Abstract

In recent years libraries have seen an increase in the number and complexity of citation management programs like Zotero, RefWorks and Endnote, and with this an expanded role for libraries in support of citation and research management. But how should libraries best support citation management and the needs of users and how do the tools fit into information literacy programs? Penn State University librarians decided to take stock of the various tools and programs available for citation management and outline how ...

Abstract

Negation occurs frequently in scientific literature, especially in biomedical literature. It has previously been reported that around 13% of sentences found in biomedical research articles contain negation. Historically, the main motivation for identifying negated events has been to ensure their exclusion from lists of extracted interactions. However, recently, there has been a growing interest in negative results, which has resulted in negation detection being identified ...

Abstract

Text mining has become an integral part of all research in the medical field. Many text analysis software platforms support particular use cases and only those. We show an example of a bibliographic tool that can be used to support virtually any use case in an agile manner. Here we focus on a Pipeline Pilot web-based application that interactively analyzes and reports on PubMed search ...

Abstract

Abstract Modern science is a main driver of technological innovation. The efficiency of the scientific system is of key importance to ensure the competitiveness of a nation or region. However, the scientific system that we use today was ...

Abstract

Conventional computer searches of the biomedical literature (e.g. MEDLINE) allow investigators to retrieve much of the information that has already been published on a given topic. However, these searches are of limited utility at the frontier of scientific discovery, when one wishes to identify and assess new, untested scientific hypotheses, or to uncover biologically significant relations between two previously disparate fields of inquiry. We have designed a set of interactive software and database search strategies, collectively called ARROWSMITH, that facilitate the ...

Abstract

Scholarly research involves a systematic study of information sources in order to establish facts and reach new conclusions. It encompasses survey, analysis, evaluation, and creation as distinct phases that are performed iteratively and often in parallel by accessing a range of local and remote resources. Throughout these activities scholars create collections of relevant work, ranging from publication references to new information acquired through experiments or correspondence with other scholars. We use the term reading list to refer to such collections. Existing ...

Abstract

To determine the accessibility of retracted articles residing on non-publisher websites and in personal libraries. Searches were performed to locate Internet copies of 1,779 retracted articles identified in MEDLINE, published between 1973 and 2010, excluding the publishers' website. Found copies were classified by article version and location. Mendeley (a bibliographic ...

Abstract

A large activity for digitization, access and preservation of cultural heritage is taking place in Europe and the United States, which involves all types of cultural institutions, i.e., galleries, libraries, museums, archives and all types of cultural content. Semantic interoperability is a key issue in these developments. Content metadata constitute the main features of cultural items that are analysed and used to interpret users’ queries, so that the most appropriate content is presented to the users. This paper presents a new ...

Abstract

Recent advances in networking and telecommunications technologies combined with the vast load of readily available scientific data, urge towards the implementation of software systems that are able to collect, combine and present information from distributed repositories. At the same time, scientists, researchers, academics and experts demand flexible infrastructures that provide just-in-time information, with reliable, peer-reviewed data, through ubiquitous interfaces. Towards this direction, several international organizations including the European Commission, promote the development of software platforms that will facilitate universal access to ...

Abstract

While mastery of the scientific literature is a strongly desirable trait for undergraduate students, the sheer volume of the current literature has complicated the challenge of teaching scientific literacy. Part of the response to this ever-increasing volume of resources includes formal instruction in the use of reference manager software while engaging students with the primary literature. This article describes the incorporation of the reference manager ...

Abstract

Current approaches to publishing scholarly work are falling behind the growing demands of modern readers, who need easy access to the underlying data, as well as the ability to consume content on an ever-growing variety of electronic devices. The pros and cons of the various formats for representing the scholarly article are hotly contested, but as yet these debates have had little tangible impact on the publishing world where, in spite of its apparent limitations, the PDF remains the dominant form ...

Abstract

In this paper, we describe a server/client literature management system specialized for the life science domain, the TogoDoc system (Togo, pronounced Toe-Go, is a romanization of a Japanese word for integration). The server and the client program cooperate closely over the Internet to provide life scientists with an effective literature recommendation service and efficient literature management. The content-based and personalized literature recommendation helps researchers to isolate interesting papers from the "tsunami" of literature, in which, on average, more than one biomedical ...

Abstract

As more information proliferates online, researchers often struggle to find an efficient way of managing their bibliographic data. Zotero presents an attractive alternative to proprietary citation tools as it is free, user-friendly, Web 2.0-compatible, and can be easily integrated with websites, online databases, catalogs, and repositories. Besides a brief review and comparative analysis of Zotero, the article highlights the science librarian's efforts to promote Zotero to students and faculty members in the College of Natural Sciences and Mathematics. While his initial ...

Abstract

The biomedical literature holds our understanding of pharmacogenomics, but it is dispersed across many journals. In order to integrate our knowledge, connect important facts across publications and generate new hypotheses we must organize and encode the contents of the literature. By creating databases of structured pharmocogenomic knowledge, we can make the value of the literature much greater than the sum of the individual reports. We ...

Abstract

Summary 10.1002/9780470669716.ch2.abs This chapter contains sections titled: * Fundamentals * Challenges in knowledge-driven approaches * Current knowledge-based bioinformatics tools * 3R systems: reading, reasoning and reporting the way towards biomedical discovery * The Hanalyzer: a proof of 3R concept * Acknowledgements * References ...

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 ...

Abstract

Zotero is a powerful free personal bibliographic manager (PBM) for writers. Use of a PBM allows the writer to focus on content, rather than the tedious details of formatting citations and references. Zotero 2.0 (http://www.zotero.org) has new features including the ability to synchronize citations with the off-site Zotero server and the ability to collaborate and share with others. An overview on how to use the software and discussion about the strengths and limitations are included. ...

Abstract

How many scholarly research articles are there in existence? Journal articles first appeared in 1665, and the cumulative total is estimated here to have passed 50 million in 2009. This sum was arrived at based on published figures for global annual output for 2006, and analyses of annual output and growth rates published in the last decade. ...

Abstract

The Entrez interface developed by the National Center for Biotechnology Information (NCBI) includes basic and advanced features that benefit novice and expert searchers alike. After NCBI made its content available as an application programming interface (API), external database developers started creating alternative interfaces to search Entrez databases. This article reviews the features and functionality of several of these alternatives (ClusterMed, eTBlast 3.0, HubMed, and SLIM v.2) and compares search results for two PubMed® strategies executed in each of the four comparison ...

Abstract

Bibliographic digital libraries play a significant role in conducting research and, in the past few years, have started to move from closed to more open social platforms. However, in this, they have faced challenges (e.g., from Web spam) in maintaining the level of scholarly precision—the ratio of relevant citations retrieved by search. This paper describes a hybrid approach that uses online social collaboration and reputation based social moderation to reduce the cost and to speed up the construction of scholarly bibliographies ...

Abstract

The new Web generations are influencing the minds and changing the habits of software developers and end users. Users, librarians, and information services professionals can interact more efficiently, creating additional information and content and generating knowledge. This new scenario is also changing the behavior of information providers and users in health sciences libraries. This article reviews the new Web environments and tools that give librarians opportunities to tailor their services better, and gives some examples of the advantages and disadvantages for ...

Abstract

The use of bibliographic management software and its internal search interfaces is now pervasive among researchers. This study compares the results between searches conducted in academic databases' search interfaces versus the EndNote search interface. The results show mixed search reliability, depending on the database and type of search performed. ...

Abstract

This paper aims to explore how the principles of a well-known Web 2.0 service, the world¿s largest social music service "Last.fm" (www.last.fm), can be applied to research, which potential it could have in the world of research (e.g. an open and interdisciplinary database, usage-based reputation metrics, and collaborative filtering) and which challenges such a model would face in academia. A real-world application of these principles, "Mendeley" (www.mendeley.com), will be demoed at the IEEE e-Science Conference 2008. ...

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 ...

Abstract

Authors' motivations for citing documents are addressed through a literature review and an empirical study. Replicating an investigation in psychology, the works of two highly-cited authors in the discipline of communication were identified, and all of the authors who cited them during the period 1995–1997 were surveyed. The instrument posed 32 questions about why a certain document was cited, plus questions about the citer's relationship to the cited author and document. Most findings were similar to the psychology study, including a ...

Abstract

Here is a truism. The function of a scientific journal is to disseminate the results of research. It also of course has a responsibility to ensure as far as possible that the results reported are valid. But it would seem from the comments of many biologists – sometimes in print [1-3] – that the policing function of journals (especially but not exclusively the high-profile journals) is in danger of overwhelming their primary function as publishers. ...

Note (first note only)

One issue in particular that we at Cell will be focusing on in 2009 is redefining what constitutes a “publishable unit” in the age of electronic journals and how we can best present the information content of a scientific article online. The vision in our crystal ball is still blurred, but some key elements are beginning to take shape. The scientific article of the future will no longer be tied to the constraints of a printing press and will take advantage

Abstract

Human beings are information omnivores: we are constantly collecting, labeling, and organizing data. But today, the shift from the physical to the digital is mixing, burning, and ripping our lives apart. In the past, everything had its one place--the physical world demanded it--but now everything has its places: multiple categories, multiple shelves. Simply put, everything is suddenly miscellaneous. In _Everything Is Miscellaneous_, David Weinberger charts the new principles of digital order that are remaking business, education, politics, science, and culture. In his rollicking tour of the rise of the ...

Abstract

BACKGROUND: The rapid growth of online publications such as the Medline and other sources raises the questions how to get the relevant information efficiently. It is important, for a bench scientist, e.g., to monitor related publications constantly. It is also important, for a clinician, e.g., to access the patient records anywhere and anytime. Although time-consuming, this kind of searching procedure is usually similar and simple. Likely, it involves a search engine and a visualization interface. Different words or combination reflects different ...

Abstract

The Digital Object Identifier (DOI) is a system for identifying content objects in the digital environment. DOIs are names assigned to any entity for use on Internet digital networks. Scientific data sets may be identified by DOIs, and several efforts are now underway in this area. This paper outlines the underlying architecture of the DOI system, and two such efforts which are applying DOIs to content objects of scientific data. ...

Note (first note only)

10.2481/dsj.4.12

Abstract

How many times has your PC crashed today? While Gordon Moore's now famous law projecting the doubling of computer power every 18 months has more than borne itself out, it's too bad that a similar trajectory projecting the reliability and usefulness of all that power didn't come to pass, as well. Advances in information technology are most often measured in the cool numbers of megahertz, throughput, and bandwidth--but, for many us, the experience of these advances may be better measured in ...

Abstract

Motivation: Internet-based electronic resources, as given by Uniform Resource Locators (URLs), are being increasingly used in scientific publications but are also becoming inaccessible in a time-dependant manner, a phenomenon documented across disciplines. Initial reports brought attention to the problem, spawning methods of effectively preserving URL content while some journals adopted policies regarding URL publication and begun storing supplementary information on journal websites. Thus, a reexamination of URL growth and decay in the literature is merited to see if the problem has ...

Note (first note only)

Proprietary data formats like Endnote may be legally defensible but open standards can be a better spur for innovation, by Zotero (for example)

Abstract

John Ioannidis and colleagues argue that the current system of publication in biomedical research provides a distorted view of the reality of scientific data. ...

Abstract

BACKGROUND:While text-mining and distributed annotation systems both aim at capturing knowledge and presenting it in a standardized form, there have been few attempts to investigate potential synergies between these two fields. For instance, distributed annotation would be very well suited for providing topic focussed, expert knowledge enriched text corpora. A key limitation for this approach is the availability of literature annotation systems that can be routinely used by groups of collaborating researchers on a day to day basis, not distracting from ...

Abstract

Information systems are critical assets for modern enterprises and incorporate key knowledge acquired over the life of an organization. These systems must be updated continuously to reflect evolving business practices. Unfortunately, repeated modification has a cumulative effect on system complexity, and the rapid evolution of technology quickly renders existing technologies obsolete. Eventually, the existing information systems become too fragile to modify and too important to discard. For this reason, organizations must consider modernizing these legacy systems to remain viable. The commercial ...

Abstract

Library 2.0: does everyone seem to know what this means except you? Or are you reasonably well informed but wondering what challenge to take on next? In this new work, Nancy Courtney has assembled some of the most forward looking thinkers in the library world to describe the next generation of online tools. Beginning with Steven J. Bell, each contributor introduces his or her favorite technology, outlines its use, and discusses its potential in today's library environment. Topical coverage includes blogs ...

Abstract

In this paper we present the Research Information Centre (RIC), a virtual research environment being jointly developed by the Technical Computing Group at Microsoft and The British Library. We view researchers as extreme information workers and the purpose of the RIC is to support researchers in managing the increasingly complex range of tasks involved in carrying out research. Our first implementation of the RIC is focused on the biomedical researcher, leveraging commercial off-the-shelf software to the extent possible. However, the base ...

Abstract

Social networking is beginning to make an impact on the drug discovery process. While bioinformatics and chemoinformatics underpin research at a scientific level, rapid communication between individual researchers across continents now allows the global exchange of ideas, tools and technologies. Networking at this level of speed and reach is quite a recent phenomenon. It facilitates the development of common interests, accelerates technology transfer and increases ...