This article presents a description and case study of CiteSpace II, a Java
application which supports visual exploration with knowledge discovery
in bibliographic databases. Highly cited and pivotal documents, areas
of specialization within a knowledge domain, and emergence of research
topics are visually mapped through a progressive knowledge domain
visualization approach to detecting and visualizing trends and patterns
in scientific literature. The test case in this study is progressive
knowledge domain visualization of the field of medical informatics. Datasets
based on publications from twelve journals in the medical informatics
field covering the time period from 1964–2004 were extracted
from PubMed and Web of Science (WOS) and developed as testbeds
for evaluation of the CiteSpace system. Two resulting document-term
co-citation and MeSH term co-occurrence visualizations are qualitatively
evaluated for identification of pivotal documents, areas of specialization, and
research trends. Practical applications in bio-medical research
settings are discussed.
Current scientific research takes place in highly specialized contexts with poor communication between disciplines as a likely consequence. Knowledge from one discipline may be useful for the other without researchers knowing it. As scientific publications are a condensation of this knowledge, literature-based discovery tools may help the individual scientist to explore new useful domains. We report on the development of the DAD-system, a concept-based Natural Language Processing system for PubMed citations that provides the biomedical researcher such a tool. We describe the general architecture and illustrate its operation by a simulation of a well-known text-based discovery: The favorable effects of fish oil on patients suffering from Raynaud's disease .
The tempo and mode of human knowledge expansion is an enduring yet poorly understood topic. Through a temporal network analysis of three decades of discoveries of protein interactions and genetic interactions in baker's yeast, we show that the growth of scientific knowledge is exponential over time and that important subjects tend to be studied earlier. However, expansions of different domains of knowledge are highly heterogeneous and episodic such that the temporal turnover of knowledge hubs is much greater than expected by chance. Familiar subjects are preferentially studied over new subjects, leading to a reduced pace of innovation. While research is increasingly done in teams, the number of discoveries per researcher is greater in smaller teams. These findings reveal collective human behaviors in scientific research and help design better strategies in future knowledge exploration.
It is of great interest to understand the patterns and mechanisms of scientific knowledge growth, but such studies have been hampered by the lack of ideal cases in which the structure of the knowledge is known, the knowledge is quantifiable, and the process of knowledge discovery is well understood and documented. The biological knowledge about a species is in part described by its protein interaction network and genetic interaction network. Here, we conduct a temporal meta-analysis of three decades of discoveries of protein interactions and genetic interactions in baker's yeast to reveal the tempo and mode of the growth of yeast biology. We show that the growth is exponential over time and that important subjects tend to be studied earlier. However, expansions of different domains of knowledge are highly heterogeneous and episodic such that the temporal turnover of knowledge hubs is much greater than that expected by chance. Familiar subjects are preferentially studied over new subjects, leading to a reduced pace of innovation. While research is increasingly done in teams, the number of discoveries per researcher is greater in smaller teams. These findings reveal collective human behaviors in scientific research and help design better strategies in future knowledge exploration.
The large amount of information contained in bibliographic databases has recently boosted the use of citations, and other indicators based on citation numbers, as tools for the quantitative assessment of scientific research. Citations counts are often interpreted as proxies for the scientific influence of papers, journals, scholars, and institutions. However, a rigorous and scientifically grounded methodology for a correct use of citation counts is still missing. In particular, cross-disciplinary comparisons in terms of raw citation counts systematically favors scientific disciplines with higher citation and publication rates. Here we perform an exhaustive study of the citation patterns of millions of papers, and derive a simple transformation of citation counts able to suppress the disproportionate citation counts among scientific domains. We find that the transformation is well described by a power-law function, and that the parameter values of the transformation are typical features of each scientific discipline. Universal properties of citation patterns descend therefore from the fact that citation distributions for papers in a specific field are all part of the same family of univariate distributions.
The promise of science lies in expectations of its benefits to societies and is matched by expectations of the realisation of the significant public investment in that science. In this paper, we undertake a methodological analysis of the science of biobanking and a sociological analysis of translational research in relation to biobanking. Part of global and local endeavours to translate raw biomedical evidence into practice, biobanks aim to provide a platform for generating new scientific knowledge to inform development of new policies, systems and interventions to enhance the public’s health. Effectively translating scientific knowledge into routine practice, however, involves more than good science. Although biobanks undoubtedly provide a fundamental resource for both clinical and public health practice, their potentiating ontology—that their outputs are perpetually a promise of scientific knowledge generation—renders translation rather less straightforward than drug discovery and treatment implementation. Biobanking science, therefore, provides a perfect counterpoint against which to test the bounds of translational research. We argue that translational research is a contextual and cumulative process: one that is necessarily dynamic and interactive and involves multiple actors. We propose a new multidimensional model of translational research which enables us to imagine a new paradigm: one that takes us from bench to bedside to backyard and beyond, that is, attentive to the social and political context of translational science, and is cognisant of all the players in that process be they researchers, health professionals, policy makers, industry representatives, members of the public or research participants, amongst others.
Innovative science frequently occurs as a result of cross-disciplinary collaboration, the importance of which is reflected by recent NIH funding initiatives that promote communication and collaboration. If shared research interests between collaborators are important for the formation of collaborations, methods for identifying these shared interests across scientific domains could potentially reveal new and useful collaboration opportunities. MEDLINE represents a comprehensive database of collaborations and research interests, as reflected by article co-authors and concept content. We analyzed six years of citations using information retrieval-based methods to compute articles’ conceptual similarity, and found that articles by basic and clinical scientists who later collaborated had significantly higher average similarity than articles by similar scientists who did not collaborate. Refinement of these methods and characterization of found conceptual overlaps could allow automated discovery of collaboration opportunities that are currently missed.
Increasing public interest in science information in a digital and 2.0 science era promotes a dramatically, rapid and deep change in science itself. The emergence and expansion of new technologies and internet-based tools is leading to new means to improve scientific methodology and communication, assessment, promotion and certification. It allows methods of acquisition, manipulation and storage, generating vast quantities of data that can further facilitate the research process. It also improves access to scientific results through information sharing and discussion. Content previously restricted only to specialists is now available to a wider audience. This context requires new management systems to make scientific knowledge more accessible and useable, including new measures to evaluate the reach of scientific information. The new science and research quality measures are strongly related to the new online technologies and services based in social media. Tools such as blogs, social bookmarks and online reference managers, Twitter and others offer alternative, transparent and more comprehensive information about the active interest, usage and reach of scientific publications. Another of these new filters is the Research Blogging platform, which was created in 2007 and now has over 1,230 active blogs, with over 26,960 entries posted about peer-reviewed research on subjects ranging from Anthropology to Zoology. This study takes a closer look at RB, in order to get insights into its contribution to the rapidly changing landscape of scientific communication.
PREOP is a prototype expert system that is designed to provide physicians with evidence-based recommendations concerning the assessment and care of patients with comorbid medical problems who are about to undergo surgery. The knowledgebase for this system is currently undergoing transition from the conventional advice of medical experts, which is variably related to evidence published in the medical literature, to a more formal approach in which the best available evidence is used for each recommendation and the quality of the evidence made apparent to the user. This work seeks to address important questions concerning improvement of the information contained in expert knowledgebases, namely, how to find and recognize new evidence when it is published, how to assess the quality of evidence in a uniform and efficient fashion, how to replace evidence in the knowledgebase efficiently when it has been superseded by higher quality evidence, and how to represent evidence in a manner that is most valuable for the user.
Objectives: The objective of this study was to identify trends in academic health sciences libraries (AHSLs) as they adapt to the shift from a print knowledgebase to an increasingly digital knowledgebase. This research was funded by the 2003 David A. Kronick Traveling Fellowship.
Methods: The author spent a day and a half interviewing professional staff at each library. The questionnaire used was sent to the directors of each library in advance of the visit, and the directors picked the staff to be interviewed and set up the schedule.
Results: Seven significant trends were identified. These trends are part of the shift of AHSLs from being facility and print oriented with a primary focus on their role as repositories of a print-based knowledgebase to a new focus on their role as the center or “nexus” for the organization, access, and use of an increasingly digital-based knowledgebase.
Conclusion: This paper calls for a national effort to develop a new model or structure for health sciences libraries to more effectively respond to the challenges of access and use of a digital knowledgebase, much the same way the National Library of Medicine did in the 1960s and 1970s in developing and implementing the National Network of Libraries of Medicine. The paper then concludes with some examples or ideas for research to assist in this process.
Nobel Prizes are commonly seen to be among the most prestigious achievements of
our times. Based on mining several million citations, we quantitatively analyze
the processes driving paradigm shifts in science. We find that groundbreaking
discoveries of Nobel Prize Laureates and other famous scientists are not only
acknowledged by many citations of their landmark papers. Surprisingly, they also
boost the citation rates of their previous publications. Given that innovations
must outcompete the rich-gets-richer effect for scientific citations, it turns
out that they can make their way only through citation cascades. A quantitative
analysis reveals how and why they happen. Science appears to behave like a
self-organized critical system, in which citation cascades of all sizes occur,
from continuous scientific progress all the way up to scientific revolutions,
which change the way we see our world. Measuring the “boosting
effect” of landmark papers, our analysis reveals how new ideas and new
players can make their way and finally triumph in a world dominated by
established paradigms. The underlying “boost factor” is also useful
to discover scientific breakthroughs and talents much earlier than through
classical citation analysis, which by now has become a widespread method to
measure scientific excellence, influencing scientific careers and the
distribution of research funds. Our findings reveal patterns of collective
social behavior, which are also interesting from an attention economics
perspective. Understanding the origin of scientific authority may therefore
ultimately help to explain how social influence comes about and why the value of
goods depends so strongly on the attention they attract.
The overarching informatics grand challenge facing society is the creation of knowledge management systems that can acquire, conserve, organize, retrieve, display, and distribute what is known today in a manner that informs and educates, facilitates the discovery and creation of new knowledge, and contributes to the health and welfare of the planet. At one time the private, national, and university libraries of the world collectively constituted the memory of society's intellectual history. In the future, these new digital knowledge management systems will constitute human memory in its entirety. The current model of multiple local collections of duplicated resources will give way to specialized sole-source servers. In this new environment all scholarly scientific knowledge should be public domain knowledge: managed by scientists, organized for the advancement of knowledge, and readily available to all. Over the next decade, the challenge for the field of medical informatics and for the libraries that serve as the continuous memory for the biomedical sciences will be to come together to form a new organization that will lead to the development of postmodern digital knowledge management systems for medicine. These systems will form a portion of the evolving world brain of the 21st century.
Peer-reviewed scientific literature is a prime source for accessing knowledge in the biomedical field. Its rapid growth and diverse domain coverage require systematic efforts in developing interactive tools for efficiently searching and summarizing current advances for acquiring knowledge and referencing, and for furthering scientific discovery. Although information retrieval systems exist, the conventional tools and systems remain difficult for biomedical investigators to use. There remain gaps even in the state-of-the-art systems as little attention has been devoted to understanding the needs of biomedical researchers.
Our work attempts to bridge the gap between the needs of biomedical users and systems design efforts. We first study the needs of users and then design a simple visual analytic application tool, SEACOIN. A key motivation stems from biomedical researchers’ request for a “simple interface” that is suitable for novice users in information technology. The system minimizes information overload, and allows users to search easily even in time-constrained situations. Users can manipulate the depth of information according to the purpose of usage. SEACOIN enables interactive exploration and filtering of search results via “metamorphose topological visualization” and “tag cloud,” visualization tools that are commonly used in social network sites. We illustrate SEACOIN’s usage through applications on PubMed publications on heart disease, cancer, Alzheimer’s disease, diabetes, and asthma.
ScanProsite——is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For a number of PROSITE profiles, the tool now makes use of ProRules—context-dependent annotation templates—to detect functional and structural intra-domain residues. The detection of those features enhances the power of function prediction based on profiles. Both user-defined sequences and sequences from the UniProt Knowledgebase can be matched against custom patterns, or against PROSITE signatures. To improve response times, matches of sequences from UniProtKB against PROSITE signatures are now retrieved from a pre-computed match database. Several output modes are available including simple text views and a rich mode providing an interactive match and feature viewer with a graphical representation of results.
Scientific research is heavily dependent on communication and collaboration. Research does not exist in a bubble; scientific work must be communicated in order to add it to the body of knowledge within a scientific community, so that its members may ‘stand on the shoulders of giants’ and benefit from all that has come before. The effectiveness of scientific communication is crucial to the pace of scientific progress: in all its forms it enables ideas to be formulated, results to be compared, and replications and improvements to be made. The sharing of science is a foundational aspect of the scientific method. This paper, part of the policy research within the FP7 EUROCANCERCOMS project, discusses how the Internet has changed communication by cancer researchers and how it has the potential to change it still more in the future. It will detail two broad types of communication: formal and informal, and how these are changing with the use of new web tools and technologies.
The availability of scientific bibliographies through online databases provides a rich source of information for scientists to support their research. However, the risk of this pervasive availability is that an individual researcher may fail to find relevant information that is outside the direct scope of interest. Following Swanson’s ABC model of disjoint but complementary structures in the biomedical literature, we have developed a discovery support tool to systematically analyze the scientific literature in order to generate novel and plausible hypotheses. In this case report, we employ the system to find potentially new target diseases for the drug thalidomide. We find solid bibliographic evidence suggesting that thalidomide might be useful for treating acute pancreatitis, chronic hepatitis C, Helicobacter pylori-induced gastritis, and myasthenia gravis. However, experimental and clinical evaluation is needed to validate these hypotheses and to assess the trade-off between therapeutic benefits and toxicities.
Preventing cancer, downstaging disease at diagnosis, and reducing mortality require that relevant research findings be translated across scientific disciplines and into clinical and public health practice. Interdisciplinary research focuses on using the languages of different scientific disciplines to share techniques and philosophical perspectives to enhance discovery and development of innovations; (i.e., from the “left end” of the research continuum). Community-based participatory research (CBPR), whose relevance often is relegated to the “right end” (i.e., delivery and dissemination) of the research continuum, represents an important means for understanding how many cancers are caused as well as for ensuring that basic science research findings affect cancer outcomes in materially important ways. Effective interdisciplinary research and CBPR both require an ability to communicate effectively across groups that often start out neither understanding each other’s worldviews nor even speaking the same language. Both demand an ability and willingness to treat individuals from other communities with respect and understanding. We describe the similarities between CBPR and both translational and interdisciplinary research, and then illustrate our points using squamous cell carcinoma of the esophagus as an example of how to deepen understanding and increase relevance by applying techniques of CBPR and interdisciplinary engagement.
The answer to the question of what a database is and what is its relevance to the scientific research is not easy. We may not be wrong if we say that it is, basically, a kind of information resource, often incomparably richer than it is, for example, a single book or magazine.
Discussion and conclusion
As a form of storing and retrieval of the knowledge, appeared in the information age, which we’ve just participated and witnesses. In it, thanks to the technical possibilities of information networks, it can be searched for a number of more or less relevant information, and that scientific and profound content. Databases are divided into: bibliographic databases, citation databases and databases containing full-text. In the paper are shortly presented most important on-line databases with their web site links. Thanks to those online databases scientific knowledge is spreading much more easy and useful.
ICT; IMRAD; quoting literature; review of the articles; publications
Contemporary biological research integrates neighboring scientific domains to answer complex questions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks.
Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and alignments.
Bioclipse 2 is equipped with advanced tools required to carry out complex analysis in the fields of bio- and cheminformatics. Developed as a Rich Client based on Eclipse, Bioclipse 2 leverages on today's powerful desktop computers for providing a responsive user interface, but also takes full advantage of the Web and networked (Web/Cloud) services for more demanding calculations or retrieval of data. The fact that Bioclipse 2 is based on an advanced and widely used service platform ensures wide extensibility, making it easy to add new algorithms, visualizations, as well as scripting commands. The intuitive tools for end users and the extensible architecture make Bioclipse 2 ideal for interdisciplinary and integrative research.
Bioclipse 2 is released under the Eclipse Public License (EPL), a flexible open source license that allows additional plugins to be of any license. Bioclipse 2 is implemented in Java and supported on all major platforms; Source code and binaries are freely available at http://www.bioclipse.net.
Objectives: Medicine must keep current with the research literature, and keeping current requires continuously updating the clinical knowledgebase (i.e., references that provide answers to clinical questions). The authors estimated the volume of medical literature potentially relevant to primary care published in a month and the time required for physicians trained in medical epidemiology to evaluate it for updating a clinical knowledgebase.
Methods: We included journals listed in five primary care journal review services (ACP Journal Club, DynaMed, Evidence-Based Practice, Journal Watch, and QuickScan Reviews). Finding little overlap, we added the 2001 “Brandon/Hill Selected List of Print Books and Journals for the Small Medical Library.” We counted articles (including letters, editorials, and other commentaries) published in March 2002, using bibliographic software where possible and hand counting when necessary. For journals not published in March 2002, we reviewed the nearest issue. Five primary care physicians independently evaluated fifty randomly selected articles and timed the process.
Results: The combined list contained 341 currently active journals with 8,265 articles. Adjusting for publication frequency, we estimate 7,287 articles are published monthly in this set of journals. Physicians trained in epidemiology would take an estimated 627.5 hours per month to evaluate these articles.
Conclusions: To provide practicing clinicians with the best current evidence, more comprehensive and systematic literature surveillance efforts are needed.
Discovery, as a public attribution, and discovering, the act of conducting research, are
experiences that entail “languaging” the unknown. This distinguishing property of language ‐ its
ability to bring forth, out of the unspoken realm, new knowledge, original ideas, and novel
thinking – is essential to the discovery process. In sharing their ideas and views, scientists
create co‐negotiated linguistic distinctions that prompt the revision of established mental maps
and the adoption of new ones. While scientific mastery entails command of the conversational
domain unique to a specific discipline, there is an emerging conversational domain that must be
mastered that goes beyond the language unique to any particular specialty. Mastery of this
new conversational domain gives researchers access to their hidden mental maps that limit
their ways of thinking about and doing science. The most effective scientists use language to
recontextualize their approach to problem‐solving, which triggers new insights (previously
unavailable) that result in new discoveries. While language is not a replacement for intuition
and other means of knowing, when we try to understand what’s outside of language we have
to use language to do so.
Knowledge production and evaluation are two important functions of health research system (HRS). In this article, we aimed to reveal the correlation between evaluation of health research organizations and health knowledge production promotion.
A comprehensive evaluation system was developed to evaluate the academic performance of national medical science universities on an annual basis. It assess following domains; stewardship, capacity building and knowledge production. Measurable indicators for each domain were assigned, a ‘research profile’ for each department was provided. In this study, we compared the results of annually national Health Research System evaluation findings during 2005–2008.
The number of scientific articles has been increased from 4672 to 8816 during 2005 to 2008. It is mentionable that, the number of articles which has been published in indexed data bases has risen too. This fact could be related to directed policy for more international publication of scientific articles from Iran. The proportion of total articles to the number of academic members was 1.14 in 2008, comparing to 0.84 in 2005. It means that this proportion have increased about twice (0.7 Vs 0.45) during mentioned time. Moreover, other scientific products such as authored books based on domestic researches and cited articles in textbooks have increased according to special attention to knowledge production by policy makers.
We conclude that Health System Research evaluation could be used as a mean for implementing policies and promoting knowledge production.
Health; Research; Evaluation; Knowledge; Production; Iran
The term blue skies research implies a freedom to carry out flexible, curiosity-driven research that leads to outcomes not envisaged at the outset. This research often challenges accepted thinking and introduces new fields of study. Science policy in the UK has given growing support for short-term goal-oriented scientific research projects, with pressure being applied on researchers to demonstrate the future application of their work. These policies carry the risk of restricting freedom, curbing research direction, and stifling rather than stimulating the creativity needed for scientific discovery.
This study tracks the tortuous routes that led to three major discoveries in cardiology. It then investigates the constraints in current research, and opportunities that may be lost with existing funding processes, by interviewing selected scientists and fund providers for their views on curiosity-driven research and the freedom needed to allow science to flourish. The transcripts were analysed using a grounded theory approach to gather recurrent themes from the interviews.
The results from these interviews suggest that scientists often cannot predict the future applications of research. Constraints such as lack of scientific freedom, and a narrow focus on relevance and accountability were believed to stifle the discovery process. Although it was acknowledged that some research projects do need a clear and measurable framework, the interviewees saw a need for inquisitive, blue skies research to be managed in a different way. They provided examples of situations where money allocated to 'safe' funding was used for more innovative research.
This sample of key UK scientists and grant providers acknowledge the importance of basic blue skies research. Yet the current evaluation process often requires that scientists predict their likely findings and estimate short-term impact, which does not permit freedom of research direction. There is a vital need for prominent scientists and for universities to help the media, the public, and policy makers to understand the importance of innovative thought along with the need for scientists to have the freedom to challenge accepted thinking. Encouraging an avenue for blue skies research could have immense influence over future scientific discoveries.
Shewanellae are facultative γ-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy metals and radionuclides and for energy generation in microbial fuel cells. Extensive experimental efforts over the last several years and the availability of 21 sequenced Shewanella genomes made it possible to collect and integrate a wealth of information on the genus into one public resource providing new avenues for making biological discoveries and for developing a system level understanding of the cellular processes. The Shewanella knowledgebase was established in 2005 to provide a framework for integrated genome-based studies on Shewanella ecophysiology. The present version of the knowledgebase provides access to a diverse set of experimental and genomic data along with tools for curation of genome annotations and visualization and integration of genomic data with experimental data. As a demonstration of the utility of this resource, we examined a single microarray data set from Shewanella oneidensis MR-1 for new insights into regulatory processes. The integrated analysis of the data predicted a new type of bacterial transcriptional regulation involving co-transcription of the intergenic region with the downstream gene and suggested a biological role for co-transcription that likely prevents the binding of a regulator of the upstream gene to the regulator binding site located in the intergenic region.
Database URL: http://shewanella-knowledgebase.org:8080/Shewanella/ or http://spruce.ornl.gov:8080/Shewanella/
Electronic-nose devices have received considerable attention in the field of sensor technology during the past twenty years, largely due to the discovery of numerous applications derived from research in diverse fields of applied sciences. Recent applications of electronic nose technologies have come through advances in sensor design, material improvements, software innovations and progress in microcircuitry design and systems integration. The invention of many new e-nose sensor types and arrays, based on different detection principles and mechanisms, is closely correlated with the expansion of new applications. Electronic noses have provided a plethora of benefits to a variety of commercial industries, including the agricultural, biomedical, cosmetics, environmental, food, manufacturing, military, pharmaceutical, regulatory, and various scientific research fields. Advances have improved product attributes, uniformity, and consistency as a result of increases in quality control capabilities afforded by electronic-nose monitoring of all phases of industrial manufacturing processes. This paper is a review of the major electronic-nose technologies, developed since this specialized field was born and became prominent in the mid 1980s, and a summarization of some of the more important and useful applications that have been of greatest benefit to man.
artificial olfaction; conducting polymers; electronic aroma detection; e-nose