A refinement strategy for identification of scientific software from bioinformatics publications

In the field of bioinformatics, a large number of classical software becomes a necessary research tool. To measure the influence of scientific software as one kind of important intellectual products, a few strategies have been proposed to identify the software names from full texts of papers to collect the usage data of packages in bioinformatics research. However, the performance of these strategies is limited because of the highly imbalance of data in the full texts. This study proposes EnsembleSVMs-CRF, a two-step refinement strategy based on ensemble learning that gradually increases the sentences that contain software mentions to improve the performance of named entity recognition. The experiment on the bioinformatics corpus shows that the performance of EnsembleSVMs-CRF, in terms of the local F1 (78.81%) and the global F1-A (73.49%), is superior to the rule-based bootstrapping method and direct CRF. Application of this strategy to the articles published between 2013 and 2017 in 27 bioinformatics journals extracted 8,239 unique packages. The most popular 50 packages thus identified demonstrate that most of them are professional software which generally requires inter-discipline knowledge, rather than programming skill. Meanwhile, we found that researchers in bioinformatics tend to use free scientific software, and the application of general software is increasing compared with professional software.

     

Learning about learning: patterns of sharing of research knowledge among Education,Border, and Cognitive Science fields

This study explores the patterns of exchange of research knowledge among Education Research, Cognitive Science, and what we call “Border Fields.” We analyze a set of 32,121 articles from 177 selected journals, drawn from five sample years between 1994 and 2014. We profile the references that those articles cite, and the papers that cite them. We characterize connections among the fields in sources indexed by Web of Science (WoS) (e.g., peer-reviewed journal articles and proceedings), and connections in sources that are not (e.g., conference talks, chapters, books, and reports). We note five findings—first, over time the percentage of Education Research papers that extensively cite Cognitive Science has increased, but the reverse is not true. Second, a high percentage of Border Field papers extensively cite and are cited by the other fields. Border Field authors’ most cited papers overlap those most cited by Education Research and Cognitive Science. There are fewer commonalities between Educational research and Cognitive Science most cited papers. This is consistent with Border Fields being a bridge between fields. Third, over time the Border Fields have moved closer to Education Research than to Cognitive Science, and their publications increasingly cite, and are cited by, other Border Field publications. Fourth, Education Research is especially strongly represented in the literature published outside those WoS-indexed publications. Fifth, the rough patterns observed among these three fields when using a more restricted dataset drawn from the WoS are similar to those observed with the dataset lying outside the WoS, but Education Research shows a far heavier influence than would be indicated by looking at WoS records alone.

     

Scopes of accounting journals and published papers: what do they signalize?

Our main objective is to create a framework to analyze signals sent from academic journals. The signals chosen for the framework were: journal’ scopes; and the latest published papers. We apply the framework to the field of accounting with the main focus of categorizing the journal scopes and the latest published articles into research topics by using text mining techniques. We analyze the published papers of research topics in accounting journals during the 2016–2018 period. Another objective is to compare research topics from the last published papers with research topics identified in accounting journal scopes. We found a majority of journals with a broader scope in terms of accounting research areas, but we see a concentration on specific research topics by analyzing the papers. In addition, the most signaled accounting areas in scopes are financial accounting and auditing. The framework helps us categorize 5270 research papers into accounting research topics correctly, faster than manually reading titles, abstracts, and keywords. While specific scopes may carry the risk of missing new research trends, broad scopes may require more reviewers from different research areas. Diversity can be seen as applying other methodological choices, theoretical lenses, and conceptual or empirical research approaches. We believe that academic diversity is for the benefit of accounting research.

     

Industrial Engineering and Research Oriented Journal I Operations I Literature: A Statistical Analysis

This paper reports the results of a statistical analysis of literature published in three journals important to OR-oriented Industrial Engineers. Over 1500 journal articles, technical notes, and letters to the editor published during the five-year period 1969-1973 were scanned for specific elements of information by which OR research and literature could be characterized. Some of the factors examined were (1) the theory/application emphasis, (2) author affiliation, (3) source of any research funding, and (4) time interval between submission and publication. This analysis reveals the IE role in OR research and publications, pointing out the applications orientation of IE-contributed literature.     

Modeling the obsolescence of research literature in disciplinary journals through the age of their cited references

There are different citation habits in the research fields that influence the obsolescence of the research literature. We analyze the distinctive obsolescence of research literature in disciplinary journals in eight scientific subfields based on cited references distribution, as a synchronous approach. We use both negative binomial (NB) and Poisson distributions to capture this obsolescence. The corpus being examined is published in 2019 and covers 22,559 papers citing 872,442 references. Moreover, three measures to analyze the tail of the distribution are proposed: (i) cited reference survival rate, (ii) cited reference mortality rate, and (iii) cited reference percentile. These measures are interesting because the tail of the distribution collects the behavior of the citations at the time when the document starts to get obsolete in the sense that it is little cited (used). As main conclusion, the differences observed in obsolescence are so important even between disciplinary journals in the same subfield, that it would be necessary to use some measure for the tail of the citation distribution, such as those proposed in this paper, when analyzing in an appropriate way the long time impact of a journal.

     

Industrial Engineering and Research Oriented Journal I Operations I Literature: A Statistical Analysis

This paper reports the results of a statistical analysis of literature published in three journals important to OR-oriented Industrial Engineers. Over 1500 journal articles, technical notes, and letters to the editor published during the five-year period 1969-1973 were scanned for specific elements of information by which OR research and literature could be characterized. Some of the factors examined were (1) the theory/application emphasis, (2) author affiliation, (3) source of any research funding, and (4) time interval between submission and publication. This analysis reveals the IE role in OR research and publications, pointing out the applications orientation of IE-contributed literature.     

Information extraction from scientific articles: a survey

In last few decades, with the advent of World Wide Web (WWW), world is being overloaded with huge data. This huge data carries potential information that once extracted, can be used for betterment of humanity. Information from this data can be extracted using manual and automatic analysis. Manual analysis is not scalable and efficient, whereas, the automatic analysis involves computing mechanisms that aid in automatic information extraction over huge amount of data. WWW has also affected overall growth in scientific literature that makes the process of literature review quite laborious, time consuming and cumbersome job for researchers. Hence a dire need is felt to automatically extract potential information out of immense set of scientific articles to automate the process of literature review. Therefore, in this study, aim is to present the overall progress concerning automatic information extraction from scientific articles. The information insights extracted from scientific articles are classified in two broad categories i.e. metadata and key-insights. As available benchmark datasets carry a significant role in overall development in this research domain, existing datasets against both categories are extensively reviewed. Later, research studies in literature that have applied various computational approaches applied on these datasets are consolidated. Major computational approaches in this regard include Rule-based approaches, Hidden Markov Models, Conditional Random Fields, Support Vector Machines, Naïve-Bayes classification and Deep Learning approaches. Currently, there are multiple projects going on that are focused towards the dataset construction tailored to specific information needs from scientific articles. Hence, in this study, state-of-the-art regarding information extraction from scientific articles is covered. This study also consolidates evolving datasets as well as various toolkits and code-bases that can be used for information extraction from scientific articles.

     

The story behind Oncotarget? A bibliometric analysis

Being the most proliferative journal of oncology a cancer research of the past decade, the Open Access journal Oncotarget had reached more than 20,000 publications and a relatively high impact factor score in the past years. In 2018, the journal citation report decided to withdraw the status of an impact factor journal. Since there was a large discussion in the scientific community and specific reasons for the withdrawal were not stated, this bibliometric analysis was performed to assess if Oncotarget exhibits any differences in its bibliometric structure compared to other journals. For this purpose, we used the “New Quality and Quantity Indices in Sciences” platform and analyzed 20,000 Oncotarget articles. Density equalizing mapping technique helps to construct maps of cancer research in Oncotarget and shows that it has led to a unique global landscape which is not asymmetrically dominated by the Western hemisphere but exhibits a publishing architecture with a pronounced emphasis on Chinese articles.

     

Bibliometric analysis of the journal literature on women’s studies

This study uses bibliometric techniques to investigate the characteristics and implications of women’s studies literature over the period from 1900 to 2013. Using computer analysis for bibliometric techniques, the results of the present study demonstrate that the journal literature on women’s studies has grown exponentially, with an annual growth rate of 10.6% for over one century. Most of the document types in the area of women’s studies are in the form of research articles, review articles and book reviews. The United States of America and the United Kingdom contribute the largest number of articles. One hundred and seventeen core journals containing 33% of the women’s studies journal articles have been identified through the application of Bradford’s law on journal distribution. More than half of the 117 core journals began publishing from 1970 to 1990, and most of these core journals deal with the humanities (including literature, history and philosophy), women’s studies, medical science, psychology, political science and sociology. The highly productive journals associated with highly cited times are Signs: Journal of Women in Culture and Society, Women’s Studies International Forum, Sex Roles, Feminism and Psychology, Gender and Society, European Journal of Women’s Studies, American Historical Review, Psychology of Women Quarterly and Feminist Studies.     

Citation patterns in the Kuwaiti journal Medical Principles and Practice: The first 12 years, 1989-2000

This study investigates the citation patterns in the journal, Medical Principles and Practice from its inception in 1989 through 2000 (volumes 1-9). The data set includes 4740 references appended to the 221 original research articles. All of the citations were entered into a ProCite database for analysis. Specifically, this study addresses: (1) bibliometric patterns of cited works in terms of publication format, subject scatter, authorship characteristics, age of citations, geographic distribution, and language distribution; (2) productivity of journal titles; (3) the role of self-citation; and (4) how selected bibliometric indicators apply. Some of the findings include: journal articles are most frequently cited; English language publications dominate the literature; there is a trend of multiple authorship; and the pattern of aging is below the norm for medical literature. The results of the study can provide a benchmark to measure the user behavior of a particular group of researchers as well as for the provision of collection development and management decisions. This revised version was published online in August 2006 with corrections to the Cover Date.     

Studying the international diffusion of a national scientific journal

The purpose of this paper is to apply concepts of the diffusion of innovations research in thestudy of the international diffusion of a formerly national scientific journal, Annales ZoologiciFennici. The study was conducted using bibliometric methodology. The diffusion of the journalwas described through citations of the journal and through the development of the nationaldistribution of its contributors. The compatibility of the journal as well as the decrease ofcomplexity were found to have an influence on diffusion. Bibliometric methods were able torepresent the international diffusion of a scientific journal.     

Knowledge context,learning and innovation: an integrating framework

Abstract

In this conceptual paper, we develop a framework which identifies those elements of firms’ knowledge context which are important for innovation, and the mechanisms through which that knowledge impacts on firms’ innovation performance. We make four main contributions to the existing literature. First, our characterisation of knowledge context provides the basis for a more specific identification of which elements of firms’ knowledge environment are important for innovation, discriminating between spatial, sectoral and network influences. Second, we reflect the role of innovation ambition in shaping firms’ knowledge search strategies. Third, we differentiate between firms’ interactive and non-interactive knowledge search activities and recognise that these may be complemented by unanticipated and serendipitous knowledge spillovers. Finally, we employ the notion of encoding capacity to reflect firms’ internal ability to assimilate and apply external knowledge, and clarify its distinctiveness from the more general concept of absorptive capacity. Our framework provides an integrating mechanism for existing empirical studies, and suggests a number of new research directions related to the determinants of innovation performance and the heterogeneity of innovation outcomes.     

The blockbuster hypothesis: influencing the boundaries of knowledge

We argue that the creation of new knowledge is both difficult and rare. More specifically, we posit that the creation of new knowledge is dominated by a few key insights that challenge the way people think about an idea; generating high interest and use. We label this the blockbuster hypothesis. Using two large samples of published management studies over the period 1998–2007 we find support for the blockbuster hypothesis. We also find that numerous studies in the leading management journals are flops, having little impact on the profession as measured using citation data. Additional tests indicate that journal “quality” is related to the ratio of blockbusters to flops a journal publishes and that journal rankings are a poor proxy for study influence. Consistent with the notion that editorial boards are able to identify new knowledge, we find that research notes significantly under-perform articles in both the same journal and articles published in lower ranked journals. Taken together, the results imply that only a few scientific studies, out of the thousands published in a given area, change or influence the boundaries of knowledge, with many appearing to have little impact on the frontiers of knowledge. Overall, this analysis indicates that the development of new knowledge is rare even though it appears to be recognizable to knowledge gatekeepers like journal editors.     

Research status and characteristics of library and information science in Taiwan: a bibliometric analysis

This study determines how library and information science (LIS) research in Taiwan has changed between 2001 and 2010. The major research questions address the research status of LIS in Taiwan, how the Taiwanese government supports the field, and the collaborative authorship of LIS journal articles in Taiwan. Bibliometric and content analysis methods were conducted to analyze 2,494 journal articles, 983 theses, and 191 research projects between 2001 and 2010. The results show LIS and Technology to be the most popular topics in journal articles. The most well-received thesis topics are LIS and Technology and User Services, accounting for more than 50?% of graduate theses. The same is true for research projects, with the subjects of LIS and Technology, LIS Theory and Foundation, and User Services having a ratio of more than 70?%. In government-sponsored research projects, the average amount of funding obtained had no significant differences or tendencies for various subjects over time. In authorship of journal articles, individual researchers conducted 66.11?% of articles in key LIS scholarly journals in Taiwan between 2001 and 2010.     

When the search for truth fails: A computer simulation of the impact of the publication bias on the meta-analysis of scientific literature

The production of scientific knowledge is a complex social process, where many actors contribute by their publications to the disclosure of the hidden truth. However, due to different methods, analysed samples, and control variables, empirical findings from this process are often contradictory. Thus, quantitative sciences use meta-analyses in order to extract the likely truth from a corpus of publications about a given research question. Unfortunately, this procedure is often impaired by different forms of the so-called publication bias: papers with null-results are sometimes not published due to the publication policy of journal editors and their boards. Similarly, articles with a high news value may have a better chance of being published, even if their findings finally prove to be wrong. Thus the publications used for meta-analyses are often distorted and lead to wrong conclusions about the truth. For this reason the present article develops a formal model of the effects of the publication bias on the results of meta-analyses. It is successfully tested with empirical data and used for studying the conditions, under which meta-analyses disclose, obscure, or revert the underlying truth. As a main result of the related computer simulations it turns out that the publication bias has for true zero-relations other consequences than for true non-zero relations. Moreover, there are situations where certain forms of the publication bias have unexpectedly favourable effects on the disclosure of the truth by meta-analyses.

     

Materials influence on design: A decade of development

This review paper evaluates the current status of the exploitation of engineering materials for design purposes with respect to developments in the respective disciplines, through a structured review of the content of Materials & Design journal over 30 years of publication. This review updates strategically the two previous reviews, with an emphasis this time placed on changes occurring over the last 10 years, making appropriate reference to the earlier investigations to explain noteworthy developments. The new information presented is again derived from the abundance of technical knowledge contained from within the many varied and growing number of high quality articles in the journal, supplemented by the author’s personal comments and experience of the field.     

Open access uptake in Germany 2010–2018: adoption in a diverse research landscape

This study investigates the development of open access (OA) to journal articles from authors affiliated with German universities and non-university research institutions in the period 2010–2018. Beyond determining the overall share of openly available articles, a systematic classification of distinct categories of OA publishing allowed us to identify different patterns of adoption of OA. Taking into account the particularities of the German research landscape, variations in terms of productivity, OA uptake and approaches to OA are examined at the meso-level and possible explanations are discussed. The development of the OA uptake is analysed for the different research sectors in Germany (universities, non-university research institutes of the Helmholtz Association, Fraunhofer Society, Max Planck Society, Leibniz Association, and government research agencies). Combining several data sources (incl. Web of Science, Unpaywall, an authority file of standardised German affiliation information, the ISSN-Gold-OA 3.0 list, and OpenDOAR), the study confirms the growth of the OA share mirroring the international trend reported in related studies. We found that 45% of all considered articles during the observed period were openly available at the time of analysis. Our findings show that subject-specific repositories are the most prevalent type of OA. However, the percentages for publication in fully OA journals and OA via institutional repositories show similarly steep increases. Enabling data-driven decision-making regarding the implementation of OA in Germany at the institutional level, the results of this study furthermore can serve as a baseline to assess the impact recent transformative agreements with major publishers will likely have on scholarly communication.

     

An innovative approach to identify the knowledge diffusion path: the case of resource-based theory

This study presents an innovative approach for identifying the knowledge diffusion path of a target research field. We take the resource-based theory (RBT) as an example to demonstrate the usefulness of this methodology. Several survey studies have provided valuable summarization and commentaries to the RBT from different perspectives. These analyses are useful and pertinent for understanding the development of RBT. However, limited by the methodologies they used, previous scholars can only select part of the RBT literature to conduct the survey work. To eliminate the limitation, this study develops an innovative approach which can handle thousands of articles. This study analyzes a dataset including 2,105 theoretical developments, empirical studies, and review papers to explore the knowledge diffusion path of the RBT. Citation data are used to build the citation network. Main paths are then probed and visualized via social network analysis methodology. To figure out the total picture of the knowledge diffusion path, this study integrates various main path analyses to supplement the traditional approach. The traditional main path analysis investigates the knowledge diffusion from a local view. The global analysis provides a main path from a macro view. The key-route analysis helps explore and clarify a complete picture of the convergence-divergence phenomena. We believe that through this novel tool, new researchers can easily identify the papers that have made major contributions to RBT knowledge diffusion and uncover the interrelationships among them.