BRIF: Bioresource Research Impact Factor - Anne Cambon-Thomsen - INSERM

BRIF: Bioresource research impact factor (framework)

Dr. Anne Cambon-Thomsen, CNRS DREMUMR 1027 Inserm and Univ Toulouse III – Epidemiology & public health

Genotoul societal platform, Toulouse: « Genetics & society »BBMRI-ERIC, Graz, Austria: Common Service ELSI

BioSHaRE conference LATEST TOOLS and SERVICES for DATA SHARING July 28th, 2015 in Milan, Italy

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from invisibility cloak to full screen

Bioresources under the invisibility cloak

BioSHaRE Conference, Milano 28/7/15

https://www.youtube.com/watch?v=8gcmbBlZfbM





https://www.youtube.com/watch?v=mbhj3UF3mHE



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WHY?not visible enough; not acknowledged adequately; difficult to trace; difficult to assess their usage reliably

Human bioresources are key components of biomedical research. Yet, their role is underestimated and the work provided to setting up and maintaining a valid bioresource is not recognized. Cambon-Thomsen et al. Nat Genet 2003, 34:25–26

• biological samples with associated data (medical/epidemiological, social),

• databases independent of physical samples

• other biomolecular and bioinformatics research tools

BIORESOURCES (BR)

- lack of indicators describing efficient usage and management of BR

- lack of a unique BR identification system to trace them precisely

- lack of standards for BR citation in the scientific literaturehttp://www.gigasciencejournal.com/content/2/1/7BioSHaRE Conference, Milano 28/7/15

BioSHaRE Conference, Milano 28/7/15 4

Different levels to consider

• Data and bioresources in genomics– essential

• What makes them being used? – Visibility, accessibility and sharing, quality.

• What makes them being visible? – Infrastructures, catalogues, description (metadata)

• What makes them being shared? – Scientific interest, recognition, sustainability

• What makes them being cited/acknowledged ? - MTA, DTA, agreements, methodology in articles, collaboration good practice. No standard.

What are the blocking factors of the shared use of bioresources

• Technical ones (quality etc.)• Institutional ones

– No exchange, sharing or access policy– No practical help– Cost

• Intellectual property ones• Information ones

– No easily available information on content– Restricted use to pre-defined professional circles

• No obvious positive spin off : incentives? 5BioSHaRE Conference, Milano 28/7/15


Lack of incentives and tools

• The movement of open access• Sharing policies versus collaborative practices• Sharing is not just giving access: an active

process• Harmonisation and diversity • Tools for sharing are needed at various levels


Final objective:

The initiativeThe Bioresource Research Impact Factor initiativeWork in progress, currently developing a framework for recognising the specific contribution of bioresources to Research (in scientific literature)

To create tools that will:

- facilitate the practice of sharing policies for data and samples

- promote a philosophy of sharing in the biomedical community

Anne Cambon-Thomsen Laurence Mabileproject manager Contacts: [email protected] , [email protected]

mailto:[email protected]

mailto:[email protected]


By creating a set of adequate standardized tools:

•standards for citation / acknowledgement of bioresources in scientific articles in order to trace their use on the web

• BRIF indicator: a tool to establish frequency of BR use and evaluate their impact based on metrics and on the use of a unique digital resource identifier

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HOW? The initiative


Objective: increase sharingPurpose: recognition of the effort involved in establishing, maintaining and sharing resourcesChallenge: how to overcome the feeling of loss that may prevail

Idea: Transforming a loss into an advantage.« The more it is shared, the more it contributes to science, the more it is recognised »Virtuous circle!

http://www.gen2phen.org/groups/brif-bio-resource-impact-factor

Currently being transferred to BBMRI-ERIC




Working subgroups

‘BRIF & Digital Identifiers’co-chaired by G. A. Thorisson, University of Leicester, UK and P.A. Gourraud, University of California SF, USA [email protected]

‘BRIF Parameters’chaired by B. Parodi, National Inst. Cancer Res. Genoa, IT [email protected]

‘BRIF in Access & Sharing Policies’co-chaired by E. Rial-Sebbag, Inserm UMR1027, Toulouse, FR and J. Harris, Norwegian Institute of Public Health, Oslo, Norway [email protected], [email protected]

‘BRIF and Journal Editors’co-chaired by A. Cambon-Thomsen, Inserm UMR1027, Tlse, FR and E. Bravo, Istituto Superiore di Sanità, Rome, IT [email protected], [email protected]

‘BRIF dissemination’chaired by L. Mabile, Inserm UMR1027, Tlse, FR [email protected]

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BioSHaRE BRIF pilot

• BioSHaRE BRIF pilot study formalised in the « Publication policy » and available on the P3G website in 2013

• Given first steps results and publication of the CoBRA guideline, updated BioSHaRE BRIF pilot study protocol in 2015


‘BRIF dissemination’ subgroup

► BRIF newsletters ► BRIF publications

► Conferences

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ACTIONS developed by the BRIF Journal Editors’ subgroup

Sensitizing editors and their associations about BR issues

Dissemination of BRIF in international Science Edition Conferences

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Organize a restricted workshop addressed to Journal editors and experts (Rome, June 21, 2013)

Work out a guideline for citation of bioresources and publish it

Launching an open access journal for describing bioresources with re-use potential


STANDARD BIORESOURCE CITATION BRIF workshop in Rome, June 2013Poster Presentation in Chicago at Peer review congress September 2013Publication in 2015 in BMC Medicine

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BMC Medicine, 17 Feb 2014 : http://www.biomedcentral.com/1741-7015/13/33

Developing a guideline to standardize the citation of bioresources in journal articles (CoBRA)

Elena Bravo1§, Alessia Calzolari1, Paola De Castro1, Laurence Mabile2, Federica Napolitani1,

Anna Maria Rossi1 and Anne Cambon-Thomsen2

1Istituto Superiore di Sanità, Rome, Italy

2UMR U 1027, Inserm, Université Toulouse III - Paul Sabatier, Toulouse, France

http://www.biomedcentral.com/1741-7015/13/33


CoBRA checklist Citation Of BioResources in scientific journal Articles

• Article text section Guidance• Abstract Indicate whether the work has used one or more bioresources, and

specify the number of bioresources 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 extant, and - by a single bibliographic reference.

• References 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]

• Specifications for ID: Unique ID can be DOI (Digital Object Identifier), catalogue number, or the name only.

• If the only ID is the name then add Town and Country.• In the case of bioresources not used as a source of material for the study, but only

referred to, follow the citation format: ID/Bioresource Name (acronym if available)/organisation or network partnership


Format of the 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]

• Specifications for ID: – Unique ID can be DOI (Digital Object Identifier),

catalogue number, or the name only.– If the only ID is the name then add Town and

Country.• In the case of bioresources not used as a source of

material for the study, but only referred to, follow the citation format: ID/Bioresource Name (acronym if available)/organisation or network partnership


BOX 1. Examples of how to cite a bioresource in the references of articles

- All examples assume that the bioresource was actively used to complete the research .- Examples assume that two different accesses to the bioresource occurred, one on March 3, 2013 and one on April 15, 2014.- Examples 1, 2 and 3 assume that cited bioresources are committed to report their partnership with BBMRI-ERIC.- Acronyms will be added only in cases of consolidated use by the biobank.

Example 1: The bioresource has an ID and a consolidated acronymBioresource: Microisolates in South Tyrol Study (MICROS), Bolzano, Italy; ID: BRIF2155 Citation: BRIF2155; Microisolates in South Tyrol Study (MICROS); BBMRI-ERIC; No. Access: 2, Last: April 15, 2014. [BIORESOURCE]

Example 2: The bioresource has been described by a marker paper with a DOI, and has a consolidated acronymBioresource: The Australian Breast Cancer Tissue Bank (ABCTB), Australia Citation: Carpenter JE, Marsh D, Mariasegaram M and Clarke CL. The Australian Breast Cancer Tissue Bank (ABCTB). Open Journal of Bioresources 1:e1; 2014. DOI: http://dx.doi.org/10.5334/ojb.aa; No. Access: 2, Last: April 15, 2014. [BIORESOURCE]

Example 3: The bioresource does not have a DOI, nor an IDBioresource: BioBanca Istituzionale of Naples, Italy Citation: BioBanca Istituzionale (BBI), Naples, Italy; BBMRI-ERIC; No. Access: 2, Last: April 15, 2014. [BIORESOURCE]

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Launch of an open access data journal dedicated to the publication of description of bioresources “featuring peer-reviewed short papers helping researchers to locate and cite bioresources with high reuse potential. “

‘Open Journal of Bioresources’http://openbioresources.metajnl.com/

Aim: - Increase the visibility of bioresources by offering the possibility of an open access “marker paper” , according to an established template of description- Provides a bioresource with a DOI

Collaboration with Ubiquity Press

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http://openbioresources.metajnl.com/


Bioresource paper template for submission to the OJB

(1) Bioresource Overview

(3) Bioresource description

(2) Methods (4) Reuse

potential

(5) Copyright Notice19


Bioresource paper template for submission to the OJB

(1) Bioresource Overview TitlePaper AuthorsPaper Author AffiliationsAbstractProject descriptionClassificationKeywordsContext: Spatial & temporal coverage

(3) Bioresource description Bioresource name Bioresource location Bioresource contact Bioresource URLIdentifier used Bioresource type Type of sampling Disease status of patients/sourceClinical characteristics of patients/source: age, gender, treatment information, etc.

Vital state of patients/sourceClinical diagnosis of patients/sourcePathology diagnosisControl samplesBiospecimen type Anatomical site Release dateAccess restrictions

(2) Methods StepsStabilization/preservationType of long-term preservation Storage temperature Shipping temperature from patient/source to preservation or research use

Shipping temperature from storage to research use

Quality assurance measuresEthics StatementConstraints

(4) Reuse potential AcknowledgementsFunding statementAuthor RolesReferences(5) Copyright Notice

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• Infrastructures• Professional

management• Traceability not only of

samples/data for quality or reproductibility purposes, but

• Traceability of the uses of the resources by systematic standardised citations

• Calculation of impact through uses

• Recognition of the resources as contribution to science

• Specific publications for describing resources

• Link between contributors and bioresources (e.g. through ORCID)

Full screen


Next: implementationWhat policy actions?

• A guideline that is not implemented is of no use• What mechanisms: endorsement at various levels

– Institutional (Universities, national institutes, infrastructures...)

– Scientific (Scientific consortia, scientific and professional societies…)

– Editorial (instruction to authors, website of reference guidelines to be used)

– Administrative : Inclusion of the reference to use – Educational : good practices taught to PhD students using

bioresources


Guideline in EQUATOR

• The EQUATOR network : http://www.equator-network.org/• Enhancing the QUAlity and Transparency Of health

Research – Contains the major reporting guidelines internationally

recognised – Editors frequently require such guidelines to be used in

manuscripts– CoBRA was developed in contact with EQUATOR and now appear

on this websitehttp://www.equator-network.org/reporting-guidelines/cobra/


Next steps• Various actions of dissemination (Newsletters,

posters in scientific conferences, presentations)• Two workshops in Toulouse

– Together with EASE (European Association of Science Editors) – October 9, 2015 http://www.ease.org.uk/ ”Editors as promoters of good practices in bioresource

research”– Together with BBMRI-ERIC: December 4, 2015 : BRIF

workshop « From identifiers, parameters and sharing policies,

towards metrics »

http://www.ease.org.uk/


Key points/conclusion• To share or not to share: not anymore the question • The question is facilitating and rewarding sharing• Barriers to sharing : complex • A key element is to cite what has been shared • The recommendation CoBRA • Necessity to use it also in MTA and DTA • This rationalisation and standardisation of

bioresource citation is part of a chain of public policies for the recognition of the various ways of contributing to genomics research and to society


Register to BRIF group at:ubscribe to the BRIF Newsletter at:http://listes.univ-tlse3.fr/wws/subscribe/brif.infoContact us:[email protected] [email protected]

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THANK YOU!


References used• Bravo E, Calzolari A, De Castro P, Mabile L, Napolitani F, Rossi AM, Cambon-Thomsen A.

Developing a guideline to standardize the citation of bioresources in journal articles (CoBRA). BMC Med. 2015;13(1):266.

• Bravo et al Citation of bioresources in biomedical journals: moving towards standardization for an impact evaluation. European Science Editing 2013;39(2): 36-38.

• De Castro et al. Open Data Sharing in the Context of Bioresources. Acta Inform Med. 2013, 21(4): 291-292.

• Mabile et al. Quantifying the use of bioresources for promoting their sharing in scientific research. GigaScience 2013, 2:7.

• Cambon-Thomsen et al The role of a Bioresource Research Impact Factor as an incentive to share human bioresources. Nature Genetics. 2011, 43(6):503-4.

• Kauffmann F., Cambon-Thomsen A. Tracing biological collections: between books and clinical trials. JAMA, 2008;299(19): 2316-2318.

• Cambon-Thomsen A. Assessing the impact of biobanks. Nature Genetics (Correspondence), 2003, 34, (1) : 25-26.

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BRIF: Bioresource Research Impact Factor - Anne Cambon-Thomsen - INSERM