Presentation by Elena Bravo, ISS, at RDA National event in Florence, Italy, 14-15 November 2016

1. CoBRA guideline : a tool to facilitate
sharing, reuse, and reproducibility of
bioresource-based research
Elena Bravo
elena.bravo@iss.it
RDA National Event in Italy | 14 -15 November 2016, Florence
FAIR data management: best practices and open issues

2. *researchers ask the wrong
questions
*study designs are
inadequate or
inappropriate
*studies are not reported
appropriately,
or are either not
published
*Publish or perish -
Predatory journals
* Misconduct, metrics
85% OF RESEARCH IS WASTE
WHY?
October 19th 2013
PERSPECTIVE
The Economics of Reproducibility in
Preclinical Research
Leonard P. Freedman1*, Iain M. Cockburn2, Timothy S. Simcoe2,3
SimcoePLoSBiol13(6):2015
How science
goes wrong:
Scientific
research has
changed the
world. Now it
needs to
change itself
Reduce

3. CoBRA is a Reporting Guideline
for the Standardized
Citation Of BioResources in scientific journal Articles
What is CoBRA
Author guidelines promote open research culture
help transparency, openness, and reproducibility of the results
SCIENTIFIC STANDARDS POLICY (B. A. Nosek et alScience 26 Jun 2015)
 The Reporting Guidelines help to improve completeness and
clearness of research articles.
 The Reporting Guidelines are essential resources for writing and
publishing health research.

4. Fam. history
Lab. param.
Treatm. outcome
Lifestyle
PBMC
Serum
FFPE
tissues
Frozen
tissues
Cells
Antibodies
Affinity binders
Recomb. proteins
Gene clone collections*
siRNA libraries*
Cell lines*
Model organisms*
Sample storage
Healthy
Population
Patients
Analysis tools Application
Basic research
Life sciences
Targets for
Drug discovery
Biomarkers for
Drug development
New diagnostics
Personalized medicine
Public health
Infrastructure
Data storage
Biocomputing
DNA
Key Components of human
biobanking

5. The biological material is essential
raw material for research and for
development of biotechnological
applications
It is crucial to share this
patrimony

6. Biological samples
with associated data
Health Databases
organized collection of data and
information by inputting, storing,
retrieving and managing and updating,
registry
Bioresources
Bioresources: It includes biological samples and associated data
(classification / characterization, epidemiological and /or clinical
data as well as omics, imaging etc)..
The “concrete” part of sample decrease in quantity
The “data” associated to sample, that is the "knowledge" of the
sample, increase over the time.
the samples are transformed in data and data…do not move!!

7. Bioresources data are :
 static (i.e.: provenance, primary material description)
 dynamic (i.e.: sequence of steps is relevant
 some steps occur repeatedly (transport – processing – storage)

8. Limitations of existing concepts
● inconsistent data items
● no common vocabulary
● highly application and/or domain specific
● scarce information on handling, processing,
storage
● no indicators for data quality
● data measured, inferred, guessed?
● sequence of actions not documented
● lacking information on time course (only
duration)
● predominantly free text
⇒ not interoperable
⇒ digital processing difficult.
File format needed
● reflecting the whole
sequence of
processing
● including methods (eg.
by stable reference)
● continued collection of
data along the
process path (from
acquisition to analysis)
● full traceability
comparability of samples from different sources
reproducibility of data generated from the samples
Sample data

9. Advantages of data sharing
OA as a moral imperative 2000
OA policies – institutions, funding bodies, governments
Size of OA citation advantage when found
(and where explicitly stated by discipline)
% increase
in citations
with Open
Access
Physics/astronomy 170 to 580
Mathematics 35 to 91
Biology -5 to 36
Electrical engineering 51
Computer science 157
Political science 86
Philosophy 45
Medicine 300 to 450
Communications studies (IT) 200
Agricultural sciences 200 to 600
Citation advantage
Swan, Alma (2010) The Open Access citation advantage

10. BRIF initiative is a an international and multidisciplinary work in
progress initiative that is developing a framework for recognition of
bioresources contribution to Research
Final objective is to create tools that will:
- Facilitate the practice of sharing policies for data and samples
- Promote a philosophy of sharing in the biomedical community
- Facilitate accurate acknowledgement of resource use
in scientific publications and grants via unique resource identifiers
- Develop tools that enable to establish frequency of use of
bioresources and evaluate their impact (develop algorithm metrics)
• Biobank partners
• Computational biologists
• Computer scientists
• Genome/genetics scientists
• Epidemiologists
• Jurists, lawyers
• Ethicists
• Experts in impact factors
• Bibliometricists
• Journal Editors, Publisher
• Researchers/users
The Bioresource Research Impact Factor initiative (BRIF)

11. * Organization : Working subgroups
‘BRIF & Digital Identifiers’
‘BRIF Parameters’
‘BRIF in Access & Sharing Policies’
‘BRIF dissemination’
‘BRIF and Journal Editors’
 Sensitize journal editors to BRIF issues
 Standardize citations in journal articles
 To develop tool for literature tracing of the bioresource use

12. * Current citation of bioresources use in scientific
literature
- multiplicity of sections where
bioresources are acknowledged
(Material & Methods,
Acknowledgements, References…)
- bioresource acknowledgement or
citation placed outside the main paper
(or in online supplementary materials)
- typing errors or approximation of the
bioresource name/identification:
multiplicity of names for a given
bioresource; different languages;
- cascade use of resources (e.g. Family
samples that are themselves part of
several other projects
- absence of citation (negligence)
- acknowledgement of persons
instead of bioresources itself
- absence of acknowledgement for
the bioresource used (negligence)
- suitable to refer to one type of
bioresource but not for any
derived, or secondary
bioresources
- No standardized way to
incentivise researchers to
acknowledge properly the
bioresource used
- Websites that no more exist
With minor changes from.: Mabile et al. GigaScience 2013, 2:7
Most of the citation can be detected via full-text mining (not
indexed in Pubmed or Web of Science)

13.  Literature tracking inadequate, difficult to trace
(not indexed in PubMed or Web of Science)
 Scarce Visibility of researcher, institution, sponsor
 Lack of recognition for work of setting up and
maintaining a valid bioresource
 Biobank USE has not measureable value for career
development (bibliometric issues)
 Lack of incentives for sharing – Underutilization of
bioresources – Waste of existing patrimony
 Lack of simple formats to give information on samples
and data used for research - Reduced reproducibility
* Citation: Lack of standard,
lack of incentives

14. * Citation of BioResources
in journal Articles
The more you give access to the resources
the more you are cited !!!
standardizing citation of bioresources in
scientific trace their use on the web and
promote access

15. * CoBRA checklist
Article text section Guidance
* Abstract Indicate whether the work has used one or more bioresources,
and specify their number if relevant.
* Introduction Indicate that the work used one or more bioresources.
Specify the type.
* Methods Report each individual bioresource used to perform the study:
- by their name and other ID, if existent, and
- by a single bibliographic reference.
*(Bioresource) Reference
Cite each bioresource used as follows:
 ID/Bioresource Name (acronym if available)/
 Organisation or network partnership/
 Number of access(es), Date of last access;
 [BIORESOURCE]

16. *Main CoBRA features
The [BIORESOURCE] reference:
 ID/ DOI/ Bioresource Name (acronym if available)/
How: specific indications for ID / DOI / Name
Significance: It is immediately implementable
 Organisation or network partnership/
How: report membership / partnership in consortia / networks
organizations
Significance: The biobank is individually cited and recognized
Recognize value of partnership /networking
Number of access(es), Date of last access
How: Number of access(es); date of last access
Significance: Recognition of “quantitative work” and appreciation
connected to routinely specialized activities
[BIORESOURCE]
How: Add the tag [BIORESOURCE] ONLY for bioresource USED for
Significance: TRACK the USE of bioresource for research/ application

17. (bioresource) Reference
Example 5: The bioresource has a DOI and has to be cited
 Case 1: NO-USE: Citation for any case but “use” of the bioresource.
Consuegra I, Jimenez J L, D. The Spanish HIV HGM BioBank (SHIVBB). Biopreservation
and Biobanking. 2013, 11(4): 253-254. doi:10.1089/bio.2013.1133.
Case 2: USE: Citation for a bioresource that contributed to the article with samples and /
or data.
Consuegra I, Jimenez J L,D. The Spanish HIV HGM BioBank (SHIVBB). Biopreservation
and Biobanking. 2013, 11(4): 253-254. doi:10.1089/bio.2013.1133; No. Access: 2, Last:
April 15, 2014. [BIORESOURCE]
[BIORESOURCE]
tag to indicate USE of the bioresource
To differentiate citation of bioresources not used from citation of bioresource
used as a source of material for the study
CoBRA : Example

18. EQUATOR supports wider practical implementation of
reporting guidelines by all relevant parties to increase the
usability and value of health research
EQUATOR

20. The EASE Guidelines for Authors and
Translators of Scientific Articles to be
Published in English provide simple, clear
advice aimed at making international scientific
communication more efficient. The updated
edition is freely available in more than 20
languages:
•English (December 2015)
•Arabic (December 2015)
•Bangla (December 2015)
•Bosnian (December 2015)
•Bulgarian (December 2015)
•Chinese (December 2015)
•Croatian (December 2015)
•Czech (December 2015)
•Estonian (December 2015)
•French (December 2015)
•German (December 2015)
•Hungarian (December 2015)
•Italian (December 2015)
•Japanese (December 2015)
•Korean (December 2015)
•Persian (December 2015)
•Polish (December 2015)
•Portuguese (December 2015)
•Romanian (December 2015)
•Russian (December 2015)
•Serbian (December 2015)
•Spanish (December 2015)
•Turkish (December 2015)
•Vietnamese (December 2015)
Methods: ….
”All factors that could have
affected the results need to be
considered. Sources of
experimental materials obtained
from biobanks should be mentioned
with full names and identifiers, if
available (Bravo et al 2015)".
EASE

21. CoBRA endorsement by IRDIC

22. Biobank Education Tools
https://zenodo.org/record/55785
Title: How to use the CoBRA guideline
Alessia Calzolari, Filippo Santoro, Elena Bravo
What it is:
Scope: to facilitate the use of the CoBRA guideline
Presented at ISBER 2016
Format: Full HD (1080p), MPEG-4 Part 10 (H.264)
Screencasting: video and audio tracks were recorded in digital
multimedia format, by using Camtasia Studio (trial version,
TechSmith Corporation, Okemos MI, US).
FREE e-learning tool :
Disseminate and facilitate

23. European Research Infrastructure Consortium (ERIC)
in Biomedicine
At the end of 2013, BBMRI, EATRIS and ECRIN were officially
awarded the Community legal framework and ISS has the mandate
to ensure Italian participation
The ERIC Legal framework
 Internationally recognized legal entity
 ERIC facilitate the joint establishment and operation of research
infrastructures of European interest (ESFRI roadmap)
 Member States annual fee ensure long-term economic sustainability
 Operational sites (National Node) in different countries that operate
under one legislation
 VAT exemption
• BBMRI (Research Biobanks)
• ECRIN (clinical studies and biotherapies)
• EATRIS (translational research)

24. *BBMRI-ERIC
BBMRI-ERIC promotes CoBRA and
suggests to include the
specification of the reference to be
used in MTA/DTA templates
CoBRA as a service

25. RDA builds the social and technical bridges
that enable open sharing of data
CoBRA implementation is a tool
to track the use and favor the access to samples
and data
.. complementarity, synergy and collaboration
among the initiatives are necessary to move
forward
* a long list of things to do…

26. Thank you
CoBRA: BRIF Journal Editor
Paola De Castro
Federica Napolitani
Anna Maria Rossi
Alessia Calzolari
Istituto Superiore di Sanita (ISS), Rome, IT
Anne Cambon-Thomsen
Laurence Mabile
UMR1027 Inserm-Université Toulouse III, FR