BioSharing Registry: connecting data policies, standards & databases in life sciences WG

WG

Group details

Chair(s): 
Susanna-Assunta Sansone, Rebecca Lawrence, Simon Hodson & Peter McQuilton
Secretariat Liaison: 
Lynn Yarmey
TAB Liaison: 
Paul Uhlir
Case Statement: 
 

The products of this WG will be principles for linking information about databases, content standards and journal and funder policies in the life sciences, and a curated and prototype registry, to access and cross-search the information, on which a variety of stakeholders can base their decisions. Specifically, journals, researchers and funders will be able to recommend or select mature and community endorsed databases and standards, and developers and curators of repositories and content standards will be aware of the requirements they need to meet to ensure their products are discoverable and well described so that they can be used by researchers or recommended by journals and funders.
 

To ensure a manageable project size and delivery within the 18-month timeframe, the WG will leverage the existing BioSharing initiative, already embedded into international infrastructure programmes.The principles and the registry, however, will be developed in a way that is extendable to other areas of science. This use cases-driven WG is a joint effort with Force11 and it is led and constituted by prospective adopters as well as technical implementers, many of whom are also leading and/or actively involved in other relevant RDA IGs and WGs, whose activities this WG complements and with which this WG will work closely. For more details, please refer to our Case Statement, found in the right-hand column.

 


Through the BioSharing WG’s 18 month timeframe, we have built upon the existing BioSharing registry and transformed it into a searchable network of 800+ databases, 650+ data standards, and 80+ journal and funder data policies in the life, biomedical and environmental science domains.

During this time, the BioSharing portal has been adopted by a number of journal publishers, research data management programmes, community groups and infrastructure, research and funding programmes. These are shown in the table below.

 

Please note: We are gaining new adopters all the time. To see the most up-to-date version of this table, please see our communities page.

 

Adopter Type Associated BioSharing Record
Biotechnology and Biological Sciences Research Council (BBSRC) Funder Data Policy  
BioMedCentral (BMC) Journal Data Policy Recommendation
EMBO Press Journal Data Policy Recommendation
Faculty of 1000 (F1000) Journal Data Policy Recommendation
GigaScience Journal Data Policy Recommendation
Scientific Data Journal Data Policy Recommendation
Springer Nature Journal Data Policy -
Wellcome Open Research Journal Data Policy Recommendation
ELIXIR Europe$ Infrastructure -
ELIXIR UK Infrastructure -
JISC UK Infrastructure -
Cell Migration Standardisation Organisation (CMSO) Organisation Collection
Taxonomic Databases Working Group (TDWG)* Organisation Collection
EMBL-Australia Bioinformatics Resource Organisation Collection
Clinical Data Interchange Standards Consortium (CDISC) Organisation Collection
FAIRDOM Project Collection
Euro-BioImaging$ Project Collection
University of Cambridge Research Data Management -
University of Oxford Research Data Management -
Stanford University Research Data Management -

 

* TDWG RDA Working Group

$ Part of RDA GEDE Coordination Group

Want to join our list of adopters? Contact us here.

 

We have helped these journal publishers develop their data policies, and have mirrored these on BioSharing with our ‘recommendations’ feature, collating all the BioSharing records mentioned in their data policy into one place, and importantly, linking them with other data in BioSharing, so showing those resources in context. For example, a journal may recommend the deposition of your proteomics data in a particular database, but what standards does that database use? This information is not available on the journal’s data policy page, but is available through BioSharing.

 

BioSharing is also embedded in and contributes to a number of infrastructure programmes, such as the EMBL-ABR (https://biosharing.org/collection/EMBLABR), curating and showcasing Bioinformatics resources in Australia, funding programmes such as the NIH LINCS program (https://biosharing.org/collection/LINCS), and research programmes such as the GEDE Euro-BioImaging initiative (https://biosharing.org/collection/EuroBioImaging). In addition, BioSharing is an ELIXIR-UK Node resource (http://www.elixir-uk.org/resources/biosharing) and actively participates in ELIXIR, the pan-European bioinformatics life science infrastructure, as the ELIXIR Standards registry.

 

BioSharing has always been a community-driven project and this is illustrated by the large number of community groups and projects that we work with, such as the TDWG Biodiversity standards group (which also has a RDA WG - https://www.rd-alliance.org/groups/metadata-standards-attribution-physic...), FAIRDOM, CDISC, and others. See https://biosharing.org/collections/ for a full list of our collections and recommendations.

 

Working with our community, we are now drafting the outputs of this WG for consideration at the RDA 9th Plenary in Barcelona. We look forward to see as many of you as possible there!

 

 

In the meantime, please contact us via this WG, the BioSharing website or biosharing-contact-us@lists.sf.net if you would like to join our growing list of adopters and/or have a collection or recommendation in BioSharing for your project.

 

 

 

Key outputs (August 2016):

 

BioSharing is now an:

 

1. Informative resource

A web-based, searchable portal of 3 interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards (https://biosharing.org/standards), databases (https://biosharing.org/databases) and data policies (https://biosharing.org/policies), also combined in an integrated view across all 3 registries (https://biosharing.org/search)

Every standard and database record is annotated with a tag indicating the readiness of that resource for implementation or use (status checked with the community). Currently we have 4 indicators, that can be found in the top left of each record card (Grid view) or in the column on the right (Table view): R - ready; Dev - in development; U - status uncertain; D - deprecated. These tags also assist the Educational side, below.

 

 

2. Educational resource

 

 

From the homepage user can access the:

- Educational section. A collection of over 40 frequently asked questions that cover the whats and whys of standards, how BioSharing can help users navigate standards, databases and data policies in the life sciences, and how to use and cite BioSharing: https://biosharing.org/educational

- Recommendations. Standards and/or databases recommended by journal or funder data policy, e.g. PLOS: https://biosharing.org/recommendation/PLOS

- Collections. Standards and/or databases grouped by domain, species or organization, e.g. see the Biodiversity Standards, a group linked to the RDA IG: https://biosharing.org/collection/TDWGBiodiversity


<

Upcoming events:

RDA 9th Plenary (5-7th April) Barcelona (ES) - participation in two sessions:

Joint session with the ELIXIR Bridging Force IG - What's happened in the Life Sciences? - see here for more information.

Joint session with the Data policy standardisation and implementation IG - using the life and biomedical sciences as a domain-specific example - see here for more information.


2016 Events we have attended and presented at

NETTAB/CHARME workshop (Oct 25-26, 2016) Rome (IT) - Reproducibility, standards and SOP in bioinformatics - slides here

ECCB (Sept 6, 2016) The Hague (NL) ELIXIR talk 11 - The BioSharing registry: mapping the landscape of standards and database resources in the life sciences - slides here

CHARME workshop - (June 22, 2016) Warsaw (PL) - a presentation on BioSharing at the kick-off COST-CHARME workshop on Standards - slides here

ISB2016 Conference - Geneva (CH) where we presented a poster on the BioSharing database registry (Tuesday 12th April) and ran a workshop on BioSharing, community curation and the BioDBcore guidelines (Wednesday 13th April)

UKON2016 Conference - Newcastle (UK) for a short talk on BioSharing on Thursday 14th April

FORCE2016 Conference - Portland (OR) at the Propelled by FORCE session on Tuesday April 19th at 10am


Activities at RDA Plenary 8 and IDW

We co-organized and presented at the following sessions:


Activities pre-plenary 8

1. Pre-defined Recommendations: A core-set of resources (databases and/or standards) that have been selected and recommended by relevant groups or organizations. 

2. Wizard Tool (beta): The wizard guides users step-by-step through the resources captured in BioSharing. 

3. BioSharing Standards Registry Survey: We have just closed our BioSharing Standards Registry survey, where we have assessed your needs for a registry of data/content standards in the life, environmental and biomedical sciences. We have had over 530 responses. We're now analysing the survey and will shortly publicize an executive summary of the results, along with the raw data.


Activities at Plenary 7

Where can you find us

Activities pre-plenary 7

To prioritize BioSharing registry's content and capabilities, in a way most appropriate to your needs, we have run a 10 questions survey and received 530 replies!

Here you can see a 3 slides update on our progresses to date.


Activities at RDA Plenary 6

Presentations

Thank-you for your feedback at the 6th Plenary meeting in Paris. It was great to catch up with everyone and to hear about the innovative and challenging work everyone is doing. If you didn’t manage to catch us at the meeting, our slides and our leaflet are available on Slideshare, as follows:

Where can you find us

Activities pre-RDA plenary 6 

Help us prioritize improvements to BioSharing's capabilities as a Standards Information Resource, in a way most appropriate to your needs. ​Take a few minutes to answer few questions, please!


Activities at RDA Plenary 5


Activities at RDA Plenary 4


Activities at RDA Plenary 3

Recent Activity

04 Nov 2016

Interoperability standards - review for the Wellcome Trust

Dear BioSharing WGs members,
given the relevance of the topic, I would like to flag a review we have
done for the Wellcome Trust
*"Interoperability Standards - Digital Objects in Their Own
Right"***https://dx.doi.org/10.6084/m9.figshare.4055496.v1
part of a set of reports just released on related topics:
https://wellcome.ac.uk/what-we-do/our-work/open-research#what-we’re-doing
Susanna
--
--

13 Sep 2016

See you in Denver!

Dear BioSharing WG members,
We have just over 6 months left for this working group to run. With this
in mind, we're presenting the many outputs of this working group in a
number of sessions in the upcoming 8th RDA plenary in Denver, CO.
Here is a full list of the sessions in which we'll be presenting:
Thursday 15th September:
- Session 2 - 2-3:30pm - The data diversity problem in biomedicine,
a joint session among IG Elixir Bridging Force, WG Biosharing,WG Data
Type Registries,WG Metadata Standards Catalog

06 Sep 2016

Demo you Software at RDA: Better Description/ Retrieval of Online Scientific Data

Dear Colleagues,
there is an *opportunity to showcase your software* (prototype pr
mature) to:
- enhance the authoring of comprehensive metadata using
community-endorsed standards
- to ensure the annotation of data with terms from standard ontologies
and terminologies, and
- to aid the identification and retrieval of relevant datasets for
exploration and re-analysis.
*BOF: Software for Better Description and Retrieval of Online
Scientific Data*

12 Aug 2016

August update: Outputs and presentations

Dear RDA BioSharing WG members,
Hope you're all well.
Here's a short update detailing our progress over the last few months
and highlighting where we'll be presenting BioSharing over the coming
months.
Thanks,
Pete
*************************
*FEATURES*
*1. BioSharing Educational - /New/
*
A collection of over _40 frequently asked questions_ that cover the
whats and whys of standards, how BioSharing can help users navigate
standards, databases and data policies in the life sciences, and how to

11 Apr 2016

April Update: Recommendations and a wizard

Dear BioSharing WG members,
Hope you're all well.
This email is a short update on both the technical and content progress
we've made over the last few weeks.
*1. AskBioSharing ***https://biosharing.org/askbiosharing
**Provides improved functionality that leverages our existing and
continually curated records. This helps users to _*navigate*_ our
growing content, _*find*_ what they need and _*learn*_ about the
landscape of standards and databases in the life sciences. AskBioSharing

07 Mar 2016

Update Mar 2016 - New homepage and more...

Dear RDA BioSharing WG members,
Hope you are all well and that those of you lucky enough to be at the
RDA 7 Plenary in Tokyo managed to catch Susanna's talk at the joint
ELIXIR IG-BioSharing WG session (and if not, here are the slides
).
Here are a few updates from the BioSharing registry:
* *New Homepage and overall site clean-up (see attached screenshot)* -
The homepage is now more intuitive, informative, and allows for more
easy access to the data. In addition, biosharing.org
should now work well on mobile and

01 Mar 2016

BioSharing WG - RDA 7 Update

Dear RDA BioSharing WG members,
here the slides for this afternoon joint session between ELIXIR IG and
BioSharing WG.
If you are at RDA, hope to see you there!
http://www.slideshare.net/SusannaSansone/biosharing-wg-elixir-ig-rda-ple...
Kind regards,
Susanna (on behalf of the BioSharing team)
--
--
Susanna-Assunta Sansone, PhD
skype: susanna-a.sansone
ORCiD: 0000-0001-5306-5690

05 Feb 2016

BioSharing WG - Update Feb 2016

Dear RDA BioSharing WG members,
Hope you are all well. Here is a brief update on our progress with the
BioSharing registry.
1. New documents for your information:
* **BioSharing Primer*
-
Ever wish you had a handy primer on BioSharing? Somewhere that
details what BioSharing is, what it does, some use cases and
statistics? We did, so we created one. This document will be updated
periodically.*
* **BioSharing leaflet
*- A

14 Jan 2016

BioSharing Registry of Standards survey - your input required

Dear RDA-BioSharing WG members,
As you may recall, in December we launched a 10 question survey to
assess the needs for a *registry of standards in the life and biomedical
sciences*, to help enhance BioSharing as part of our work in the ELIXIR
and NIH BD2K infrastructure programmes.
Despite a good response so far, we feel we can do better! Could we ask
to you /*c*//*omplete the survey (if you haven't already) and
disseminate it*/ among your peers? I have copied some text below, that
you may wish to use when spreading the word.