Indicators for the Data Usage Index (DUI): an incentive for publishing primary biodiversity data through global information infrastructure.

BACKGROUND: A professional recognition mechanism is required to encourage expedited publishing of an adequate volume of 'fit-for-use' biodiversity data. As a component of such a recognition mechanism, we propose the development of the Data Usage Index (DUI) to demonstrate to data publishers that their efforts of creating biodiversity datasets have impact by being accessed and used by a wide spectrum of user communities. DISCUSSION: We propose and give examples of a range of 14 absolute and normalized biodiversity dataset usage indicators for the development of a DUI based on search events and dataset download instances. The DUI is proposed to include relative as well as species profile weighted comparative indicators. CONCLUSIONS: We believe that in addition to the recognition to the data publisher and all players involved in the data life cycle, a DUI will also provide much needed yet novel insight into how users use primary biodiversity data. A DUI consisting of a range of usage indicators obtained from the GBIF network and other relevant access points is within reach. The usage of biodiversity datasets leads to the development of a family of indicators in line with well known citation-based measurements of recognition.

Towards mainstreaming of biodiversity data publishing: recommendations of the GBIF Data Publishing Framework Task Group.

BACKGROUND: Data are the evidentiary basis for scientific hypotheses, analyses and publication, for policy formation and for decision-making. They are essential to the evaluation and testing of results by peer scientists both present and future. There is broad consensus in the scientific and conservation communities that data should be freely, openly available in a sustained, persistent and secure way, and thus standards for 'free' and 'open' access to data have become well developed in recent years. The question of effective access to data remains highly problematic. DISCUSSION: Specifically with respect to scientific publishing, the ability to critically evaluate a published scientific hypothesis or scientific report is contingent on the examination, analysis, evaluation - and if feasible - on the re-generation of data on which conclusions are based. It is not coincidental that in the recent 'climategate' controversies, the quality and integrity of data and their analytical treatment were central to the debate. There is recent evidence that even when scientific data are requested for evaluation they may not be available. The history of dissemination of scientific results has been marked by paradigm shifts driven by the emergence of new technologies. In recent decades, the advance of computer-based technology linked to global communications networks has created the potential for broader and more consistent dissemination of scientific information and data. Yet, in this digital era, scientists and conservationists, organizations and institutions have often been slow to make data available. Community studies suggest that the withholding of data can be attributed to a lack of awareness, to a lack of technical capacity, to concerns that data should be withheld for reasons of perceived personal or organizational self interest, or to lack of adequate mechanisms for attribution. CONCLUSIONS: There is a clear need for institutionalization of a 'data publishing framework' that can address sociocultural, technical-infrastructural, policy, political and legal constraints, as well as addressing issues of sustainability and financial support. To address these aspects of a data publishing framework - a systematic, standard approach to the formal definition and public disclosure of data - in the context of biodiversity data, the Global Biodiversity Information Facility (GBIF, the single inter-governmental body most clearly mandated to undertake such an effort) convened a Data Publishing Framework Task Group. We conceive this data publishing framework as an environment conducive to ensure free and open access to world's biodiversity data. Here, we present the recommendations of that Task Group, which are intended to encourage free and open access to the worlds' biodiversity data.

Do journals and corporate sponsors back certain views in topics where disagreement prevails?

The article focuses on scientific disagreement about the use of statin-related drugs in the prevention of cardiovascular events. The study forms part of an exploration of the broader principle of research polarization, foremost in medicine. The hypothesis is that statin-positive and statin-critical researchers publish in different committed central journals, and that they are financially supported by different dedicated corporate sources. Methodologically we use Web of Science (WoS) analytic tools to perform publication analysis of a time series covering 1998-2018 in three seven-year windows. For each window data is captured based on sets of known statin-positive and statin-critical articles and researchers, and their primary and secondary co-authors. Standard deviation is used as a focused normalization and visual instrument together with Spearman's correlation coefficient in order to compare frequency distributions of statin-positive and critical journal and sponsor articles. Z-test p-values are used to assess the probability of error concerning the distributions. Findings at general topical level showed that a few journals consistently and significantly occupied top positions, 2 of which, American Journal of Cardiology and Circulation, published articles from both positions. Besides, Journal of the American College of Cardiology served as a major publisher of statin-positive research from 2005, as did European Heart Journal from 2012, replacing American Journal of Cardiology at the top. From 2012 Atherosclerosis and European Journal of Preventive Cardiology served as top-publishers of statin-critical articles. Two central US funding agencies, US Department of Health Human Services and National Institutes of Health (NIH), operated at general topical level across the time series, but the agencies played only a minor role in the divergent research positions. From 2005 statin-positive as well as statin-critical research was mainly sponsored by multinational pharmaceutical companies, predominantly Merck, AstraZeneca and Pfizer. In conclusion, the initial hypothesis about dedicated journals and sponsors was entirely substantiated at the general topical level and at the journal level of research disagreement, but not at sponsor level. Distinct dedicated journals were extracted separately from the 2 divergent statin positions. Since the WoS coverage of sponsor data 1998-2004 was sporadic sponsor data are analyzed from 2005. Only from 2012 the WoS sponsor coverage of the topic is consistently at 60%.

Towards a data publishing framework for primary biodiversity data: challenges and potentials for the biodiversity informatics community.

BACKGROUND: Currently primary scientific data, especially that dealing with biodiversity, is neither easily discoverable nor accessible. Amongst several impediments, one is a lack of professional recognition of scientific data publishing efforts. A possible solution is establishment of a 'Data Publishing Framework' which would encourage and recognise investments and efforts by institutions and individuals towards management, and publishing of primary scientific data potentially on a par with recognitions received for scholarly publications. DISCUSSION: This paper reviews the state-of-the-art of primary biodiversity data publishing, and conceptualises a 'Data Publishing Framework' that would help incentivise efforts and investments by institutions and individuals in facilitating free and open access to biodiversity data. It further postulates the institutionalisation of a 'Data Usage Index (DUI)', that would attribute due recognition to multiple players in the data collection/creation, management and publishing cycle. CONCLUSION: We believe that institutionalisation of such a 'Data Publishing Framework' that offers socio-cultural, legal, technical, economic and policy environment conducive for data publishing will facilitate expedited discovery and mobilisation of an exponential increase in quantity of 'fit-for-use' primary biodiversity data, much of which is currently invisible.

FindZebra: a search engine for rare diseases.

BACKGROUND: The web has become a primary information resource about illnesses and treatments for both medical and non-medical users. Standard web search is by far the most common interface to this information. It is therefore of interest to find out how well web search engines work for diagnostic queries and what factors contribute to successes and failures. Among diseases, rare (or orphan) diseases represent an especially challenging and thus interesting class to diagnose as each is rare, diverse in symptoms and usually has scattered resources associated with it. METHODS: We design an evaluation approach for web search engines for rare disease diagnosis which includes 56 real life diagnostic cases, performance measures, information resources and guidelines for customising Google Search to this task. In addition, we introduce FindZebra, a specialized (vertical) rare disease search engine. FindZebra is powered by open source search technology and uses curated freely available online medical information. RESULTS: FindZebra outperforms Google Search in both default set-up and customised to the resources used by FindZebra. We extend FindZebra with specialized functionalities exploiting medical ontological information and UMLS medical concepts to demonstrate different ways of displaying the retrieved results to medical experts. CONCLUSIONS: Our results indicate that a specialized search engine can improve the diagnostic quality without compromising the ease of use of the currently widely popular standard web search. The proposed evaluation approach can be valuable for future development and benchmarking. The FindZebra search engine is available at http://www.findzebra.com/.

Specialized tools are needed when searching the web for rare disease diagnoses.

In our recent paper, we study web search as an aid in the process of diagnosing rare diseases. To answer the question of how well Google Search and PubMed perform, we created an evaluation framework with 56 diagnostic cases and made our own specialized search engine, FindZebra (findzebra.com). FindZebra uses a set of publicly available curated sources on rare diseases and an open-source information retrieval system, Indri. Our evaluation and the feedback received after the publication of our paper both show that FindZebra outperforms Google Search and PubMed. In this paper, we summarize the original findings and the response to FindZebra, discuss why Google Search is not designed for specialized tasks and outline some of the current trends in using web resources and social media for medical diagnosis.

[Research activity in clinical biochemistry]. / Forskningsaktiviteten for speciallaeger i klinisk biokemi.

BACKGROUND: Quantitative bibliometric measurements of research activity are frequently used, e.g. for evaluating applicants for academic positions. The purpose of this investigation is to assess research activity within the medical speciality of Clinical Biochemistry by comparing it with a matched control group from other medical specialities in Denmark. MATERIALS AND METHODS: A list of all physicians registered in Denmark (23,127 persons) was drawn from the database "Laeger.dk". Of these, 5,202 were generalists (not included) while 11,691 were from other specialities. Of the 126 specialists from Clinical Biochemistry, 57 fulfilled the inclusion criteria. Each of these 57 was matched according to medical title with two randomly chosen specialists from other specialities, totaling 114. Using Medline and the Web of Science, the number of publications and the number of citations were then ascertained. RESULTS: 25% of the 11,691 specialists held a PhD degree or doctoral degree, DMSci, (Clinical Biochemistry: 61%). The 171 specialists included in the study had 9,823 papers in Medline and 10,140 papers in the Web of Science. The number of Medline papers per specialist was 71 for Clinical Biochemistry compared to 51 for the control group. The number of citations per specialist was 1,844 for Clinical Biochemistry compared to 816 for the control group. The top ten H-indices (of which 8 were in Clinical Biochemistry) ranged from 30 to 69. CONCLUSION: Both the number of papers and the number of citations were higher for Clinical Biochemistry than for the control group. The difference was most pronounced among professors.