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1.  Welcome to Journal of Ethnobiology and Ethnomedicine 
Ethnobiology is a multidisciplinary field of study that draws on approaches and methods from both the social and biological sciences. Ethnobiology aims at investigating culturally based biological and environmental knowledge, cultural perception and cognition of the natural world, and associated behaviours and practices. Ethnomedicine is concerned with the cultural interpretations of health, disease and illness and also addresses the health care seeking process and healing practices. Research interest and activities in the areas of ethnobiology and ethnomedicine have increased tremendously in the last decade. Since the inception of the disciplines, scientific research in ethnobiology and ethnomedicine has made important contributions to understanding traditional subsistence and medical knowledge and practice. The Journal of Ethnobiology and Ethnomedicine (JEE) invites manuscripts and reviews based on original interdisciplinary research from around the world on the inextricable relationships between human cultures and nature, on Traditional Environmental Knowledge (TEK), folk and traditional medical knowledge, as well as on the relevance of the above for Primary Health Care (PHC) policies in developing countries.
PMCID: PMC1266047
2.  The philosophy of scientific experimentation: a review 
Practicing and studying automated experimentation may benefit from philosophical reflection on experimental science in general. This paper reviews the relevant literature and discusses central issues in the philosophy of scientific experimentation. The first two sections present brief accounts of the rise of experimental science and of its philosophical study. The next sections discuss three central issues of scientific experimentation: the scientific and philosophical significance of intervention and production, the relationship between experimental science and technology, and the interactions between experimental and theoretical work. The concluding section identifies three issues for further research: the role of computing and, more specifically, automating, in experimental research, the nature of experimentation in the social and human sciences, and the significance of normative, including ethical, problems in experimental science.
PMCID: PMC2809324  PMID: 20098589
3.  Welcome to Journal of Foot and Ankle Research: a new open access journal for foot health professionals 
Journal of Foot and Ankle Research (JFAR) is a new, open access, peer-reviewed online journal that encompasses all aspects of policy, organisation, delivery and clinical practice related to the assessment, diagnosis, prevention and management of foot and ankle disorders. JFAR will cover a wide range of clinical subject areas, including diabetology, paediatrics, sports medicine, gerontology and geriatrics, foot surgery, physical therapy, dermatology, wound management, radiology, biomechanics and bioengineering, orthotics and prosthetics, as well the broad areas of epidemiology, policy, organisation and delivery of services related to foot and ankle care. The journal encourages submission from all health professionals who manage lower limb conditions, including podiatrists, nurses, physical therapists and physiotherapists, orthopaedists, manual therapists, medical specialists and general medical practitioners, as well as health service researchers concerned with foot and ankle care. All manuscripts will undergo open peer review, and all accepted manuscripts will be freely available on-line using the open access platform of BioMed Central.
PMCID: PMC2547890  PMID: 18822156
4.  Bioenergy research: a new paradigm in multidisciplinary research 
The field of biology is becoming increasingly interdisciplinary and cross-cutting. This changing research atmosphere is creating the way for a new kind of enquiry that while building upon the traditional research establishment is providing a new multidisciplinary framework to more effectively address scientific grand challenges. Using the US Department of Energy sponsored BioEnergy Science Center as an example, we highlight how impactful breakthroughs in biofuel science can be achieved within a large cross-disciplinary team environment. Such transformational insights are key to furthering our understanding and in generating models, theories and processes that can be used to overcome recalcitrance of biomass for sustainable biofuel production. Multidisciplinary approaches have an increasingly greater role to play in meeting rising demands for food, fibre, energy, clean environment and good health. Discoveries achieved by diverse minds and cross-applications of tools and analytical approaches have tremendous potential to fill existing knowledge gaps, clear roadblocks and facilitate translation of basic sciences discoveries as solutions towards addressing some of the most pressing global issues.
PMCID: PMC3227023  PMID: 20542958
bioenergy; ethanol; plant; microbe; integrated science
5.  Journal of Ethnobiology and Ethnomedicine – achievements and perspectives 
Last summer we officially launched the Journal of Ethnobiology and Ethnomedicine, published by BioMedCentral, with the aim of establishing a serious, peer-reviewed, open-access online journal that focuses on the multidisciplinary, interdisciplinary, and transdisciplinary fields of ethnobiology and ethnomedicine, drawing on approaches and methods from both the social and biological sciences. The strong start vindicates the widely held belief that the journal responds to a real need within the research community.
The success of the journal has been most gratifying. The steady influx of submissions of high scientific standards illustrates the strong demand for a dynamic, proactive, and open-minded scientific journal in these research areas. Our aim has been to dedicate JEE to the "scientific communities" worldwide, particularly those in the developing countries.
PMCID: PMC1383503  PMID: 16460576
6.  The surveillance state of behavioral automation 
Current Opinion in Neurobiology  2012;22(1):170-176.
► Behavioral automation is accelerating experimental throughput. ► Automation is integrating behavior with physiology. ► Comprehensive observation allows quantitative description of complex behaviors. ► Observational methods are being integrated with psychology experiments.
Genetics’ demand for increased throughput is driving automatization of behavior analysis far beyond experimental workhorses like circadian monitors and the operant conditioning box. However, the new automation is not just faster: it is also allowing new kinds of experiments, many of which erase the boundaries of the traditional neuroscience disciplines (psychology, ethology and physiology) while producing insight into problems that were otherwise opaque. Ironically, a central theme of current automatization is to improve observation of animals in increasingly naturalistic environments. This is not just a return to 19th century priorities: the new observational methods provide unprecedented quantitation of actions and ever-closer integration with experimentation.
PMCID: PMC3398388  PMID: 22119142
7.  Korean Association of Medical Journal Editors at the Forefront of Improving the Quality and Indexing Chances of its Member Journals 
Journal of Korean Medical Science  2013;28(5):648-650.
The article overviews some achievements and problems of Korean medical journals published in the highly competitive journal environment. Activities of Korean Association of Medical Journal Editors (KAMJE) are viewed as instrumental for improving the quality of Korean articles, indexing large number of local journals in prestigious bibliographic databases and launching new abstract and citation tracking databases or platforms (eg KoreaMed, KoreaMed Synapse, the Western Pacific Regional Index Medicus [WPRIM]). KAMJE encourages its member journals to upgrade science editing standards and to legitimately increase citation rates, primarily by publishing more great articles with global influence. Experience gained by KAMJE and problems faced by Korean editors may have global implications.
PMCID: PMC3653074  PMID: 23678253
Periodicals as Topic; Medicine; Learned Associations; Journal Indexing; Science Communication; Korea
8.  Welcome to Biomatter 
Biomatter  2011;1(1):1-2.
It is with great pleasure and honor that I introduce Biomatter, a new international and transdisciplinary journal for the publication of peer-reviewed original research exploring the clinical and laboratory investigations in the field of science and application of biomaterials.
Recent developments in medicine have resulted in a considerable and unprecedented increase in lifespan. The invention of artificial implants made from biomaterials in the 1960s created a whole new scientific field and resulted in revolutionary technologies that strongly contributed to this increase in life expectancy. Since then, many exciting advancements shaped modern biomaterials science, which itself originated several new fields, with biology playing a major role and where the separation between engineering and health sciences can hardly be distinguished. Current and future research efforts in this field are believed to result in new therapeutic approaches to prevent and treat debilitating and life-threatening diseases.Biomatter intends to be on the forefront of disclosing these developments.
Biomatter appears as a forum to discuss and disclose the relevant advancements in the exciting and fast-growing field of science and application of biomaterials. It is widely anticipated that current and upcoming advances will soon result in products with potential to dramatically change the way in which we live, probably with yet-unimaginable future implications in healthcare.
PMCID: PMC3548248  PMID: 23507725
9.  Welcome To International Seminars In Surgical Oncology 
This editorial marks the launch of a new online journal for surgical and medical oncology. The internet has produced a profound shift in the way in which clinicians, researchers and patients seek, interpret and utilise medical information and research. The launch of our journal comes at a time when these changes are in a rapid phase of development and consolidation.
PMCID: PMC483031  PMID: 15285811
10.  Welcome to Implementation Science 
Implementation research is the scientific study of methods to promote the systematic uptake of research findings and other evidence-based practices into routine practice, and, hence, to improve the quality and effectiveness of health services and care. This relatively new field includes the study of influences on healthcare professional and organisational behaviour.
Implementation Science will encompass all aspects of research in this field, in clinical, community and policy contexts. This online journal will provide a unique platform for this type of research and will publish a broad range of articles – study protocols, debate, theoretical and conceptual articles, rigorous evaluations of the process of change, and articles on methodology and rigorously developed tools – that will enhance the development and refinement of implementation research. No one discipline, research design, or paradigm will be favoured.
Implementation Science looks forward to receiving manuscripts that facilitate the continued development of the field, and contribute to healthcare policy and practice.
PMCID: PMC1436009
11.  Bridging the Divide between Science and Journalism 
There are countless reasons nearly every scientist should learn how to communicate effectively with the media, including increased understanding of critical research findings to attract or sustain funding and build new professional partnerships that will further propel forward research. But where do scientists begin? Bridging the Divide between Science and Journalism offers practical tips for any scientist looking to work with the media.
Given the traditional and internet-based sources for medical research and healthcare-related news now available, it is imperative that scientists know how to communicate their latest findings through the appropriate channels. The credible media channels are managed by working journalists, so learning how to package vast, technical research in a form that is appetizing and "bite-sized" in order to get their attention, is an art. Reducing years of research into a headline can be extremely difficult and certainly doesn't come naturally to every scientist, so this article provides suggestions on how to work with the media to communicate your findings.
PMCID: PMC2847545  PMID: 20219123
12.  Evaluation Criteria for Publishing in Top-Tier Journals in Environmental Health Sciences and Toxicology 
Environmental Health Perspectives  2011;119(7):896-899.
Background: Trying to publish a paper in a top-rated peer-reviewed journal can be a difficult and frustrating experience for authors. It is important that authors understand the general review process before submitting manuscripts for publication.
Objectives: Editors-in-chief and associate editors from top-tier journals such as Environmental Health Perspectives (EHP), Toxicological Sciences, Journal of Pharmacology and Experimental Therapeutics, and Chemical Research in Toxicology were asked to provide guidance concerning the writing and submission of papers to their journals.
Discussion: The editors reviewed the manuscript review process for their journals, elaborated on the evaluation criteria for reviewing papers, and provided advice for future authors in preparing their papers.
Conclusions: The manuscript submission process was similar for all of the journals with the exception of EHP that includes an initial screening in which about two-thirds of submitted papers are returned to the authors without review. The evaluation criteria used by the journals were also similar. Papers that are relevant to the scope of the journal, are innovative, significantly advance the field, are well written, and adhere to the instructions to authors have a higher likelihood of being accepted. The editors advised potential authors to ensure that the topic of the paper is within the scope of the journal, represents an important problem, is carefully prepared according to the instructions to authors, and to seek editorial assistance if English is not the primary language of the authors.
PMCID: PMC3222983  PMID: 21414890
environmental health sciences; evaluation criteria; peer review; top-tier journals; toxicology
13.  A new journal – "Theoretical Biology and Medical Modelling" 
Biology has a conceptual basis that allows one to build models and theorize across many life sciences, including medicine and medically-related disciplines. A dearth of good venues for publication has been perceived during a period when bioinformatics, systems analysis and biomathematics are burgeoning.
Steps have been taken to provide the sort of journal with a quick turnaround time for manuscripts which is online and freely accessible to all readers, whatever their persuasion or discipline. We have now been running for some time a journal which has had many good papers presented pre-launch, and a steady stream of papers thereafter. The value of this journal as a new venue has already been vindicated.
Within a short space of time, we have founded a state-of-the-art electronic journal freely accessible to all in a much sort-after interdisciplinary field that will be of benefit to the thinking life scientist, which must include medically qualified doctors as well as scientists who prefer to build their new hypotheses on basic principles and sound concepts underpinning biology. At the same time, these principles are not sacrosanct and require critical analysis. The journal promises to deliver many exciting ideas in the future.
PMCID: PMC1156957  PMID: 15949046
14.  Towards a new kind of experimental psycho-aesthetics? Reflections on the Parallellepipeda project 
i-Perception  2011;2(6):648-678.
Experimental psycho-aesthetics—the science aimed at understanding the factors that determine aesthetic experience—is reviewed briefly as background to describe the Parallellepipeda project, a cross-over project between artists and scientists in Leuven. In particular, I sketch how it started and developed further, with close interactions between the participating artists and scientists. A few examples of specific research projects are mentioned to illustrate the kind of research questions we address and the methodological approach we have taken. We often found an effect of providing participants with additional information, a difference between novice and expert participants, and a shift with increasing experience with an artwork, in the direction of tolerating more complexity and acquiring more order from it. By establishing more connections between parts of an artwork and more associations to the artwork, it becomes a stronger Gestalt, which is more easily mastered by the viewer and leads to increased appreciation. In the final part of the paper, I extract some general lessons from the project regarding a possible new way of doing psycho-aesthetics research, which is able to solve some of the problems of traditional experimental psycho-aesthetics (eg, trade-off between experimental control and ecological validity).
PMCID: PMC3485798  PMID: 23145251
art; perception; eye movements; aesthetics; ecological validity; expertise; Gestalt; mid-level vision
15.  Welcome Message from the Scientific Programme Committee 
It gives us great pleasure to welcome you to MEDNET99 - The 4th World Congress on the Internet in Medicine.
MEDNET99 is an international meeting which aims to bring together researchers, developers and users involved in the application of the Internet in Medicine. The Congress - this year under the theme "Towards the Millennium of Cybermedicine - will provide a forum for exploration of the rapidly developing relationship between medical sciences and the Internet, and is relevant to all medical and health care professionals, as well as those involved in the development and application of the new technological opportunities offered to the medical field by the Internet and the World Wide Web.
This year's Congress will take place over three full days, 19th - 21st September 1999, in the small and beautiful town of Heidelberg, one of the most famous tourist destinations in Germany and the town with the oldest German University.
MEDNET99 follows on from three successful MEDNET meetings, all held in the United Kingdom, which were attended by large international and multi-disciplinary groups of delegates. MEDNET98 was attended by more than 250 participants. After these three successful conferences in the United Kingdom, this year's MEDNET will for the first time be hosted outside of the UK. It will therefore hopefully be the first in a long series of World Congresses of Internet in Medicine hosted in different countries around the globe.
MEDNET99 will be preceded by several events on Saturday, 18th September: In a series of tutorials, experts in the field share their knowledge. To take account of local developments in the Internet scene we also organised a satellite symposium on "Internet and Medicine in Germany". A further novum is the "patient afternoon", where we bring together health care professionals with consumers to talk about medical information — in particular cancer information — on the Internet.
MEDNET99 will be focusing on the following themes:
applications of the Internet in medical information exchange and medical education
role of Internet and information exchange in evidence-based healthcare
use of the Internet for consumer health promotion and impact of the Internet on public health
global and regional health information networks
commercial information systems and portal sites for physicians
eJournals and scientific publishing on the Internet, online peer-review, impact of Internet on traditional medical publishing
search engines, search agents and other search tools
electronic mail
using the Internet for medical research and clinical trials
quality of Internet information
Internet usage statistics and demographics
clinical information systems and Intranets
system design issues
legal and ethical issues
As well as providing a forum for delegates to exchange valuable information, MEDNET99 will provide a varied program of social events and interesting workshops.
On behalf of the organisers and the Scientific Programme Committee of MEDNET99, we would like to extend a warm welcome to Heidelberg and we hope that you will all have a stimulating and rewarding Congress.
PMCID: PMC1761831
16.  Welcome to Thyroid Research 
Thyroid Research  2008;1:1.
Welcome to the first issue of Thyroid Research, a new journal published by BioMed Central, which aims at providing a platform for both researchers and clinicians to discuss a broad spectrum of thyroidology and related issues. These include physiological mechanisms of thyroid hormone action, secretory regulations, immunological and genetic aspects and, finally, news and information on state-of-the-art diagnostic equipment and treatment protocols for more effective management of thyroid disorders.
PMCID: PMC2577041  PMID: 19014644
17.  Journal of Experimental & Clinical Assisted Reproduction: shaping the future of research and practice in reproductive endocrinology/infertility 
Journal of Experimental & Clinical Assisted Reproduction is an open access, online, peer-review journal publishing papers on all aspects of research into reproductive endocrinology, infertility, bioethics and the advanced reproductive technologies. The journal reports on important developments impacting the field of human reproductive medicine and surgery. The field exists as a sub-specialty of obstetrics & gynecology, focusing on the diagnosis and treatment of complex human reproductive problems. The continued growth of this relatively new field depends on quality research by proven scientists as well as junior investigators who, together, make contributions to this area of medical and surgical practice. The publishing revolution made possible by internet technology presages a bright future for continued interdisciplinary collaboration among researchers. Against this background, Journal of Experimental & Clinical Assisted Reproduction exists for the scientific community to facilitate this scholarly dialogue.
PMCID: PMC524035  PMID: 15507153
publishing; reproductive medicine; internet; research; trends
18.  Treatment Integrity of School-Based Interventions with Children in the Journal of Applied Behavior Analysis 1991-2005 
We reviewed all school-based experimental studies with individuals 0 to 18 years published in the Journal of Applied Behavior Analysis (JABA) between 1991 and 2005. A total of 142 articles (152 studies) that met review criteria were included. Nearly all (95%) of these experiments provided an operational definition of the independent variable, but only 30% of the studies provided treatment integrity data. Nearly half of studies (45%) were judged to be at high risk for treatment inaccuracies. Treatment integrity data were more likely to be included in studies that used teachers, multiple treatment agents, or both. Although there was a substantial increase in reporting operational definitions of independent variables, results suggest that there was only a modest improvement in reported integrity over the past 30 years of JABA studies. Recommendations for research and practice are discussed.
PMCID: PMC2078573  PMID: 18189097
treatment integrity; child studies; school interventions; applied behavior analysis
19.  Properties of journal impact in relation to bibliometric research group performance indicators 
Scientometrics  2012;92(2):457-469.
In this paper we present a compilation of journal impact properties in relation to other bibliometric indicators as found in our earlier studies together with new results. We argue that journal impact, even calculated in a sufficiently advanced way, becomes important in evaluation practices based on bibliometric analysis only at an aggregate level. In the relation between average journal impact and actual citation impact of groups, the influence of research performance is substantial. Top-performance as well as lower performance groups publish in more or less the same range of journal impact values, but top-performance groups are, on average, more successful in the entire range of journal impact. We find that for the high field citation-density groups a larger size implies a lower average journal impact. For groups in the low field citation-density regions however a larger size implies a considerably higher average journal impact. Finally, we found that top-performance groups have relatively less self-citations than the lower performance groups and this fraction is decreasing with journal impact.
PMCID: PMC3399073  PMID: 22844167
Impact factor; Journal impact; Bibliometric analysis; Research group performance
20.  Collaboration for Improved Disease Surveillance Literature Review 
To improve the method of automated retrieval of surveillance-related literature from a wide range of indexed repositories.
The ISDS Research Committee (RC) is an interdisciplinary group of researchers interested in various topics related to disease surveillance. The RC hosts a literature review process with a permanent repository of relevant journal articles and bimonthly calls that provide a forum for discussion and author engagement. The calls have led to workgroups and society-wide events, boosted interest in the ISDS Conference, and fostered networking among participants.
Since 2007, the RC has identified and classified published articles using an automated search method with the aim of progressing ISDS’s mission of advancing the science and practice of disease surveillance by fostering collaboration and increasing awareness of innovations in the field of surveillance. The RC literature review efforts have provided an opportunity for interprofessional collaboration and have resulted in a repository of over 1,000 articles, but feedback from ISDS members indicated relevant articles were not captured by the existing methodology. The method of automated literature retrieval was thus refined to improve efficiency and inclusiveness of stakeholder interests.
The earlier literature review method was implemented from March 2007 to March 2012. PubCrawler [1] (articles indexed in Medline) and Google Scholar [2] search results were sent to the RC via automated e-mail. To refine this method, the RC developed search strings in PubMed [3], Embase [4], and Scopus [5], consisting of over 100 terms suggested by members. After evaluating these methods, we found that the Scopus search is the most comprehensive and improved the cross-disciplinary scope. Scopus results allowed filtering of 50–100 titles and abstracts in fewer than 30 minutes each week for the identification of relevant articles (Figure).
Journal titles were categorized to assess the increased range of fields covered; categories include epidemiology, agriculture, economics, and medicine (51 categories total).
Since implementing the new method, potentially relevant articles identified per month increased from an average of 19 (SD: 13; n= 31) to 159 (SD: 63; n= 3). Both methods identified articles in the health sciences, but the new search also captured articles in the life, physical, and social sciences. Between March 2007 and March 2012, articles selected were classified into an average of 10 different categories per literature review (SD: 4; n= 31) versus an average of 33 categories (SD: 5; n= 3) with the updated process.
The new search method improves upon the previous method – it captures relevant articles indexed in health science and other secondary databases beyond Medline. The new method has resulted in a greater number of relevant literature articles, from a broader range of disciplines, and in reduced amount of preparation time as compared to the results of the previous search method. This improvement may increase multi-disciplinary discussions and partnerships, but changes in online publishing pose challenges to continued access of the new range of articles.
PMCID: PMC3692894
Disease surveillance literature; ISDS Research Committee; Literature search
21.  What The Cognitive Neurosciences Mean To Me 
Mens Sana Monographs  2007;5(1):158-168.
Cognitive Neuroscience is an interdisciplinary area of research that combines measurement of brain activity (mostly by means of neuroimaging) with a simultaneous performance of cognitive tasks by human subjects. These investigations have been successful in the task of connecting the sciences of the brain (Neurosciences) and the sciences of the mind (Cognitive Sciences). Advances on this kind of research provide a map of localization of cognitive functions in the human brain. Do these results help us to understand how mind relates to the brain? In my view, the results obtained by the Cognitive Neurosciences lead to new investigations in the domain of Molecular Neurobiology, aimed at discovering biophysical mechanisms that generate the activity measured by neuroimaging instruments. In this context, I argue that the understanding of how ionic/molecular processes support cognition and consciousness cannot be made by means of the standard reductionist explanations. Knowledge of ionic/molecular mechanisms can contribute to our understanding of the human mind as long as we assume an alternative form of explanation, based on psycho-physical similarities, together with an ontological view of mentality and spirituality as embedded in physical nature (and not outside nature, as frequently assumed in western culture).
PMCID: PMC3192380  PMID: 22058629
“Covering law” model; cognitive molecular neurobiology; cognitive neuroscience; embedded and embodied cognition; homeoresis; philosophy of mind; reductionism; structuralism; structuralist-naturalistic approach
22.  Establishing a new journal for systematic review products 
Systematic Reviews  2012;1:1.
Welcome to a new age in publishing systematic reviews. We hope the launch of Systematic Reviews will resonate with a broad spectrum of readers interested in using them in a variety of ways, such as providing comprehensive and up to date evidence for patient management, informing health policy, and developing rigorous practice guidelines. Systematic reviews are increasingly popular. Our journal is committed to publishing a wide variety of well conducted and transparently reported systematic reviews and associated research. We are open access and electronic and not confined by space and so offer scope for publishing reviews in detail and providing a modern and innovative approach to publishing. We look forward to participating in the voyage with all of our readers.
PMCID: PMC3348672  PMID: 22587946
new journal; systematic reviews; open access
23.  Epidemiology: second-rate science? 
Public Health Reports  1998;113(4):312-320.
In recent years epidemiology has come under increasing criticism in regulatory and public arenas for being "unscientific." The tobacco industry has taken advantage of this, insisting for decades that evidence linking cigarettes and lung cancer falls short of proof. Moreover, many epidemiologists remain unduly skeptical and self-conscious about the status of their own causal claims. This situation persists in part because of a widespread belief that only the laboratory can provide evidence sufficient for scientific proof. Adherents of this view erroneously believe that there is no element of uncertainty or inductive inference in the "direct observation" of the laboratory researcher and that epidemiology provides mere "circumstantial" evidence. The historical roots of this attitude can be traced to philosopher John Stuart Mill and physiologist Claude Bernard and their influence on modern experimental thinking. The author uses the debate over cigarettes and lung cancer to examine ideas of proof in medical science and public health, concluding that inductive inference from a limited sample to a larger population is an element in all empirical science.
PMCID: PMC1308387  PMID: 9672568
24.  Assessment of community-submitted ontology annotations from a novel database-journal partnership 
As the scientific literature grows, leading to an increasing volume of published experimental data, so does the need to access and analyze this data using computational tools. The most commonly used method to convert published experimental data on gene function into controlled vocabulary annotations relies on a professional curator, employed by a model organism database or a more general resource such as UniProt, to read published articles and compose annotation statements based on the articles' contents. A more cost-effective and scalable approach capable of capturing gene function data across the whole range of biological research organisms in computable form is urgently needed. We have analyzed a set of ontology annotations generated through collaborations between the Arabidopsis Information Resource and several plant science journals. Analysis of the submissions entered using the online submission tool shows that most community annotations were well supported and the ontology terms chosen were at an appropriate level of specificity. Of the 503 individual annotations that were submitted, 97% were approved and community submissions captured 72% of all possible annotations. This new method for capturing experimental results in a computable form provides a cost-effective way to greatly increase the available body of annotations without sacrificing annotation quality.
Database URL:
PMCID: PMC3410254  PMID: 22859749
25.  Toward an interactive article: integrating journals and biological databases 
BMC Bioinformatics  2011;12:175.
Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture.
We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases.
Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.
PMCID: PMC3213741  PMID: 21595960

Results 1-25 (607299)