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

*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 duplication –

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.

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

The biological material is essential

raw material for research and for

development of biotechnological

applications

It is crucial to share this

patrimony

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!!

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)

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

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

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)

* 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

* 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)

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

* 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

* 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]

*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

(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

EQUATOR supports wider practical implementation of

reporting guidelines by all relevant parties to increase the

usability and value of health research

EQUATOR

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

CoBRA endorsement by IRDIC

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

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)

*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

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…

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