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by Kshitish Acharya, Akhilesh Bajpai, Sravanthi Davuluri, et al.Haritha Haridas, Greta Kasliwal, Deepti, Sreelakshmi Ks, Darshan Chandrashekar, Pranami Bora, Mohammed Farouk, Neelima Chitturi, Samudyata, ArunNehru Kp, Kshitish Acharya, Akhilesh K. Bajpai, Sravanthi Davuluri, Haritha Haridas, Greta Kasliwal, H. Deepti, K. S. Sreelakshmi, Darshan S. Chandrashekar, Pranami Bora, Mohammed Farouk, Neelima Chitturi, V. Samudyata, K. P. ArunNehru, Kshitish K. Acharya
Abstract
BackgroundCollecting scientific publications related to a specific topic is crucial for different phases of research, health care and ‘effective text mining’. Available bio-literature search engines vary in their ability to scan different sections of articles, for the user-provided search terms and/or phrases. Since a thorough scientific analysis of all major bibliographic tools has not been done, their selection has often remained subjective. We have considered most of the existing bio-literature search engines (http://www.shodhaka.com/startbioinfo/LitSearch.html) and performed an extensive analysis of 18 literature ...
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Abstract
The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology ...
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Serials: The Journal for the Serials Community, Vol. 24, No. 1. (1 March 2011), pp. 21-25, doi:10.1629/2421
Abstract
The web has changed our information-seeking behaviour radically, yet scholarly communication remains firmly embedded in the traditions of the print world. Here, I argue that the dropping costs of publication and distribution mean that effort and resource expended on preventing publication is wasted and that developing the tools and culture for post-publication annotation, curation and ranking is more productive. Rather than see this as information overload, or in Clay Shirky's words, a ‘filter failure’, I propose that it is more useful ...
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Abstract
Recent developments in Web technology can be used for semantic enhancement of scholarly journal articles, by aiding publication of data and metadata and providing 'lively' interactive access to content. Such semantic enhancements are already being undertaken by leading STM publishers, and automated text processing will help these enhancements become affordable and routine. Publisher, editor, and author all have primary roles in that process; an incremental approach is needed. Publication of data and metadata to the Web make possible added-value 'ecosystem services'; ...
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J Participat Med, Vol. 1, No. 1. (2009)
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by P. S. Blackawton, S. Airzee, A. Allen, et al.S. Baker, A. Berrow, C. Blair, M. Churchill, J. Coles, -J, L. Fraquelli, C. Hackford, A. Hinton Mellor, M. Hutchcroft, B. Ireland, D. Jewsbury, A. Littlejohns, G. M. Littlejohns, M. Lotto, J. McKeown, A. O'Toole, H. Richards, L. Robbins-Davey, S. Roblyn, H. Rodwell-Lynn, D. Schenck, J. Springer, A. Wishy, T. Rodwell-Lynn, D. Strudwick, R. B. Lotto
Abstract
Background Real science has the potential to not only amaze, but also transform the way one thinks of the world and oneself. This is because the process of science is little different from the deeply resonant, natural processes of play. Play enables humans (and other mammals) to discover (and create) relationships and patterns. When one adds rules to play, a game is created. This is science: the process of playing with rules that enables one to reveal previously unseen patterns of ...
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Abstract
This paper presents the first meta-analysis for the inter-rater reliability (IRR) of journal peer reviews. IRR is defined as the extent to which two or more independent reviews of the same scientific document agree. ...
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Abstract
Scientific writing is an essential part of a student’s and researcher’s everyday life. In this paper we investigate the particularities of scientific writing and explore the features and limitations of existing tools for scientific writing. Deriving from this analysis and an online survey of the scientific writing processes of students and researchers at the University of Paderborn, we identify key principles to simplify scientific writing and reviewing. Finally, we introduce a novel approach to support scientific writing with a tool called ...
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Abstract
We report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. The approach has been applied to the genome of Mycobacterium tuberculosis (M.tb), the causative agent of one of today's most widely spread infectious diseases. The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’. The TB-drugome reveals that approximately one-third of the drugs examined have ...
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(30 May 2005)
Abstract
This is a report about the use and misuse of citation data in the assessmentof scientific research. The idea that research assessment must be done using“simple and objective” methods is increasingly prevalent today. The “simpleand objective” methods are broadly interpreted as bibliometrics, that is,citation data and the statistics derived from them. There is a belief thatcitation statistics are inherently more accurate because they substitute simplenumbers for complex judgments, and hence overcome the possible subjectivity ofpeer review. But this belief is unfounded. ...
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posted to citation
by mfenner
to the group Gobbledygook
on 2010-11-29 22:38:04
Abstract
BACKGROUND: Most journals try to improve their articles by technical editing processes such as proof-reading, editing to conform to 'house styles', grammatical conventions and checking accuracy of cited references. Despite the considerable resources devoted to technical editing, we do not know whether it improves the accessibility of biomedical research findings or the utility of articles. This is an update of a Cochrane methodology review first published in 2003. OBJECTIVES: To assess the effects of technical editing on research reports in peer-reviewed ...
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posted to no-tag
by mfenner
to the group Gobbledygook
on 2010-11-27 10:24:11
Abstract
Abstract 10.1002/biuz.200890080.abs Mit dem im Jahr 2005 geprägten Begriff Web 2.0 ist eine veränderte Nutzung des Internets gemeint, bei der die Inhalte in zunehmendem Maße vom Nutzer selbst erstellt werden. Typische Beispiele sind Blogs und Wikis, die sich ebenso wie andere Web 2.0-Anwendungen hervorragend zur Unterstützung des Unterrichts an Schulen und Universitäten eignen. ...
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Abstract
Fertilization of mammalian eggs is followed by successive cell divisions and progressive differentiation, first into the early embryo and subsequently into all of the cell types that make up the adult animal. Transfer of a single nucleus at a specific stage of development, to an enucleated unfertilized egg, provided an opportunity to investigate whether cellular differentiation to that stage involved irreversible genetic modification. The first offspring to develop from a differentiated cell were born after nuclear transfer from an embryo-derived cell ...
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Abstract
10.1126/science.1178927 ...
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by Johanna R. McEntyre, Sophia Ananiadou, Stephen Andrews, et al.William J. Black, Richard Boulderstone, Paula Buttery, David Chaplin, Sandeepreddy Chevuru, Norman Cobley, Lee-Ann A. Coleman, Paul Davey, Bharti Gupta, Lesley Haji-Gholam, Craig Hawkins, Alan Horne, Simon J. Hubbard, Jee-Hyub H. Kim, Ian Lewin, Vic Lyte, Ross MacIntyre, Sami Mansoor, Linda Mason, John McNaught, Elizabeth Newbold, Chikashi Nobata, Ernest Ong, Sharmila Pillai, Dietrich Rebholz-Schuhmann, Heather Rosie, Rob Rowbotham, C. J. Rupp, Peter Stoehr, Philip Vaughan
Abstract
UK PubMed Central (UKPMC) is a full-text article database that extends the functionality of the original PubMed Central (PMC) repository. The UKPMC project was launched as the first 'mirror' site to PMC, which in analogy to the International Nucleotide Sequence Database Collaboration, aims to provide international preservation of the open and free-access biomedical literature. UKPMC (http://ukpmc.ac.uk) has undergone considerable development since its inception in 2007 ...
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Abstract
Is there a means of assessing research impact beyond citation analysis? The case study took place at the Washington University School of Medicine Becker Medical Library. This case study analyzed the research study process to ...
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Abstract
Transparency in reporting of conflict of interest is an increasingly important aspect of publication in medical journals. Publication of large industry-supported trials may generate many citations and journal income through reprint sales and thereby be a source of conflicts of interest for journals. We investigated industry-supported trials' influence on journal impact factors and revenue. We sampled six major medical journals (Annals of Internal Medicine, Archives of Internal Medicine, BMJ, JAMA, The Lancet, and New England Journal of Medicine [NEJM]). For each ...
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posted to open_access
by mfenner
to the group Gobbledygook
on 2010-10-26 19:35:06
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Abstract
GREGORY PETSKO BEMOANS THE RISE OF THE TWITTERING CLASSES.: ...
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Abstract
LESSONS IN PERSONAL GENOME ANALYSIS, SOCIAL NETWORKING OR HEALTH INFORMATION?: ...
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Abstract
A RECENTLY DEPARTED GENOME BIOLOGIST DISCUSSES THE IMPACT FACTOR OF HIS LIFE WITH ST PETER AT THE PEARLY GATES.: ...
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Abstract
BACKGROUND: JAMA introduced a requirement for independent statistical analysis for industry-funded trials in July 2005. We wanted to see whether this policy affected the number of industry-funded trials published by JAMA. METHODS AND FINDINGS: We undertook a retrospective, before-and-after study of published papers. Two investigators independently extracted data from all issues of JAMA published between 1 July 2002 and 30 June 2008 (i.e., three years before and after the policy). They were not blinded to publication date. The randomized controlled trials ...
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Abstract
CiTO, the Citation Typing Ontology, is an ontology for describing the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and also to Web information resources, and for publishing these descriptions on the Semantic Web. Citation are described in terms of the factual and rhetorical relationships between citing publication and cited publication, the in-text and global citation frequencies of each cited work, and the nature of the cited work itself, including its publication ...
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Abstract
AbstractObjective To understand belief in a specific scientific claim by studying the pattern of citations among papers stating it.Design A complete citation network was constructed from all PubMed indexed English literature papers addressing the belief that β amyloid, a protein accumulated in the brain in Alzheimer’s disease, is produced by and injures skeletal muscle of patients with inclusion body myositis. Social network theory and graph theory were used to analyse this network.Main outcome measures Citation bias, amplification, and invention, and their ...
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Abstract
Articles whose authors have supplemented subscription-based access to the publisher's version by self-archiving their own final draft to make it accessible free for all on the web (“Open Access”, OA) are cited significantly more than articles in the same journal and year that have not been made OA. Some have suggested that this “OA Advantage” may not be causal but just a self-selection bias, because authors preferentially make higher-quality articles OA. To test this we compared self-selective self-archiving with mandatory self-archiving ...
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Abstract
Reference management software has been used by researchers for more than 20 years to find, store, and organize references, and to write scholarly papers. Recently developed collaborative web-based tools have resulted in a number of interesting new features, and in a number of new reference managers. These developments are changing which reference managers we use, and how we use them ...
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(25 Apr 2010)
Abstract
Impact factors (and similar measures such as the Scimago Journal Rankings) suffer from two problems: (i) citation behavior varies among fields of science and therefore leads to systematic differences, and (ii) there are no statistics to inform us whether differences are significant. The recently introduced SNIP indicator of Scopus tries to remedy the first of these two problems, but a number of normalization decisions are involved which makes it impossible to test for significance. Using fractional counting of citations-based on the assumption that impact is proportionate to the ...
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Abstract
The impact of scientific publications has traditionally been expressed in terms of citation counts. However, scientific activity has moved online over the past decade. To better capture scientific impact in the digital era, a variety of new impact measures has been proposed on the basis of social network analysis and usage log data. Here we investigate how these new measures relate to each other, and how accurately and completely they express scientific impact. We performed a principal component analysis of the ...
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(23 Dec 2006)
Abstract
Academic institutions, federal agencies, publishers, editors, authors, and librarians increasingly rely on citation analysis for making hiring, promotion, tenure, funding, and/or reviewer and journal evaluation and selection decisions. The Institute for Scientific Information's (ISI) citation databases have been used for decades as a starting point and often as the only tools for locating citations and/or conducting citation analyses. ISI databases (or Web of Science), however, may no longer be adequate as the only or even the main sources of citations because new databases and tools that allow citation searching ...
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(25 Nov 2009)
Abstract
Contemporary scholarly discourse follows many alternative routes in addition to the three-century old tradition of publication in peer-reviewed journals. The field of High- Energy Physics (HEP) has explored alternative communication strategies for decades, initially via the mass mailing of paper copies of preliminary manuscripts, then via the inception of the first online repositories and digital libraries. This field is uniquely placed to answer recurrent questions raised by the current trends in scholarly communication: is there an advantage for scientists to make their work available through repositories, often in preliminary ...
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(4 Oct 2010)
by Suenje Dallmeier-Tiessen, Robert Darby, Bettina Goerner, et al.Jenni Hyppoelae, Peter Igo-Kemenes, Deborah Kahn, Simon Lambert, Anja Lengenfelder, Chris Leonard, Salvatore Mele, Panayiota Polydoratou, David Ross, Sergio Ruiz-Perez, Ralf Schimmer, Mark Swaisland, Wim van der Stelt
Abstract
The SOAP (Study of Open Access Publishing) project has compiled data on the present offer for open access publishing in online peer-reviewed journals. Starting from the Directory of Open Access Journals, several sources of data are considered, including inspection of journal web site and direct inquiries within the publishing industry. Several results are derived and discussed, together with their correlations: the number of open access journals and articles; their subject area; the starting date of open access journals; the size and business models of open access publishers; the ...
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Abstract
BACKGROUND: The impact of scientific publications has traditionally been expressed in terms of citation counts. However, scientific activity has moved online over the past decade. To better capture scientific impact in the digital era, a variety of new impact measures has been proposed on the basis of social network analysis and usage log data. Here we investigate how these new measures relate to each other, and how accurately and completely they express scientific impact. METHODOLOGY: We performed a principal component analysis ...
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First Monday, Vol. 15, No. 7. (5 July 2010)
Abstract
The growing flood of scholarly literature is exposing the weaknesses of current, citation-based methods of evaluating and filtering articles. A novel and promising approach is to examine the use and citation of articles in a new forum: Web 2.0 services like social bookmarking and microblogging. Metrics based on this data could build a “Scientometics 2.0,” supporting richer and more timely pictures of articles' impact. This paper develops the most comprehensive list of these services to date, assessing the potential value and ...
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posted to no-tag
by mfenner
to the group Gobbledygook
on 2010-09-26 17:36:25
along with 1 person
skonkiel
Abstract
We describe the ongoing citations to biomedical articles affected by scientific misconduct, and characterize the papers that cite these affected articles. The citations to 102 articles named in official findings of scientific misconduct during the period of 1993 and 2001 were identified through the Institute for Scientific Information Web of Science database. Using a stratified random sampling strategy, we performed a content analysis of 603 of the 5,393 citing papers to identify indications of awareness that the cited articles affected by ...
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Abstract
After thousands of hours of investigation, three clinical trials at Duke University in Durham, North Carolina, were suspended in late 2009 because of the irreproducibility of the genomic 'signatures' used to select cancer therapies for patients. Journals have a duty to help the community by maintaining reproducibility as a cornerstone of the scientific process. ...
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Abstract
Using an improved method of gel electrophoresis, many hitherto unknown proteins have been found in bacteriophage T4 and some of these have been identified with specific gene products. Four major components of the head are cleaved during the process of assembly, apparently after the precursor proteins have assembled into some large intermediate structure. ...
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Abstract
Our group analyzed a multi-institutional data set to address the question of how the outcomes of surgery for prostate cancer are affected by surgeon-specific factors. The cohort consists of 9076 patients treated by open radical prostatectomy at one of four US academic institutions 1987 - 2003. The primary analyses focused on 7765 patients without neoadjuvant therapy. The most well-known finding is that of a surgical "learning curve", with rates of prostate cancer cure strongly dependent on surgeon experience. In this "data ...
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Abstract
Google Wave is the kind of open-source online collaboration tool that should drive scientists to wire their research and publications into an interactive data web, says Cameron Neylon. ...
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Abstract
The authors discuss the value of article-level metrics in determining an article's scientific impact. ...
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Abstract
To capture the essence of good science, stakeholders must combine forces to create an open, sound and consistent system for measuring all the activities that make up academic productivity, says Julia Lane. Summary ...
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Abstract
Choosing good problems is essential for being a good scientist. But what is a good problem, and how do you choose one? The subject is not usually discussed explicitly within our profession. Scientists are expected to be smart enough to figure it out on their own and through the observation of their teachers. This lack of explicit discussion leaves a vacuum that can lead to approaches such as choosing problems that can give results that merit publication in valued journals, resulting ...
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Abstract
Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We ...
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Abstract
Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available. We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, ...
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