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CoBRA guideline : a tool to facilitate sharing, reuse, and reproducibility of bioresource-based research


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

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CoBRA guideline : a tool to facilitate sharing, reuse, and reproducibility of bioresource-based research

  1. 1. CoBRA guideline : a tool to facilitate sharing, reuse, and reproducibility of bioresource-based research Elena Bravo RDA National Event in Italy | 14 -15 November 2016, Florence FAIR data management: best practices and open issues
  2. 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. 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. 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. 5. The biological material is essential raw material for research and for development of biotechnological applications It is crucial to share this patrimony
  6. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 18. EQUATOR supports wider practical implementation of reporting guidelines by all relevant parties to increase the usability and value of health research EQUATOR
  19. 19. 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
  20. 20. CoBRA endorsement by IRDIC
  21. 21. Biobank Education Tools 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
  22. 22. 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)
  23. 23. *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
  24. 24. 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…
  25. 25. 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