Design and update of a classification system: the UCSD map of science

Global maps of science can be used as a reference system to chart career trajectories, the location of emerging research frontiers, or the expertise profiles of institutes or nations. This paper details data preparation, analysis, and layout performed when designing and subsequently updating the UCSD map of science and classification system. The original classification and map use 7.2 million papers and their references from Elsevier's Scopus (about 15,000 source titles, 2001-2005) and Thomson Reuters' Web of Science (WoS) Science, Social Science, Arts & Humanities Citation Indexes (about 9,000 source titles, 2001-2004)-about 16,000 unique source titles. The updated map and classification adds six years (2005-2010) of WoS data and three years (2006-2008) from Scopus to the existing category structure-increasing the number of source titles to about 25,000. To our knowledge, this is the first time that a widely used map of science was updated. A comparison of the original 5-year and the new 10-year maps and classification system show (i) an increase in the total number of journals that can be mapped by 9,409 journals (social sciences had a 80% increase, humanities a 119% increase, medical (32%) and natural science (74%)), (ii) a simplification of the map by assigning all but five highly interdisciplinary journals to exactly one discipline, (iii) a more even distribution of journals over the 554 subdisciplines and 13 disciplines when calculating the coefficient of variation, and (iv) a better reflection of journal clusters when compared with paper-level citation data. When evaluating the map with a listing of desirable features for maps of science, the updated map is shown to have higher mapping accuracy, easier understandability as fewer journals are multiply classified, and higher usability for the generation of data overlays, among others.     

I Publish in I Edit? - Do Editorial Board Members of Urologic Journals Preferentially Publish Their Own Scientific Work?

Scientists who are members of an editorial board have been accused of preferentially publishing their scientific work in the journal where they serve as editor. Reputation and academic standing do depend on an uninterrupted flow of published scientific work and the question does arise as to whether publication mainly occurs in the self-edited journal. This investigation was designed to determine whether editorial board members of five urological journals were more likely to publish their research reports in their own rather than in other journals. A retrospective analysis was conducted for all original reports published from 2001–2010 by 65 editorial board members nominated to the boards of five impact leading urologic journals in 2006. Publications before editorial board membership, 2001–2005, and publications within the period of time as an editorial board member, 2006–2010, were identified. The impact factors of the journals were also recorded over the time period 2001–2010 to see whether a change in impact factor correlated with publication locality. In the five journals as a whole, scientific work was not preferentially published in the journal in which the scientists served as editor. However, significant heterogeneity among the journals was evident. One journal showed a significant increase in the amount of published papers in the ‘own’ journal after assumption of editorship, three journals showed no change and one journal showed a highly significant decrease in publishing in the ‘own’ journal after assumption of editorship.     

Impact factor of Revista Iberoamericana de Micología

The impact factor is a bibliometric indicator published annually in the Journal Citation Reports, and widely regarded as a quality ranking of the journals included in this database. The problem with this indicator is that the impact factor of several journals not listed in the Science Citation Index database is largely unknown. The aim of this study was to analyze the 2001 national and international impact factor of Revista Iberoamericana de Micología. The National impact factor of Revista Iberoamericana de Micología was obtained by adding the number of cites in 2001 from a total of 87 Spanish medical journals of greater scientific quality. Also, bibliographical references from Spanish journals indexed in the 2001 Journal Citation reports database have been included to determine the international impact factor of this analyzed journal. Revista Iberoamericana de Micología received a total of 62 cites from published articles in 1999 to 2001, coming from 20 different journals, being their self-citation index 10.1%. The journal with the highest number of cites to Revista Iberoamericana de Micología was Journal of Clinical Microbiology, with 12 cites (19.3%). According to this findings the national and international impact factor of Revista Iberoamericana de Micología was 0.266 and 0.606, respectively. The impact factor of Revista Iberoamericana de Micología, although not included in the Science Citation Index database, was higher than other Journal Citation Reports. Moreover, Revista Iberoamericana de Micología received most of its citations from high impact factor journals included in the Journal Citation Reports database. These data support the international recognition of the scientific level of the journal.     

The rise of computational biology

The year 2001 saw a remarkable burst of interest in biological simulation, with several international meetings on the subject, and the inclusion, by journals, of web site references from which published models can be downloaded. So, why has all this happened so suddenly?     

生物信息学跨学科研究

目的:研究生物信息学起源、发展趋势,与其他学科相互交叉渗透关系的发展及强度。方法:利用美国《科学引文索引》(SCI)数据库web of science,运用文献计量学方法对8种权威生物信息学期刊2001年至2010年于2011年1月15日之前上传至webof science的全部文献进行统计及分析。通过研究生物信息学相关论文的主题分类,被引情况及施引文献的分类,寻找其跨学科的趋势及相关研究领域的进展情况、主要内容。结果:生物信息学的相关文献数在2001-2010间逐年增加,在2009-2010年达到高峰。跨学科领域广泛,并以生物化学、分子生物学、计算生物学、微生物学、数学、统计学等学科为主要交叉学科。各交叉学科与生物信息学之间跨学科研究的文献数也呈逐年递增趋势。结论:生物信息学的跨学科范围广泛,发展迅速。     

A tale of four stories: soil ecology, theory, evolution and the publication system

Background

Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals.

Findings

We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals.

Conclusion

This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate “particularity” (empirical observations) and “generality” (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary.     

Double-blind review favours increased representation of female authors

Double-blind peer review, in which neither author nor reviewer identity are revealed, is rarely practised in ecology or evolution journals. However, in 2001, double-blind review was introduced by the journal Behavioral Ecology. Following this policy change, there was a significant increase in female first-authored papers, a pattern not observed in a very similar journal that provides reviewers with author information. No negative effects could be identified, suggesting that double-blind review should be considered by other journals.     

Integrative Approach to Quality Assessment of Medical Journals Using Impact Factor,Eigenfactor, and Article Influence Scores

Background

Impact factor (IF) is a commonly used surrogate for assessing the scientific quality of journals and articles. There is growing discontent in the medical community with the use of this quality assessment tool because of its many inherent limitations. To help address such concerns, Eigenfactor (ES) and Article Influence scores (AIS) have been devised to assess scientific impact of journals. The principal aim was to compare the temporal trends in IF, ES, and AIS on the rank order of leading medical journals over time.

Methods

The 2001 to 2008 IF, ES, AIS, and number of citable items (CI) of 35 leading medical journals were collected from the Institute of Scientific Information (ISI) and the http://www.eigenfactor.org databases. The journals were ranked based on the published 2008 ES, AIS, and IF scores. Temporal score trends and variations were analyzed.

Results

In general, the AIS and IF values provided similar rank orders. Using ES values resulted in large changes in the rank orders with higher ranking being assigned to journals that publish a large volume of articles. Since 2001, the IF and AIS of most journals increased significantly; however the ES increased in only 51% of the journals in the analysis. Conversely, 26% of journals experienced a downward trend in their ES, while the rest experienced no significant changes (23%). This discordance between temporal trends in IF and ES was largely driven by temporal changes in the number of CI published by the journals.

Conclusion

The rank order of medical journals changes depending on whether IF, AIS or ES is used. All of these metrics are sensitive to the number of citable items published by journals. Consumers should thus consider all of these metrics rather than just IF alone in assessing the influence and importance of medical journals in their respective disciplines.     

Pluralism and diversity: trends in the use and application of ordination methods 1990‐2007

Question: What are the trends and patterns in the application of ordination techniques in vegetation science since 1990? Location: Worldwide literature analysis. Methods: Evaluation of five major journals of vegetation science; search of all ISI‐listed ecological journals. Data were analysed with ANCOVAs, Spearman rank correlations, GLMs, biodiversity indices and simple graphs. Results: The ISI search retrieved fewer papers that used ordinations than the manual evaluation of five selected journals. Both retrieval methods revealed a clear trend in increasing frequency of ordination applications from 1990 to the present. Canonical Correspondence Analysis was far more frequently detected by the ISI search than any other method. Applications such as Correspondence Analysis/Reciprocal Averaging and Detrended Correspondence Analysis have increasingly been used in studies published in “applied” journals, while Canonical Correspondence Analysis, Redundancy Analysis and Non‐Metric Multidimensional Scaling were more frequently used in journals focusing on more “basic” research. Overall, Detrended Correspondence Analysis was the most commonly applied method within the five major journals, although the number of publications slightly decreased over time. Use of Non‐Metric Multidimensional Scaling has increased over the last 10 years. Conclusion: The availability of suitable software packages has facilitated the application of certain techniques such as Non‐Metric Multidimensional Scaling. However, choices of ordination techniques are currently less driven by the constraints imposed by the software; there is also limited evidence that the choice of methods follows social considerations such as the need to use fashionable methods. Methodological diversity has been maintained or has even increased over time and reflects the researcher's need for diverse analytical tools suitable to address a wide range of questions.     

Negative changes in the scientific publication process in ecology: potential causes and consequences

1. Increasingly viewed to have societal impact and value, science is affected by complex changes such as globalisation and the increasing dominance of commercial interest. As a result, technical advancements, financial concerns, institutional prestige and journal proliferation have created challenges for ecological and other scientific journals and affected the perception of both researchers and the public about the science that they publish. 2. Journals are now used for more than dissemination of scientific research. Institutions use journal rankings for a variety of purposes and often require a pre‐established number of articles in hiring and budgetary decisions. Consequently, journal impact factors have achieved greater importance, and the splitting of articles into smaller parcels of information (‘salami‐slicing’) to increase numbers of publications has become more frequent. 3. Journals may prescribe upper limits to article length, even though the average length of articles for several ecological journals examined has increased over time. There are clear signs, however, that journals without length limits for articles will become rarer. In contrast to ecological journals, taxonomic journals are not following this trend. 4. Two case histories demonstrate how splitting longer ecological articles into a series of shorter ones results in both redundancy of information and actually increases the journal space used overall. Furthermore, with current rejection rates of ecological journals (often ～80%), many thin salami‐sliced articles jam the peer‐review system much longer (through resubmission after rejection) than unsliced articles previously did (e.g. when rejection rates were ～50%). In our experience, the increased pressure to publish many articles in ‘high‐impact’ journals also may decrease the attractiveness of a future scientific career in ecology to young people. 5. ‘Gatekeeping’ of journal quality has shifted from editors to reviewers, and several recent trends are apparent including: bias about appropriate statistical methods; reviewers being more rigid overall; non‐native English writers being criticised for poor communications skills; and favourable reviews being signed more often than unfavourable ones. In terms of production, outsourcing of copy editing has increased the final error rate of published material. 6. We supplemented our perceptions with those of older colleagues (～100 experienced ecologists) that responded to an informal survey on this topic (response rate: 81%). In the opinion of almost 90% of our respondents, the overall review process has changed and for 20% among them the professional quality of reviews has declined. 7. We, and many older colleagues, are convinced there have been some negative changes in the scientific publication process. If younger colleagues share this concern, we can collectively counter this deteriorating situation, because we are the key to the publishing and evaluation process.     

Research blogs and the discussion of scholarly information

The research blog has become a popular mechanism for the quick discussion of scholarly information. However, unlike peer-reviewed journals, the characteristics of this form of scientific discourse are not well understood, for example in terms of the spread of blogger levels of education, gender and institutional affiliations. In this paper we fill this gap by analyzing a sample of blog posts discussing science via an aggregator called ResearchBlogging.org (RB). ResearchBlogging.org aggregates posts based on peer-reviewed research and allows bloggers to cite their sources in a scholarly manner. We studied the bloggers, blog posts and referenced journals of bloggers who posted at least 20 items. We found that RB bloggers show a preference for papers from high-impact journals and blog mostly about research in the life and behavioral sciences. The most frequently referenced journal sources in the sample were: Science, Nature, PNAS and PLoS One. Most of the bloggers in our sample had active Twitter accounts connected with their blogs, and at least 90% of these accounts connect to at least one other RB-related Twitter account. The average RB blogger in our sample is male, either a graduate student or has been awarded a PhD and blogs under his own name.     

Editorial

These are heady times. As the new millennium dawns, the field of zoology is more exciting than ever. Phylogenetic relations among animals are rapidly being refined or revised in light of new data and powerful new analyses. These revelations in turn are rekindling interest in the function, development, and evolution of animals from all branches of the zoological tree. Tools and insights derived from work on a few model organisms are being applied widely to fill in significant gaps in our knowledge about how the astonishing diversity of animal characteristics evolved.Paralleling this new excitement is an upheaval in scientific publishing. Increasingly specialized journals are sprouting up worldwide as publishers rush to embrace emerging areas of excitement. Electronic communication is re-defining expectations about how new knowledge is disseminated both in format and in mode of transmission and about the time from submission to publication. For established journals to survive, they too must evolve.This journal, ZOOLOGY, is evolving to meet the needs and expectations of the modern community of animal biologists. It aims to promote research like that of it's founder J.W. Spengel — that explicitly emphasizes comparative aspects of animal biology. With the rapid growth of phylogenetic information, ZOOLOGY now offers a venue where the full impact of recent phylogenetic advances on our understanding of animal form, function, development, and evolution can be addressed. An ambitious new group of editors, a new advisory board, and a professionally staffed editorial office, are working to rejuvenate ZOOLOGY as an internationally recognized leader in comparative animal biology.ZOOLOGY has a distinguished place in the pantheon of animal biology journals. It ranks among the oldest continuously published journals in Germany. Founded in 1886 as Zoologische Jahrbücher it quickly rose to prominence among European zoological journals. In the early 1990's, after political and social upheavaling some European countries and after the reunification of Germany, the journal took a more international approach under a new title, ZOOLOGY — ANALYSIS OF COMPLEX SYSTEMS (ZACS). For the last four years, ZOOLOGY has also worked in close cooperation with the German Zoological Society and this tradition will continue. Once each year, it will publish review lectures presented at the annual meeting of the Society. A supplement to ZOOLOGY, containing the abstracts of oral and poster presentations of the annual meeting, will also be produced in conjunction with the German Zoological Society.But the new ZOOLOGY also recognizes the increasing importance of rapid and international communication in all areas of animal biology. It therefore aims to reduce publication time drastically and to enhance the speed and rigor of the review process. The new editors and editorial board are committed to maintaining the highest scientific standards and also to remaining flexible enough to adjust to the ever changing field of animal biology. Recognizing the increasing importance of rapid, effective, international communication, the new ZOOLOGY will offer:— the highest scientific standards— a short review time— a publication time schedule of three months after acceptance— color plates free of charge (at the editors' discretion)— an online version published in advance of the printed journal— free E-mail Table of Contents alerts so papers are widely publicized— papers abstracted/indexed by all the major scientific indexing servicesAs the new cover and the more accessible layout inside this issues show, the change has already begun. The future holds great promise for animal biology. Join us as Zoology strives to fulfil that promise.Spring 2001J. Matthias StarckThomas C. BoschA. Richard PalmerKiyokazu Agata     

Bioorganic chemistry: Institutes,journals, publications,a short scientific metric analysis <Emphasis Type="Italic">on the 50th anniversary of the Institute of Natural Compound Chemistry,Institute of Bioorganic Chemistry</Emphasis>

An attempt to illustrate the development of bioorganic chemistry in Russia and all over the world has been made. The development of a new field of science was accompanied by the emergence of specialized journals, organizations, departments and institutions for research in this field. A brief report about the four most important world journals on bioorganic chemistry is represented. The analysis of publications of world scientific institutions, having the word “bioorganic” in their title since 1972 to the middle of 2008, has been made with the help of information from Web Science. The publication distribution among countries, institutions, languages, journals, and the list of the most productive authors clearly demonstrate the leading role of the USSR and Russia and of the Institute of Natural Compound Chemistry, Institute of Bioorganic Chemistry, in the creation and development of this field of science in the world. The publication distribution among the areas of knowledge displays a close connection between bioorganic chemistry and a number of the other fields of science, first of all, biochemistry and molecular biology, and also organic chemistry.     

中国大陆鸟类栖息地选择研究十年

栖息地选择研究一直是鸟类生态学研究的重要内容之一。通过对2001年1月至2010年12月10年期间中国大陆鸟类学家在国内外期刊上发表的鸟类栖息地选择研究的论文进行分析,对我国鸟类栖息地选择研究提出展望。10年间,我国鸟类学家共发表有关鸟类栖息地选择或利用的论文170篇,共涉及到鸟类10目31科73种。在这10年里,中国大陆有关鸟类栖息地选择或利用的文章持续增长。然而,我国鸟类栖息地选择的研究也存在着如下问题:(1)存在栖息地选择和栖息地利用误用的现象,这种现象在10年内并无明显改善;(2)在选择研究方法时,很少考虑个体的可获得性、种群密度及抽样尺度对栖息地选择的影响;(3)大多数的栖息地选择的论文没有对鸟类的栖息地选择行为进行研究,也缺乏对其选择的适合度背景去进行研究。根据这些问题,对我国未来的鸟类栖息地选择研究提出了建议。     

Inflated impact factors? The true impact of evolutionary papers in non-evolutionary journals

Amongst the numerous problems associated with the use of impact factors as a measure of quality are the systematic differences in impact factors that exist among scientific fields. While in theory this can be circumvented by limiting comparisons to journals within the same field, for a diverse and multidisciplinary field like evolutionary biology, in which the majority of papers are published in journals that publish both evolutionary and non-evolutionary papers, this is impossible. However, a journal's overall impact factor may well be a poor predictor for the impact of its evolutionary papers. The extremely high impact factors of some multidisciplinary journals, for example, are by many believed to be driven mostly by publications from other fields. Despite plenty of speculation, however, we know as yet very little about the true impact of evolutionary papers in journals not specifically classified as evolutionary. Here I present, for a wide range of journals, an analysis of the number of evolutionary papers they publish and their average impact. I show that there are large differences in impact among evolutionary and non-evolutionary papers within journals; while the impact of evolutionary papers published in multidisciplinary journals is substantially overestimated by their overall impact factor, the impact of evolutionary papers in many of the more specialized, non-evolutionary journals is significantly underestimated. This suggests that, for evolutionary biologists, publishing in high-impact multidisciplinary journals should not receive as much weight as it does now, while evolutionary papers in more narrowly defined journals are currently undervalued. Importantly, however, their ranking remains largely unaffected. While journal impact factors may thus indeed provide a meaningful qualitative measure of impact, a fair quantitative comparison requires a more sophisticated journal classification system, together with multiple field-specific impact statistics per journal.     

Pseudoreplication in ecological research: the problem overlooked by Russian scientists

The use of differential statistics to test for treatment effect with data from experiments where either treatments were not replicated (though samples may be) or replicates are not statistically independent leads to serious methodological problem. This problem, discovered by Hurbert (1984), is called pseudoreplication. Due to unknown reasons, pseudoreplication issue was completely overlooked by the Russian ecologists, in spite of the fact that the international scientific community is aware of pseudoreplication for almost twenty years. As the result, up to 47% of the experimental ecological papers, published in six Russian academic journals (Botanicheskij zhurnal, Ekologia, Izvestija RAN Ser. Biol., Lesovedenie, Zhurnal Obshchei Biologii, Zooligicheskij zhurnal) in 1998-2001, are pseudoreplicated; this proportion is nearly twice as high as the proportion of pseudoreplicated studies in international journals during 1960-1980, e.g. before the problem was discovered by Hurlbert (1984). This situation is alarming, especially because a substantial part of pseudoreplication arise from incorrect use of statistics, not from incorrect designing of experiments. By using several examples from the recent papers of Russian ecologists I shortly review the situations where pseudoreplication may occur and discuss some aspects of the experimental design, which are critical for correct processing and interpretation of ecological data.     

Making a new technology work: the standardization and regulation of microarrays

The translation of laboratory innovations into clinical tools is dependent upon the development of regulatory arrangements designed to ensure that the new technology will be used reliably and consistently. A case study of a key post-genomic technology, gene chips or microarrays, exemplifies this claim. The number of microarray publications and patents has increased exponentially during the last decade and diagnostic microarray tests already are making their way into the clinic. Yet starting in the mid-1990s, scientific journals were overrun with criticism concerning the ambiguities involved in interpreting most of the assumptions of a microarray experiment. Questions concerning platform comparability and statistical calculations were and continue to be raised, in spite of the emergence by 2001 of an initial set of standards concerning several components of a microarray experiment. This article probes the history and ongoing efforts aimed at turning microarray experimentation into a viable, meaningful, and consensual technology by focusing on two related elements: