasciencejournal.com/blog/genomic-standards-community-go-shenzhen-gigascience-session-overview-from-gsc13/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.

Policies and Standards for Reproducible Research: from theory to practice

This month

 GigaScience

co-hosted a session at the Genomic Standards Consortium meeting in Shenzhen on “Policies and Standards for Reproducible Research: from theory to practice.

Publicaciones de Rogue Scholar

FAIRsharing Guestpost: What Criteria Matters with Data Repository Selection?

Genomic Standards Community Go Shenzhen: GigaScience session overview from #GSC13