BRIF MS DRAFT 27-07-11

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BRIF DRAFT MS for PLOS Med / version 27-07-2011
TO SUBMIT TO : 'Guidelines and Guidance" of PLOS Medicine http://www.plosmedicine.org/static/guidelines.action#about 2000 words, 30 ref
Title: The BRIF (Bioresource Research Impact Factor) as a (potential) tool for improving bioresource sharing in biomedical research
Authors: Named authors to be discussed according to contribution plus BRIF working group as a collective author (with named contributors) So far have contributed : Laurence mabile, Anne Cambon-Thomsen, Mylène Deschenes, Robert Hewitt, G Thorisson, Jane Carpenter, Paul Hoffman, Federica Napolitani (group led by Elena Bravo)
Table of Contents
Table of Contents......................................................................1
Introduction....................................................................................1 The BRIF concept and objectives......................................................4 Digital identifier schemes................................................................5 Parameters, measures and indicators...............................................6 Journal guidelines for resource citing and referencing.......................7 Policies for resource access and sharing...........................................7 Conclusions.....................................................................................8 REFERENCES....................................................................................9
Introduction
Definition of bioresources and their importance in biomedical research Written by Jane Carpenter, Paul Hoffman and Anne
BRIF DRAFT MS for PLOS Med / version 27-07-2011 An increasing portion of biomedical research is relying on the use of bioresources. Bioresources include both biological samples with associated data (medical/epidemiological, social), databases independent of physical samples and useful for biomedical research and other biomolecular research tools. Research tools include any data directly or undirectly derived from biosamples such as databases, locus specificdatabases, registries of disease patients and any specific tool for molecular characterization of biobanked samples. Besides some specific research infrastructures, many of the bioresources are already directly anchored in medical practice. Here we introduce the two main classes of bioresources and the issues attached to their setting up and usages. As the creation and use of biobanks increases around the world, there is an urgent need to better define what could be a biobank of high standing. Much of basic and translational research being undertaken today relies on the provision of human biological material collected from persons with specific characteristics1 - this may be disease or population based – and digital information resources accessible over the Internet. This is increasingly important in the modern era of “omics” medicine. Traditionally material was obtained by individual researchers consenting donors and collecting prospectively the appropriate samples on a project specific basis. The time taken to recruit and collect the material required added a significant time delay to when the actual laboratory work on the specimens could commence. Biobanks are essential resources and also platforms for biomedical research allowing basic, translational and clinical rearch projects by providing human biospecimens as well as offering acess to key technologies. However, research biobanks require reliable and sustainable solutions for different key issues to provide high-quality material based on optimized procedures for acquisition, storage, documentation, expert evaluation and standardized material transfer procedures. As a response to meet this urgent requirement and expedite research, the concept of collecting, storing and distributing specimens in biobanks or bioresources, was developed and established in many centres across the world. Not only does this provide a single entry point for researchers requiring high quality material and data but also allows for best practice methodologies to be followed2 and hence supply of the highest quality material for downstream testing. Individual bioresources vary in capacity, access arrangements, and disease types collected. It is also true that the development of high throughput ‘omics’ platforms requires material from large numbers of both patients and/or healthy individuals which is problematic if not impossible to obtain on an individual basis and this need is being met by “modern” bioresource facilities. The true value of bioresources will increase exponentially with time, as more long term clinical and outcome data becomes available on the donors, and data accrual is in itself a major activity of many bioresources. Also, as time progresses, projects supplied with material will return research results to the resource and thus enhance the data set available, indeed the data alone may be sufficient to mine and answer research questions. A commitment to share this information with the research community is paramount3. The 2011 Joint statement of 17 major national funders sent the most recent and powerful
BRIF DRAFT MS for PLOS Med / version 27-07-2011 signal that research resources must be shared so as to maximize the potential of publicly funded resources. However, open access environment must be correlated by appropriate measures to allow for the proper recognition of research resources being used in the development novel scientific knowledge. Failing to do so will have a major impact on the global sharing vision that funders hope to implement. Improper recognition of resource makes it more difficult for biobanks/database to justify the deployment of access and ‘users’ support and more generally, the relevance of their continued operation for the scientific community. In the context of limited funding resources, it makes their very existence precarious. While pushing on biobanks/database for opening their access, we must thus put an equal amount of pressure on the users to recognize their resources. Appropriate set of tools must be developed and implemented to allow measuring impact. Such tools currently exist, but insufficient level of coordination and systematic implementation makes it difficult to see their positive impact on the overall organization of scientific activities.
Suggested references: (1) Yu Y, Zhu Z. Significance of biological resources collection and tumour tissue bank creation. World J Gastrointest Oncol 2010; 2(1):5-8 (2) ISBER Best Practices for Repositories. Cell Preservation Technol: 2008; 6:1-58 (3) Walport M, Brest P. Sharing research data to improve public health. Lancet: 2011; 377; 9765:537-539 Knoppers BM, Harris JR, Tassé AM, Budin-Ljøsne I, Kaye J, Deschênes M, Zawati MH. Towards a data sharing Code of Conduct for international genomic research. Genome Med. 2011 Jul 14;3(7):46. [Epub ahead of print] PubMed PMID: 21787442. Joly Y, Zeps N, Knoppers BM. Genomic databases access agreements: legal validity and possible sanctions. Hum Genet. 2011 Jun 25. [Epub ahead of print] PubMed PMID: 21706183. Kaye etal. Data sharing Nat rev genet 2010 Knoppers BM, Harris JR, Tassé AM, Budin-Ljøsne I, Kaye J, Deschênes M, Zawati MH. Towards a data sharing Code of Conduct for international genomic research. Genome Med. 2011 Jul 14;3(7):46. [Epub ahead of print] PubMed PMID: 21787442. Kaye J. From single biobanks to international networks: developing e-governance. Hum Genet. 2011 Jul 23. [Epub ahead of print] PubMed PMID: 21785980. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73. Erratum in: Nature. 2011 May 26;473(7348):544. Xue, Yali [added]; Cartwright, Reed A [added]; Altshuler, David L [corrected to Altshuler, David]; Kebbel, Andrew [corrected to Keebler, Jonathan]; Koko-Gonzales, Paula [corrected to Kokko-Gonzales, Paula]; Nickerson, Debbie A [corrected to Nickerson, Deborah A]. PubMed PMID: 20981092; PubMed Central PMCID: PMC3042601. Kaye J, Heeney C, Hawkins N, de Vries J, Boddington P. Data sharing in genomics--re-shaping scientific practice. Nat Rev Genet. 2009 May;10(5):331-5. PubMed PMID: 19308065; PubMed Central PMCID: PMC2672783.
What are the obstacles for recognition of the work involved in setting up and maintaining bioresources?
BRIF DRAFT MS for PLOS Med / version 27-07-2011 Written by Robert Hewitt and Paul Hoffman Establishing a valuable bioresource requires considerable time and effort, and so it is essential that people are provided with an incentive to do the work required to a high standard. To provide appropriate rewards and recognition, it is necessary to be able to measure the performance of bioresources and there are various ways to do this. Performance can be measured using indicators that the bioresource is efficiently run and well utilized. For example, by counting the number of cases collected or distributed per year, or the number of projects supported per year. A good way could be to evaluate the ratio between the number of biospecimens entering in the biobank and the number of biospecimens which are used for developing a research project by year. Economic factors like the cost of running and maintaining the biobank can also be taken into account. Performance can be measured using indicators of the quality of the bioresource, the quantity of the bioresource available, and the value of the samples or datasets. Morphological control of frozen specimen used for “omics” program is to be considered. For example, using the results of an external assessment like certification (ISO 9001/2008) or accreditation (ISO 17025 and ISO 15189). Also, assessment of the extent and richness of the datasets collected (including follow up of patients and treatments) and the complexity of cases. Performance can also be measured using indicators of research productivity. For example, counting and measuring the impact of publications that result from research supported by the bioresource, or the number of patents that result or the number of material transfert agreement and contrat signed by year. Since the purpose of a bioresource is to enhance research productivity, this last indicator may provide the most reliable assessment. However, the process of tracking publications and quantifying their impact is not straightforward. To track the publications made possible by a bioresource, it is essential that researchers consistently acknowledge use of the bioresource by placing a unique and traceable citation in all their relevant publications. Moreover, origin of the bioresource used for research must be identified in the Material and Method section. To some extent this is already possible, if researchers acknowledge the bioresource in their papers and if the effort is made to search through publications to find appropriate acknowledgements. Once publications have been tracked, then the impact of each individual publication can be assessed in order to measure publication impact. The success of this approach depends on the compliance of the researcher in acknowledging the bioresource and the laborious efforts of the assessor. However there remains in doing so a major disadvantage of being highly sensitive to errors or inconsistencies in writing acknowledgements (typing errors, partial names etc.). This system also also breaks down in cases where the acknowledgement section of the citing paper is not accessible to the assessor (i.e. behind subscription paywall). In order to make this process efficient and less error-prone, it needs to be automated, we need to have traceable and unique identifiers for bioresources, and the scientific community needs to show support in order to encourage researcher compliance. So there are a number of obstacles to be overcome if this is to be a routine and widely accepted method of assessment.
The BRIF concept and objectives Written by Anne & Laurence
BRIF DRAFT MS for PLOS Med / version 27-07-2011 Aim : In such a context, a central concept introduced in 2003 (1), and further developed in 2004 (2, 3), is that of a bioresource research Impact factor (BRIF). The idea is to construct a quantitative parameter to describe bioresources, modeled on the publication ‘Impact Factor’. It aims to provide a guidance and a methodology for optimising recognition of bioresources, their use and their sharing at international level. Such a BRIF would make it possible to document; 1. the quantitative use of a bioresource, 2. the kind and the importance of research results involving it, and 3. the scientific and management efforts of those who set up and made available a valid bioresource and their institution. This system could be used much more rationally than “reputation” in the evaluation of bioresources activities over time. Also, if such a factor was taken into account in assessing researchers/contributors’ professional results, it would increase the quality and sharing of bioresources. In order to operationalise this concept an international working group has been set up and specific tasks assigned to sub-groups as presented below. This working group comprises 120 members from 22 countries.
References suggested: 1: Cambon-Thomsen A. Assessing the impact of biobanks. Nat Genet. 2003 May;34(1):25-6. PubMed PMID: 12721553 2: Cambon-Thomsen A. The social and ethical issues of post-genomic human biobanks. Nat Rev Genet. 2004 Nov;5(11):866-73. PubMed PMID: 15520796. 3: Cambon-Thomsen A, Thorisson GA, Mabile L, Andrieu S, Bertier G, Boeckhout M, Cambon-Thomsen A, Carpenter J, Dagher G, Dalgleish R, Deschênes M, di Donato JH, Filocamo M, Goldberg M, Hewitt R, Hofman P, Kauffmann F, Leitsalu L, Lomba I, Mabile L, Melegh B, Metspalu A, Miranda L, Napolitani F, Oestergaard MZ, Parodi B, Pasterk M, Reiche A, Rial-Sebbag E, Rivalle G, Rochaix P, Susbielle G, Tarasova L, Thomsen M, Thorisson GA, Zawati MH, Zins M; BRIF workshop group. The role of a Bioresource Research Impact Factor as an incentive to share human bioresources. Nat Genet. 2011 Jun;43(6):503-4. PubMed PMID: 21614086.
Digital identifier schemes Written by Mummi To address the various issues referred to above concerning identification, bioresources need to be assigned digital identifiers (IDs) which allow them to be reliably cited in a scholarly context. In order to fulfill the requirements of the scholarly record, bioresource IDs should be persistent, globally unique and citable. The Digital IDs subgroup focuses its work on exploring and assessing existing and emerging technical solutions to the above, as well as addressing key related questions such as what to identify (biobank projects, sample collections, databases, datasets) and which international & independent body should be responsible for assigning bioresource IDs. It is worth emphasizing here that the aim is not to create new identifier scheme specifically for BRIF. Rather, the aim is to identify frameworks which are already
BRIF DRAFT MS for PLOS Med / version 27-07-2011 established or well on their way of becoming so, and subsequently recommend their use as appropriate with respect to: • • Resource providers (e.g. what type of IDs to use for biobank projects? Refer to clinical trial system or other systems) End users (e.g. guidelines from journals to authors for how to properly cite biobank projects and databases using unique IDs)
Preliminary results from the work of the Digital IDs subgroup indicate that the field is already moving in the right direction in several areas, especially with regards to digital research outputs. Notably, the DataCite initiative (http://www.datacite.org). It currently has established a worldwide data registration agency which reuses and extends the Digital Object Identifier (DOI) scheme already widely used in the scholarly publishing domain. Datasets generated and published by biobanks via digital repositories - and possibly data collections (including biological samples databases) - could well be assigned such ‘data DOIs’, an important step towards treating these important research outputs as first-class publications (1).
1: Thorisson G. Nat Biotech 27, 984 - 985 (2009): http://dx.doi.org/10.1038/nbt1109-984b
[NB These points may well belong better in the Conclusions/Discussion section?] -highly-related issue is identification of contributors, IDs for people / persons / contributors -it’s a challenge, BUT in part because no established tech/infrastructure. This is probably out of scope of the BRIF group. But probably worth mentioning that ORCID ‘is coming’, and it’s reasonable to assume that this infrastructure will be at the heart of any attribution schemes. -BRIF should keep an eye on developments in this area, and revisit this in next year as ORCID develops. Could provide set of recommendations once situation is more clear.
Parameters, measures and indicators Written by Robert Hewitt The purpose of the BRIF Parameters subgroup is to identify the different parameters to take into account when calculating the BRIF. From initial discussions it has been decided to focus on two types of entity providing a service to the scientific community: biobanks of human biomaterials and databases of information relating to human subjects research. The aim is to provide a measure of the extent to which bioresources promote high quality and reliable research. Downstream effects on healthcare and the economy
BRIF DRAFT MS for PLOS Med / version 27-07-2011 will not be assessed. The parameters selected need to be objective and easily verifiable, and the calculation of BRIF needs to be as simple as possible. A wide range of parameters are being considered for inclusion, including indicators of bioresource quality, value, efficiency and research productivity. The possibility of having two types of BRIF is also being discussed: firstly, a simple factor based purely on publication impact and secondly, a more complex factor that also includes measurements of bioresource quality, value and efficiency.
Journal guidelines for resource citing and referencing Written by Anne Cambon-Thomsen (with the help of Federica Napolitani & Elena Bravo) Although a key element for assessing the use and the research impact of bioresources is their systematic citation in Journals articles we are far from having standards and guidelines for the citation of such contributions. A specific task is a proposal for sensitizing journal editors to BRIF issues and modifying their editorial guidelines accordingly. The necessity of recognition by editors of Journals of acknowledging properly the bioresources used, using proper terminology and/or identifiers and agreeing on standards of citation (format/marker paper, place (s), institutions, people) have been extensively discussed within the "BRIF Connection to editors" subgroup. As “Uniform Requirements for Manuscripts Submitted to Biomedical Journals” (URM, http://www.icmje.org/) already exist, a proposal has been sent to the International Committee of Medical Journal Editors for being considered in a next amendment of these requirements. It underlines some insertions that may be needed in order to address the editorial problems concerning bioresources, which are becoming of great relevance within the biomedical community.
Policies for resource access and sharing Written by Mylène Deschênes Attempting to measure the impact of a biobank supposes, as it premise, that the research resource is being used. Use of a biobank (or research database) is contingent upon many factors, but the access and sharing policies certainly play a major role in facilitating or hindering use. Various components such as the level of constraints imposed on users or the level of simplicity/complexity of the procedures to gain access are pivotal to create an environment that will stimulate or discourage use of a bioresource/research database. Sharing, access and publication policies, and the agreements that support the ‘transaction’ of sharing material or data, seem like the appropriate vehicles to consider in implementing enforceable means of measuring the impact of a biobank. Through such guidelines or contrats, a bioresources/research database can impose on eventual users requirements to empower itself to measure its impact. Let us consider two categories of tools that are likely to contribute to the capacity of a biobank to measure its impact: the dissemination and the ‘control’ measures.
BRIF DRAFT MS for PLOS Med / version 27-07-2011 (1) Publications, academic presentations and other less traditional means of disseminating research results have a prime importance in measuring the impact of a scientific contribution. Bioresources must thus ensure that users will recognize the resources that was used in whatever means of dissemination the research chooses to communicate the results to the scientific community and the public. This recognition must be written in such a way as to allow for a systematic search to track usesas described above. Bioresources might also consider requiring the users to report on their use (e.g. sending their publication or a summary report) back to its source. However, a balance must be struck between imposing a series of requirements to users and still maintaining conditions that are favourable to use. Also of importance is the burden on bioresource managers if they have many contracts to prepare. (2) Another element is the level of control that the biobank can exercise over the secondary use of its material. If a biobank hopes to keep track of the use of its material, it must ensure that all eventual users will comply with its dissemination requirements. This is particularly a challenge for research database where the data can be copied and circulated easily and at infinitum. In a context where international collaboration is increasing and pooling of research resources is necessary to conduct research on complex health disease, it might be difficult for the bioresource to keep track of eventual users. The identity of the source of a material may be lost in the chain of multiple exchanges and amalgamation with others. A biobank can thus require that users do not share with third parties the material/data. Under such circumstances, it is expected that eventual users will have to deal directly with the bioresources to gain access, and will thus have the same requirements imposed upon them to recognize the original resources. However, here again, a balance must be truck between imposing constraints to users and making use of the bioresources appealing to eventual users. This is especially the case for databases. Given the delicate equilibrium required between stimulating uses and supporting the capacity to measure the impact, the BRIF sub-group proposes to further study and develop an appropriate set of tools that could eventually be integrated in the overall access and sharing policies of the biobanks/research databases
Conclusions Written by Anne and Laurence There is a certain pressure to develop chart of principles, tools and guidelines for bioresources uses and management that the biomedical community could refer to in their research practice. However this will not become actual unless proper tools for recognising such activities are in place. This article provides the foundations/bases for such policies in order to foster discussion among relevant stakeholders themselves.
BRIF DRAFT MS for PLOS Med / version 27-07-2011 REFERENCES
To gather from the different sections