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1.  OvidSP Medline-to-PubMed search filter translation: a methodology for extending search filter range to include PubMed's unique content 
Background
PubMed translations of OvidSP Medline search filters offer searchers improved ease of access. They may also facilitate access to PubMed’s unique content, including citations for the most recently published biomedical evidence. Retrieving this content requires a search strategy comprising natural language terms (‘textwords’), rather than Medical Subject Headings (MeSH). We describe a reproducible methodology that uses a validated PubMed search filter translation to create a textword-only strategy to extend retrieval to PubMed’s unique heart failure literature.
Methods
We translated an OvidSP Medline heart failure search filter for PubMed and established version equivalence in terms of indexed literature retrieval. The PubMed version was then run within PubMed to identify citations retrieved by the filter’s MeSH terms (Heart failure, Left ventricular dysfunction, and Cardiomyopathy). It was then rerun with the same MeSH terms restricted to searching on title and abstract fields (i.e. as ‘textwords’). Citations retrieved by the MeSH search but not the textword search were isolated. Frequency analysis of their titles/abstracts identified natural language alternatives for those MeSH terms that performed less effectively as textwords. These terms were tested in combination to determine the best performing search string for reclaiming this ‘lost set’. This string, restricted to searching on PubMed’s unique content, was then combined with the validated PubMed translation to extend the filter’s performance in this database.
Results
The PubMed heart failure filter retrieved 6829 citations. Of these, 834 (12%) failed to be retrieved when MeSH terms were converted to textwords. Frequency analysis of the 834 citations identified five high frequency natural language alternatives that could improve retrieval of this set (cardiac failure, cardiac resynchronization, left ventricular systolic dysfunction, left ventricular diastolic dysfunction, and LV dysfunction). Together these terms reclaimed 157/834 (18.8%) of lost citations.
Conclusions
MeSH terms facilitate precise searching in PubMed’s indexed subset. They may, however, work less effectively as search terms prior to subject indexing. A validated PubMed search filter can be used to develop a supplementary textword-only search strategy to extend retrieval to PubMed’s unique content. A PubMed heart failure search filter is available on the CareSearch website (http://www.caresearch.com.au) providing access to both indexed and non-indexed heart failure evidence.
doi:10.1186/1471-2288-13-86
PMCID: PMC3700762  PMID: 23819658
Information Retrieval; Search Filters; Search Filter Translation; PubMed; Medline; Medical Subject Headings (MeSH)
2.  A Framework and Methodology for Navigating Disaster and Global Health in Crisis Literature 
PLoS Currents  2013;5:ecurrents.dis.9af6948e381dafdd3e877c441527cba0.
Both ‘disasters’ and ‘global health in crisis’ research has dramatically grown due to the ever-increasing frequency and magnitude of crises around the world. Large volumes of peer-reviewed literature are not only a testament to the field’s value and evolution, but also present an unprecedented outpouring of seemingly unmanageable information across a wide array of crises and disciplines. Disaster medicine, health and humanitarian assistance, global health and public health disaster literature all lie within the disaster and global health in crisis literature spectrum and are increasingly accepted as multidisciplinary and transdisciplinary disciplines. Researchers, policy makers, and practitioners now face a new challenge; that of accessing this expansive literature for decision-making and exploring new areas of research. Individuals are also reaching beyond the peer-reviewed environment to grey literature using search engines like Google Scholar to access policy documents, consensus reports and conference proceedings. What is needed is a method and mechanism with which to search and retrieve relevant articles from this expansive body of literature. This manuscript presents both a framework and workable process for a diverse group of users to navigate the growing peer-reviewed and grey disaster and global health in crises literature. Methods: Disaster terms from textbooks, peer-reviewed and grey literature were used to design a framework of thematic clusters and subject matter ‘nodes’. A set of 84 terms, selected from 143 curated terms was organized within each node reflecting topics within the disaster and global health in crisis literature. Terms were crossed with one another and the term ‘disaster’. The results were formatted into tables and matrices. This process created a roadmap of search terms that could be applied to the PubMed database. Each search in the matrix or table results in a listed number of articles. This process was applied to literature from PubMed from 2005-2011. A complementary process was also applied to Google Scholar using the same framework of clusters, nodes, and terms expanding the search process to include the broader grey literature assets. Results: A framework of four thematic clusters and twelve subject matter nodes were designed to capture diverse disaster and global health in crisis-related content. From 2005-2011 there were 18,660 articles referring to the term [disaster]. Restricting the search to human research, MeSH, and English language there remained 7,736 identified articles representing an unmanageable number to adequately process for research, policy or best practices. However, using the crossed search and matrix process revealed further examples of robust realms of research in disasters, emergency medicine, EMS, public health and global health. Examples of potential gaps in current peer-reviewed disaster and global health in crisis literature were identified as mental health, elderly care, and alternate sites of care. The same framework and process was then applied to Google Scholar, specifically for topics that resulted in few PubMed search returns. When applying the same framework and process to the Google Scholar example searches retrieved unique peer-reviewed articles not identified in PubMed and documents including books, governmental documents and consensus papers. Conclusions: The proposed framework, methodology and process using four clusters, twelve nodes and a matrix and table process applied to PubMed and Google Scholar unlocks otherwise inaccessible opportunities to better navigate the massively growing body of peer-reviewed disaster and global health in crises literature. This approach will assist researchers, policy makers, and practitioners to generate future research questions, report on the overall evolution of the disaster and global health in crisis field and further guide disaster planning, prevention, preparedness, mitigation response and recovery.
doi:10.1371/currents.dis.9af6948e381dafdd3e877c441527cba0
PMCID: PMC3625621  PMID: 23591457
3.  Twenty Years of Research on Mineral Trioxide Aggregate: A Scientometric Report 
Iranian Endodontic Journal  2013;8(1):1-5.
Introduction
Mineral trioxide aggregate (MTA) has been suggested for root-end filling, vital pulp therapy, apical plug, perforations repair, and root canal filling. Since the introduction of MTA in 1993, many studies about this material have been published. The aim of this survey was to illustrate statistical information about published articles in PubMed-index journals vis-à-vis the various aspects of this biomaterial.
Material and Methods
A PubMed search was performed to retrieve the relative articles from 1993 to August 2012. The data of each article including publication year, journal name, number of authors, first author name, affiliations and study design were recorded. Citation of each article till 2009 was obtained from Scopus and Google scholar databases. Data were analyzed to determine the related scientometric indicators.
Results
In total, 1027 articles were found in PubMed-indexed journals which show considerable increase from 2 papers in 1993 to 139 in 2011. While ~62% of articles had no level of evidence, only ~5% could be classified as having the highest level of evidence (LOE1); however, the majority of LOE1 articles originated from Iran (~1%: n=10). Journal of Endodontics, as the top rank journal, published 31.7% of MTA related articles. The majority of articles were four-authored (19.6%). Most of the articles originated from USA (21.9%), Brazil (18.5%) and Iran (8.76%). The average number of citation for the top ten articles from Scopus was 231.
Conclusion
This data demonstrates that during the past two decades, research on this novel endodontic biomaterial had a rapid positive trend especially during the last 5 years. Further high-level evidence articles for the various clinical applications of MTA would result in superior clinical decision making and stronger scientific-based endodontic practice.
PMCID: PMC3570971  PMID: 23411944
Biomaterial; Endodontic; Mineral trioxide aggregate; MTA; PubMed; Scientometric
4.  Searching PubMed during a Pandemic 
PLoS ONE  2010;5(4):e10039.
Background
The 2009 influenza A(H1N1) pandemic has generated thousands of articles and news items. However, finding relevant scientific articles in such rapidly developing health crises is a major challenge which, in turn, can affect decision-makers' ability to utilise up-to-date findings and ultimately shape public health interventions. This study set out to show the impact that the inconsistent naming of the pandemic can have on retrieving relevant scientific articles in PubMed/MEDLINE.
Methodology
We first formulated a PubMed search algorithm covering different names of the influenza pandemic and simulated the results that it would have retrieved from weekly searches for relevant new records during the first 10 weeks of the pandemic. To assess the impact of failing to include every term in this search, we then conducted the same searches but omitted in turn “h1n1,” “swine,” “influenza” and “flu” from the search string, and compared the results to those for the full string.
Principal Findings
On average, our core search string identified 44.3 potentially relevant new records at the end of each week. Of these, we determined that an average of 27.8 records were relevant. When we excluded one term from the string, the percentage of records missed out of the total number of relevant records averaged 18.7% for omitting “h1n1,” 13.6% for “swine,” 17.5% for “influenza,” and 20.6% for “flu.”
Conclusions
Due to inconsistent naming, while searching for scientific material about rapidly evolving situations such as the influenza A(H1N1) pandemic, there is a risk that one will miss relevant articles. To address this problem, the international scientific community should agree on nomenclature and the specific name to be used earlier, and the National Library of Medicine in the US could index potentially relevant materials faster and allow publishers to add alert tags to such materials.
doi:10.1371/journal.pone.0010039
PMCID: PMC2850925  PMID: 20383330
5.  GO2PUB: Querying PubMed with semantic expansion of gene ontology terms 
Background
With the development of high throughput methods of gene analyses, there is a growing need for mining tools to retrieve relevant articles in PubMed. As PubMed grows, literature searches become more complex and time-consuming. Automated search tools with good precision and recall are necessary. We developed GO2PUB to automatically enrich PubMed queries with gene names, symbols and synonyms annotated by a GO term of interest or one of its descendants.
Results
GO2PUB enriches PubMed queries based on selected GO terms and keywords. It processes the result and displays the PMID, title, authors, abstract and bibliographic references of the articles. Gene names, symbols and synonyms that have been generated as extra keywords from the GO terms are also highlighted. GO2PUB is based on a semantic expansion of PubMed queries using the semantic inheritance between terms through the GO graph. Two experts manually assessed the relevance of GO2PUB, GoPubMed and PubMed on three queries about lipid metabolism. Experts’ agreement was high (kappa = 0.88). GO2PUB returned 69% of the relevant articles, GoPubMed: 40% and PubMed: 29%. GO2PUB and GoPubMed have 17% of their results in common, corresponding to 24% of the total number of relevant results. 70% of the articles returned by more than one tool were relevant. 36% of the relevant articles were returned only by GO2PUB, 17% only by GoPubMed and 14% only by PubMed. For determining whether these results can be generalized, we generated twenty queries based on random GO terms with a granularity similar to those of the first three queries and compared the proportions of GO2PUB and GoPubMed results. These were respectively of 77% and 40% for the first queries, and of 70% and 38% for the random queries. The two experts also assessed the relevance of seven of the twenty queries (the three related to lipid metabolism and four related to other domains). Expert agreement was high (0.93 and 0.8). GO2PUB and GoPubMed performances were similar to those of the first queries.
Conclusions
We demonstrated that the use of genes annotated by either GO terms of interest or a descendant of these GO terms yields some relevant articles ignored by other tools. The comparison of GO2PUB, based on semantic expansion, with GoPubMed, based on text mining techniques, showed that both tools are complementary. The analysis of the randomly-generated queries suggests that the results obtained about lipid metabolism can be generalized to other biological processes. GO2PUB is available at http://go2pub.genouest.org.
doi:10.1186/2041-1480-3-7
PMCID: PMC3599846  PMID: 22958570
Gene ontology; Semantic expansion; Query enrichment; PubMed
6.  “A Good Personal Scientific Relationship”: Philip Morris Scientists and the Chulabhorn Research Institute, Bangkok 
PLoS Medicine  2008;5(12):e238.
Background
This paper examines the efforts of consultants affiliated with Philip Morris (PM), the world's leading transnational tobacco corporation, to influence scientific research and training in Thailand via the Chulabhorn Research Institute (CRI). A leading Southeast Asian institute for environmental health science, the CRI is headed by Professor Dr. Her Royal Highness Princess Chulabhorn, the daughter of the King of Thailand, and it has assumed international significance via its designation as a World Health Organization (WHO) Collaborating Centre in December 2005.
Methods and Findings
This paper analyses previously confidential tobacco industry documents that were made publicly available following litigation in the United States. PM documents reveal that ostensibly independent overseas scientists, now identified as industry consultants, were able to gain access to the Thai scientific community. Most significantly, PM scientist Roger Walk has established close connections with the CRI. Documents indicate that Walk was able to use such links to influence the study and teaching of environmental toxicology in the institute and to develop relations with key officials and local scientists so as to advance the interests of PM within Thailand and across Asia. While sensitivities surrounding royal patronage of the CRI make public criticism extremely difficult, indications of ongoing involvement by tobacco industry consultants suggest the need for detailed scrutiny of such relationships.
Conclusions
The establishment of close links with the CRI advances industry strategies to influence scientific research and debate around tobacco and health, particularly regarding secondhand smoke, to link with academic institutions, and to build relationships with national elites. Such strategies assume particular significance in the national and regional contexts presented here amid the globalisation of the tobacco pandemic. From an international perspective, particular concern is raised by the CRI's recently awarded status as a WHO Collaborating Centre. Since the network of WHO Collaborating Centres rests on the principle of “using national institutions for international purposes,” the documents presented below suggest that more rigorous safeguards are required to ensure that such use advances public health goals rather than the objectives of transnational corporations.
Jeff Collin and Ross MacKenzie analyze tobacco industry documents and find that Philip Morris consultants were able to gain access to a Thai research institute that is a WHO Collaborating Centre.
Editors' Summary
Background.
Tobacco use kills 5.4 million people a year (one person every six seconds) and accounts for one in ten adult deaths worldwide. Globally, the use of tobacco is on the rise, especially in developing countries, which have become a major target for tobacco industry marketing. The tobacco industry has worked hard to try and influence public perceptions about the risks of smoking and the risk of inhaling secondhand smoke (passive smoking). The industry has used a variety of tactics to downplay the health hazards of smoking or inhaling secondhand smoke—two examples are publishing articles casting doubts about the health hazards of tobacco and funding research that is biased toward giving pro-industry results. Another tactic is for tobacco industry consultants to try and gain entry to universities and other academic centers to see if they can influence research and teaching activities.
Why Was This Study Done?
The researchers were concerned that consultants from the tobacco company Philip Morris had gained access to an academic research center in Thailand called the Chulabhorn Research Institute (CRI). The CRI is an internationally renowned teaching institution for a variety of scientific disciplines, including environmental toxicology (the study of how chemicals in the environment, such as tobacco smoke, can affect human health), biomedicine, and biotechnology. The institute has secured funding from the Thai government, the Association of Southeast Nations and the United Nations Development Programme. In 2005 the institute's environmental toxicology unit was designated a World Health Organization (WHO) Collaborating Centre. WHO Collaborating Centres are “institutions such as research institutes, parts of universities or academies, that are designated by the Director-General of the WHO to carry out activities in support of the WHO's programs” (http://www.who.int/collaboratingcentres/en/). The researchers were concerned that Philip Morris consultants had been able to develop relationships with the CRI to help advance the company's interests.
What Did the Researchers Do and Find?
The researchers analyzed previously confidential tobacco industry documents that were made publicly available online following litigation in the United States. They searched two online collections of industry documents—the Legacy Tobacco Documents Library and Tobacco Documents Online—as well as the online collections operated by US-based tobacco companies. They found that consultants to Philip Morris were able to gain access to the scientific community in Thailand. A Philip Morris scientist named Roger Walk was able to establish close connections to the CRI, and he used these connections to influence research and teaching activities at the CRI on environmental toxicology. Walk was also able to build relationships with government officials and scientists in Thailand to help advance the interests of Philip Morris in the country and across Asia.
What Do these Findings Mean?
This study provides evidence that the tobacco industry has established close links with a research institute in Thailand that collaborates with the WHO, and has been able to influence the institute's teaching curriculum and research. Such links are of great concern to the public health community, which is working hard to reduce deaths and disease due to tobacco. These links raise the possibility that the tobacco industry is managing to influence medical research and teaching at academic institutions. The WHO has stated that a firewall is in place between itself and the tobacco industry—but the study authors argue, based on their findings, that “this firewall is not impenetrable.” The study findings, they conclude, highlight a challenge posed to international tobacco control efforts, especially with respect to Article 5.3 of an international treaty called the WHO Framework Convention on Tobacco Control; Article 5.3 addresses the need to protect public health policies from the vested interests of the tobacco industry. The authors say that better safeguards must be put in place to prevent tobacco companies from thwarting public health goals.
Additional Information.
Please access these Web sites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.0050238.
The Legacy Tobacco Documents Library contains over 9.7 million documents created by tobacco companies
Tobacco Documents Online contains over 4 million tobacco industry documents
Over 900 WHO Collaborating Centres are at work in 99 Member States on many health disciplines
The WHO held an inquiry in 2000 into possible tobacco industry influence over the organization (and over other UN agencies), and has published its recommendations in response to this inquiry
The WHO Framework Convention on Tobacco Control is an international treaty on controlling tobacco
doi:10.1371/journal.pmed.0050238
PMCID: PMC2605886  PMID: 19108600
7.  NEMO: Extraction and normalization of organization names from PubMed affiliation strings 
Background. We are witnessing an exponential increase in biomedical research citations in PubMed. However, translating biomedical discoveries into practical treatments is estimated to take around 17 years, according to the 2000 Yearbook of Medical Informatics, and much information is lost during this transition. Pharmaceutical companies spend huge sums to identify opinion leaders and centers of excellence. Conventional methods such as literature search, survey, observation, self-identification, expert opinion, and sociometry not only need much human effort, but are also noncomprehensive. Such huge delays and costs can be reduced by “connecting those who produce the knowledge with those who apply it”. A humble step in this direction is large scale discovery of persons and organizations involved in specific areas of research. This can be achieved by automatically extracting and disambiguating author names and affiliation strings retrieved through Medical Subject Heading (MeSH) terms and other keywords associated with articles in PubMed. In this study, we propose NEMO (Normalization Engine for Matching Organizations), a system for extracting organization names from the affiliation strings provided in PubMed abstracts, building a thesaurus (list of synonyms) of organization names, and subsequently normalizing them to a canonical organization name using the thesaurus.
Results: We used a parsing process that involves multi-layered rule matching with multiple dictionaries. The normalization process involves clustering based on weighted local sequence alignment metrics to address synonymy at word level, and local learning based on finding connected components to address synonymy. The graphical user interface and java client library of NEMO are available at http://lnxnemo.sourceforge.net .
Conclusion: NEMO is developed to associate each biomedical paper and its authors with a unique organization name and the geopolitical location of that organization. This system provides more accurate information about organizations than the raw affiliation strings provided in PubMed abstracts. It can be used for : a) bimodal social network analysis that evaluates the research relationships between individual researchers and their institutions; b) improving author name disambiguation; c) augmenting National Library of Medicine (NLM)’s Medical Articles Record System (MARS) system for correcting errors due to OCR on affiliation strings that are in small fonts; and d) improving PubMed citation indexing strategies (authority control) based on normalized organization name and country.
PMCID: PMC2990275  PMID: 20922666
8.  The Scientific Conferences Organized During War Time (1992-1995) in Sarajevo 
Materia Socio-Medica  2011;23(4):238-248.
Author of this paper spent 1479 days in the siege of Sarajevo, during the period of war time in Bosnia and Herzegovina (B&H). This siege, lasting from 1992 to 1995 (e.g. Dayton Piece agreement was signed in November, 1995) represents the longest siege in the history of the world. Besides usual daily work, as the associate professor of Health education, Medical deontology and Medical informatics for the students of the Faculty of medicine, Faculty of dental medicine, Faculty of Pharmacy and Nursing college of University of Sarajevo, the author organized by himself and contributors, 10 scientific conferences in a sieged Sarajevo. All presented papers at those conferences are published in Proceedings abstract books, as the proof of continuing scientific work, in Sarajevo and other cities in B&H. Additionally, the author continued to publish, in that time, unique PubMed/MedLine indexed journal, - Medical Archives, (i.e. established in 1947) and, in 1993 formed a new journal named - “Acta Informatica Medica” (AIM) , as the Journal of the Bosnian Society of Medical informatics. Bosnian Society of Medical Informatics, thus became the first scientific association from Bosnia and Herzegovina, included in 1994, in the European Federation of Medical Informatics (EFMI) and the International Medical Informatics Assiciation (IMIA) , which was “miracle” from the besieged Sarajevo and war time result of aggression on Bosnia and Herzegovina. It should be noted that the importance of maintaining these academic gatherings, in the circumstances of war, was multifaceted. First of all, thanks to these meetings, the continuity of scientific meetings and activities in the besieged city of Sarajevo was not broken, as well as the continuity of scientific publication, which was crucial for the maintenance of the teaching staff at the university and, finally, in the expansion of the “scientific truth” about what happened in Sarajevo and B&H in these difficult times. All of this was critical to the “survival” of B&H and its people. Some of the published articles, especially in the Medical Archives journal, which even in difficult war conditions did not break the continuity of its publication, and then it was the only scientific journal indexed in B&H, having been consequently cited in the major biomedical data bases in the world. Many scientists abroad have had the opportunity to learn about some of the wonders of Sarajevo “war medicine”, thanks to this journal. Finally, despite the fact that it is another way of expressing its resistance to the aggression on B&H, the organized symposia in the war represented the continuity of the scientific research activities. Bosnia and Herzegovina and Sarajevo under siege, in this way, kept in touch with the civilized world and modern achievements, despite the fact that they were victims of medieval barbarism. In addition, these meetings sent a powerful message to the world about the willingness to register and systematize all the war experiences, especially those related to medicine and medical practice, in terms of what Europe has not known, since the Second World War. Partially, we succeeded in that. The total number of 286 presentations were presented in seven war Conferences, as quantitative and qualitative contribution to the scientific activities, despite the inhuman conditions, in which these articles emerged. These presentations and Conferences testify to the enthusiasm of B&H community and academic institutions that have collaborated with it. Authors and co-authors presented the “war” articles that deserve to be mentioned in the monograph “1479 days of the siege of Sarajevo”. Unfortunately, many of these brave authors are not alive and cannot read this. The task for us remains to remember them by their own good. Old Persian proverb says; “The event which is not recorded is as like it had never happened”. Sapienti sat.
doi:10.5455/msm.2011.23.238-248
PMCID: PMC3633541  PMID: 23678305
Bosnia and Herzegovina; siege; scientific meetings during wartime.
9.  Financial Conflicts of Interest and Reporting Bias Regarding the Association between Sugar-Sweetened Beverages and Weight Gain: A Systematic Review of Systematic Reviews 
PLoS Medicine  2013;10(12):e1001578.
Maira Bes-Rastrollo and colleagues examine whether financial conflicts of interest are likely to bias conclusions from systematic reviews that investigate the relationship between sugar-sweetened beverages and weight gain or obesity.
Please see later in the article for the Editors' Summary
Background
Industry sponsors' financial interests might bias the conclusions of scientific research. We examined whether financial industry funding or the disclosure of potential conflicts of interest influenced the results of published systematic reviews (SRs) conducted in the field of sugar-sweetened beverages (SSBs) and weight gain or obesity.
Methods and Findings
We conducted a search of the PubMed, Cochrane Library, and Scopus databases to identify published SRs from the inception of the databases to August 31, 2013, on the association between SSB consumption and weight gain or obesity. SR conclusions were independently classified by two researchers into two groups: those that found a positive association and those that did not. These two reviewers were blinded with respect to the stated source of funding and the disclosure of conflicts of interest.
We identified 17 SRs (with 18 conclusions). In six of the SRs a financial conflict of interest with some food industry was disclosed. Among those reviews without any reported conflict of interest, 83.3% of the conclusions (10/12) were that SSB consumption could be a potential risk factor for weight gain. In contrast, the same percentage of conclusions, 83.3% (5/6), of those SRs disclosing some financial conflict of interest with the food industry were that the scientific evidence was insufficient to support a positive association between SSB consumption and weight gain or obesity. Those reviews with conflicts of interest were five times more likely to present a conclusion of no positive association than those without them (relative risk: 5.0, 95% CI: 1.3–19.3).
An important limitation of this study is the impossibility of ruling out the existence of publication bias among those studies not declaring any conflict of interest. However, the best large randomized trials also support a direct association between SSB consumption and weight gain or obesity.
Conclusions
Financial conflicts of interest may bias conclusions from SRs on SSB consumption and weight gain or obesity.
Please see later in the article for the Editors' Summary
Editors' Summary
Background
In our daily lives, we frequently rely on the results of scientific research to make decisions about our health. If we are healthy, we may seek out scientific advice about how much exercise to do to reduce our risk of a heart attack, and we may follow dietary advice issued by public health bodies to help us maintain a healthy weight. If we are ill, we expect our treatment to be based on the results of clinical trials and other studies. We assume that the scientific research that underlies our decisions about health-related issues is unbiased and accurate. However, there is increasing evidence that the conclusions of industry-sponsored scientific research are sometimes biased. So, for example, reports of drug trials sponsored by pharmaceutical companies sometimes emphasize the positive results of trials and “hide” unwanted side effects deep within the report or omit them altogether.
Why Was This Study Done?
Although the effects of company sponsors on the conclusions of pharmaceutical research have been extensively examined, little is known about the effects of industry sponsorship on nutrition research, even though large commercial entities are increasingly involved in global food and drink production. It is important to know whether the scientific evidence about nutrition is free of bias because biased information might negatively affect the health of entire populations. Moreover, scientific evidence from nutrition research underlies the formulation of governmental dietary guidelines and food-related public health interventions. In this systematic review, the researchers investigate whether the disclosure of potential financial conflicts of interest (for example, research funding by a beverage company) has influenced the results of systematic reviews undertaken to examine the association between the consumption of highly lucrative sugar-sweetened beverages (SSBs) and weight gain or obesity. Systematic reviews identify all the research on a given topic using predefined criteria. In an ideal world, systematic reviews provide access to all the available evidence on specific exposure–disease associations, but publication bias related to authors' conflicts of interest may affect the reliability of the conclusions of such studies.
What Did the Researchers Do and Find?
The researchers identified 18 conclusions from 17 systematic reviews that had investigated the association between SSB consumption and weight gain or obesity. In six of these reviews, a financial conflict of interest with a food industry was disclosed. Among the reviews that reported having no conflict of interest, 83.3% of the conclusions were that SSB consumption could be a potential risk factor for weight gain. By contrast, the same percentage of reviews in which a potential financial conflict of interest was disclosed concluded that the scientific evidence was insufficient to support a positive association between SSB consumption and weight gain, or reported contradictory results and did not state any definitive conclusion about the association between SSB consumption and weight gain. Reviews in which a potential conflict of interest was disclosed were five times more likely to present a conclusion of no positive association between SSB consumption and weight gain than reviews that reported having no financial conflict of interest.
What Do These Findings Mean?
These findings indicate that systematic reviews that reported financial conflicts of interest or sponsorship from food or drink companies were more likely to reach a conclusion of no positive association between SSB consumption and weight gain than reviews that reported having no conflicts of interest. A major limitation of this study is that it cannot assess which interpretation of the available evidence is truly accurate. For example, the scientists involved in the systematic reviews that reported having no conflict of interest may have had preexisting prejudices that affected their interpretation of their findings. However, the interests of the food industry (increased sales of their products) are very different from those of most researchers (the honest pursuit of knowledge), and recent randomized trials support a positive association between SSB consumption and overweight/obesity. Thus, these findings draw attention to possible inaccuracies in scientific evidence from research funded by the food and drink industry. They do not imply that industry sponsorship of nutrition research should be avoided entirely. Rather, as in other research areas, clear guidelines and principles (for example, sponsors should sign contracts that state that they will not be involved in the interpretation of results) need to be established to avoid dangerous conflicts of interest.
Additional Information
Please access these websites via the online version of this summary at http://dx.doi.org/10.1371/journal.pmed.1001578.
The Research Ethics Program at the University of California, San Diego provides an overview of conflicts of interest for researchers and details of US regulations and guidelines
The PLOS Medicine series on Big Food examines the activities and influence of the food industry in global health
A PLOS Medicine Research Article by Basu et al. uses mathematical modeling to investigate whether SSB taxation would avert obesity and diabetes in India
A 2012 policy brief from the Yale Rudd Center for Food Policy and Obesity discusses current evidence regarding SSB taxes
The US National Institutes of Health has regulations on financial conflicts of interest for institutions applying to receive funding
Wikipedia has pages on conflict of interest, reporting bias, systematic review, and SSBs (note that Wikipedia is a free online encyclopedia that anyone can edit; available in several languages)
doi:10.1371/journal.pmed.1001578
PMCID: PMC3876974  PMID: 24391479
10.  Characteristics and Trends of Orthopedic Publications between 2000 and 2009 
Clinics in Orthopedic Surgery  2011;3(3):225-229.
Background
This study was undertaken to investigate the trends of orthopedic publications during the last decade, and to document the country of origin, journal, funding source, and language of contribution using PubMed.
Methods
Orthopedic articles published between 2000 and 2009 were retrieved from PubMed using the following search terms: "orthopaedic[Affiliation] AND ("2000/1/1"[PDAT]: "2009/12/31"[PDAT])" and "orthopedic[Affiliation] AND ("2000/1/1"[PDAT]: "2009/12/31"[PDAT])." The articles were downloaded in XML file format, which contained the following information: article title, author names, journal names, publication dates, article types, languages, authors' affiliations and funding sources. These information was extracted, sorted, and rearranged using the database's management software. We investigated the annual number of published orthopedic articles worldwide and the annual rate of increase. Furthermore, the country of publication origin, journal, funding source, and language of contribution were also investigated.
Results
A total of 46,322 orthopedic articles were published and registered in PubMed in the last 10 years. The worldwide number of published orthopedic articles increased from 2,889 in 2000 to 6,909 in 2009, showing an annual increase of 384.6 articles, or an annualized compound rate of 10.2%. The United States ranked highest in the number of published orthopedic articles, followed by Japan, the United Kingdom, Germany, and the Republic of Korea. Among the orthopedic articles published worldwide during the last 10 years, 37.9% pertained studies performed in the United States. Fifty-seven point three percent (57.3%) of articles were published in journals established in the United States. Among the published orthopaedic articles, 4,747 articles (10.2%) disclosed financial support by research funds, of which 4,688 (98.8%) articles utilized research funds from the United States. Most articles were published in English (97.2%, 45,030 articles).
Conclusions
The number of published orthopedic articles has been increasing over the last decade. The number of orthopedic articles, journals publication, and funding sources were dominated by research conducted in the United States, while share and growth of Asian countries including Japan, the Republic of Korea, and China were notable.
doi:10.4055/cios.2011.3.3.225
PMCID: PMC3162203  PMID: 21909470
Bibliometrics; Orthopedics; Research trend; Periodicals as topics
11.  OReFiL: an online resource finder for life sciences 
BMC Bioinformatics  2007;8:287.
Background
Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced in special journal issues or websites with a search function, but others remain scattered throughout the Internet and in the published literature. The searchable resources on these sites are collected and maintained manually and are therefore of higher quality than automatically updated sites, but also require more time and effort.
Description
We developed an online resource search system called OReFiL to address these issues. We developed a crawler to gather all of the web pages whose URLs appear in MEDLINE abstracts and full-text papers on the BioMed Central open-access journals. The URLs were extracted using regular expressions and rules based on our heuristic knowledge. We then indexed the online resources to facilitate their retrieval and comparison by researchers. Because every online resource has at least one PubMed ID, we can easily acquire its summary with Medical Subject Headings (MeSH) terms and confirm its credibility through reference to the corresponding PubMed entry. In addition, because OReFiL automatically extracts URLs and updates the index, minimal time and effort is needed to maintain the system.
Conclusion
We developed OReFiL, a search system for online life science resources, which is freely available. The system's distinctive features include the ability to return up-to-date query-relevant online resources introduced in peer-reviewed papers; the ability to search using free words, MeSH terms, or author names; easy verification of each hit following links to the corresponding PubMed entry or to papers citing the URL through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar; and quick confirmation of the existence of an online resource web page.
doi:10.1186/1471-2105-8-287
PMCID: PMC1976328  PMID: 17683589
12.  Understanding PubMed® user search behavior through log analysis 
This article reports on a detailed investigation of PubMed users’ needs and behavior as a step toward improving biomedical information retrieval. PubMed is providing free service to researchers with access to more than 19 million citations for biomedical articles from MEDLINE and life science journals. It is accessed by millions of users each day. Efficient search tools are crucial for biomedical researchers to keep abreast of the biomedical literature relating to their own research. This study provides insight into PubMed users’ needs and their behavior. This investigation was conducted through the analysis of one month of log data, consisting of more than 23 million user sessions and more than 58 million user queries. Multiple aspects of users’ interactions with PubMed are characterized in detail with evidence from these logs. Despite having many features in common with general Web searches, biomedical information searches have unique characteristics that are made evident in this study. PubMed users are more persistent in seeking information and they reformulate queries often. The three most frequent types of search are search by author name, search by gene/protein, and search by disease. Use of abbreviation in queries is very frequent. Factors such as result set size influence users’ decisions. Analysis of characteristics such as these plays a critical role in identifying users’ information needs and their search habits. In turn, such an analysis also provides useful insight for improving biomedical information retrieval.
Database URL: http://www.ncbi.nlm.nih.gov/PubMed
doi:10.1093/database/bap018
PMCID: PMC2797455  PMID: 20157491
13.  Psychometric Properties of Self-Report Concussion Scales and Checklists 
Journal of Athletic Training  2012;47(2):221-223.
Reference/Citation:
Alla S, Sullivan SJ, Hale L, McCrory P. Self-report scales/checklists for the measurement of concussion symptoms: a systematic review. Br J Sports Med. 2009;43 (suppl 1):i3–i12.
Clinical Question:
Which self-report symptom scales or checklists are psychometrically sound for clinical use to assess sport-related concussion?
Data Sources:
Articles available in full text, published from the establishment of each database through December 2008, were identified from PubMed, Medline, CINAHL, Scopus, Web of Science, SPORTDiscus, PsycINFO, and AMED. Search terms included brain concussion, signs or symptoms, and athletic injuries, in combination with the AND Boolean operator, and were limited to studies published in English. The authors also hand searched the reference lists of retrieved articles. Additional searches of books, conference proceedings, theses, and Web sites of commercial scales were done to provide additional information about the psychometric properties and development for those scales when needed in articles meeting the inclusion criteria.
Study Selection:
Articles were included if they identified all the items on the scale and the article was either an original research report describing the use of scales in the evaluation of concussion symptoms or a review article that discussed the use or development of concussion symptom scales. Only articles published in English and available in full text were included.
Data Extraction:
From each study, the following information was extracted by the primary author using a standardized protocol: study design, publication year, participant characteristics, reliability of the scale, and details of the scale or checklist, including name, number of items, time of measurement, format, mode of report, data analysis, scoring, and psychometric properties. A quality assessment of included studies was done using 16 items from the Downs and Black checklist1 and assessed reporting, internal validity, and external validity.
Main Results:
The initial database search identified 421 articles. After 131 duplicate articles were removed, 290 articles remained and were added to 17 articles found during the hand search, for a total of 307 articles; of those, 295 were available in full text. Sixty articles met the inclusion criteria and were used in the systematic review. The quality of the included studies ranged from 9 to 15 points out of a maximum quality score of 17. The included articles were published between 1995 and 2008 and included a collective total of 5864 concussed athletes and 5032 nonconcussed controls, most of whom participated in American football. The majority of the studies were descriptive studies monitoring the resolution of concussive self-report symptoms compared with either a preseason baseline or healthy control group, with a smaller number of studies (n = 8) investigating the development of a scale.
The authors initially identified 20 scales that were used among the 60 included articles. Further review revealed that 14 scales were variations of the Pittsburgh Steelers postconcussion scale (the Post-Concussion Scale, Post-Concussion Scale: Revised, Post-Concussion Scale: ImPACT, Post-Concussion Symptom Scale: Vienna, Graded Symptom Checklist [GSC], Head Injury Scale, McGill ACE Post-Concussion Symptoms Scale, and CogState Sport Symptom Checklist), narrowing down to 6 core scales, which the authors discussed further. The 6 core scales were the Pittsburgh Steelers Post-Concussion Scale (17 items), Post-Concussion Symptom Assessment Questionnaire (10 items), Concussion Resolution Index postconcussion questionnaire (15 items), Signs and Symptoms Checklist (34 items), Sport Concussion Assessment Tool (SCAT) postconcussion symptom scale (25 items), and Concussion Symptom Inventory (12 items). Each of the 6 core scales includes symptoms associated with sport-related concussion; however, the number of items on each scale varied. A 7-point Likert scale was used on most scales, with a smaller number using a dichotomous (yes/no) classification.
Only 7 of the 20 scales had published psychometric properties, and only 1 scale, the Concussion Symptom Inventory, was empirically driven (Rasch analysis), with development of the scale occurring before its clinical use. Internal consistency (Cronbach α) was reported for the Post-Concussion Scale (.87), Post-Concussion Scale: ImPACT 22-item (.88–.94), Head Injury Scale 9-item (.78), and Head Injury Scale 16-item (.84). Test-retest reliability has been reported only for the Post-Concussion Scale (Spearman r = .55) and the Post-Concussion Scale: ImPACT 21-item (Pearson r = .65). With respect to validity, the SCAT postconcussion scale has demonstrated face and content validity, the Post-Concussion Scale: ImPACT 22-item and Head Injury Scale 9-item have reported construct validity, and the Head Injury Scale 9-item and 16-item have published factorial validity.
Sensitivity and specificity have been reported only with the GSC (0.89 and 1.0, respectively) and the Post-Concussion Scale: ImPACT 21-item when combined with the neurocognitive component of ImPACT (0.819 and 0.849, respectively). Meaningful change scores were reported for the Post-Concussion Scale (14.8 points), Post-Concussion Scale: ImPACT 22-item (6.8 points), and Post-Concussion Scale: ImPACT 21-item (standard error of the difference = 7.17; 80% confidence interval = 9.18).
Conclusions:
Numerous scales exist for measuring the number and severity of concussion-related symptoms, with most evolving from the neuropsychology literature pertaining to head-injured populations. However, very few of these were created in a systematic manner that follows scale development processes and have published psychometric properties. Clinicians need to understand these limitations when choosing and using a symptom scale for inclusion in a concussion assessment battery. Future authors should assess the underlying constructs and measurement properties of currently available scales and use the ever-increasing prospective data pools of concussed athlete information to develop scales following appropriate, systematic processes.
PMCID: PMC3418135  PMID: 22488289
mild traumatic brain injuries; evaluation; reliability; validity; sensitivity; specificity
14.  The physician–scientist in Canadian psychiatry 
Objective
The objective of the study was to determine whether physician–scientists in psychiatry in Canada are in decline, as was reported for medicine overall during the 1990s in the United States.
Design
Federal databases were searched to study grant applications in the area of mental health submitted by physician–scientists compared with PhD–scientists for the period 1985–2001. A survey of Canadian Residency Training Program Directors was carried out for the graduating class of 2000.
Setting
The Canadian publicly funded university system.
Participants
Applicants to the Medical Research Council of Canada and its successor, the Canadian Institutes of Health Research, for operating grant support and Residency Training Program Directors.
Interventions
None.
Outcome measures
Comparison over time between MD and PhD applicants regarding the number of grant applications submitted, the proportion of applications funded and the number of new applications submitted, with separation of applications submitted to a predominantly “biomedical” peer review committee and to a predominantly “clinical research” peer review committee. The survey obtained information about a number of variables related to research training.
Results
The situation for physician–scientists in psychiatry in Canada appeared remarkably similar to general findings in US studies. Relative to PhD applicants, fewer grant proposals were being made by physicians (paired t16 = 7.08, p < 0.001) and, in consequence, fewer proposals were funded. The proportion of proposals funded was similar for MD and PhD applicants (paired t16 = 0.27, p = 0.79). Grant applications made to the predominantly biomedical committee were more likely to be funded than applications to the committee with an orientation toward clinical research (paired t7 = 5.53, p < 0.001). Applications by PhD–scientists to the biomedical committee showed the largest increase over time and were the most successful. From the survey of graduating classes, close to one-third of residents had authored or co-authored a publication during residency. Only 7% were proceeding to research fellowship training. The remuneration available for fellowship training was about one-third of what graduating classmates could expect to earn in the first year of practice.
Conclusions
Quantitative data indicate that physician–scientists in psychiatry in Canada are experiencing the same pressures and challenges as physician–scientists in the United States. A plan of action tailored to the needs of the psychiatric community in Canada needs to be developed.
PMCID: PMC305270  PMID: 14719050
education, medical; internship and residency; policy making; research
15.  Publication Rate of Abstracts Presented at the Shoulder and Elbow Session of the American Academy of Orthopaedic Surgery 
Many shoulder and elbow abstracts presented at the American Academy of Orthopaedic Surgeons (AAOS) annual meeting are cited in the orthopaedic literature or are used to guide orthopaedic practice, but not all of these abstracts are submitted, survive peer review, or eventually are published. Presuming unpublished works have not been scientifically confirmed, one could question whether it is academically responsible to cite abstracts presented at the AAOS before they are peer-reviewed and published. To partly address this issue we determined the peer-reviewed publication rate for 558 abstracts (233 papers and 325 posters) presented at the shoulder and elbow sessions of the AAOS from 1999 to 2004. In April 2007, we searched the computerized database MEDLINE® and PubMed® for published articles based on these abstracts. We examined the published articles to assess publication rate, time to publication, change in contents, change in authors, and change in conclusions of abstracts. The overall publication rate in peer-reviewed journals was 58% (321 of 558), similar to other orthopaedic meetings and medical disciplines. We believe it is unacceptable to cite shoulder and elbow abstracts submitted to the AAOS because only slightly more than ½ (58%) of them are authenticated scientifically.
doi:10.1007/s11999-008-0474-2
PMCID: PMC2674152  PMID: 18769988
16.  How Complementary and Alternative Medicine Practitioners Use PubMed 
Background
PubMed is the largest bibliographic index in the life sciences. It is freely available online and is used by professionals and the public to learn more about medical research. While primarily intended to serve researchers, PubMed provides an array of tools and services that can help a wider readership in the location, comprehension, evaluation, and utilization of medical research.
Objective
This study sought to establish the potential contributions made by a range of PubMed tools and services to the use of the database by complementary and alternative medicine practitioners.
Methods
In this study, 10 chiropractors, 7 registered massage therapists, and a homeopath (N = 18), 11 with prior research training and 7 without, were taken through a 2-hour introductory session with PubMed. The 10 PubMed tools and services considered in this study can be divided into three functions: (1) information retrieval (Boolean Search, Limits, Related Articles, Author Links, MeSH), (2) information access (Publisher Link, LinkOut, Bookshelf ), and (3) information management (History, Send To, Email Alert). Participants were introduced to between six and 10 of these tools and services. The participants were asked to provide feedback on the value of each tool or service in terms of their information needs, which was ranked as positive, positive with emphasis, negative, or indifferent.
Results
The participants in this study expressed an interest in the three types of PubMed tools and services (information retrieval, access, and management), with less well-regarded tools including MeSH Database and Bookshelf. In terms of their comprehension of the research, the tools and services led the participants to reflect on their understanding as well as their critical reading and use of the research. There was universal support among the participants for greater access to complete articles, beyond the approximately 15% that are currently open access. The abstracts provided by PubMed were felt to be necessary in selecting literature to read but entirely inadequate for both evaluating and learning from the research. Thus, the restrictions and fees the participants faced in accessing full-text articles were points of frustration.
Conclusions
The study found strong indications of PubMed’s potential value in the professional development of these complementary and alternative medicine practitioners in terms of engaging with and understanding research. It provides support for the various initiatives intended to increase access, including a recommendation that the National Library of Medicine tap into the published research that is being archived by authors in institutional archives and through other websites.
doi:10.2196/jmir.9.2.e19
PMCID: PMC1913941  PMID: 17613489
PubMed; research dissemination; complementary and alternative medicine; open access; professional development; information retrieval; information management; literacy
17.  The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews 
Systematic Reviews  2013;2:115.
Background
The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs.
Methods
The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database.
Results
GS’ overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%.
Conclusions
Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be performed by experienced searchers creating searches that maximize recall for as many databases as deemed necessary by the search expert.
doi:10.1186/2046-4053-2-115
PMCID: PMC3882110  PMID: 24360284
Bibliographic databases; Information retrieval; Systematic reviews; Methodology; Literature searching; Reproducibility
18.  Publication Rates of Public Health Theses in International and National Peer-Review Journals in Turkey 
Background:
Thesis is an important part of specialisation and doctorate education and requires intense work. The aim of this study was to investigate the publication rates of Turkish Public Health Doctorate Theses (PHDT) and Public Health Specialization (PHST) theses in international and Turkish national peer-review journals and to analyze the distribution of research areas.
Methods:
List of all theses upto 30 September 2009 were retrieved from theses database of the Council of Higher Education of the Republic of Turkey. The publication rates of these theses were found by searching PubMed, Science Citation Index-Expanded, Turkish Academic Network and Information Center (ULAKBIM) Turkish Medical Database, and Turkish Medline databases for the names of thesis author and mentor. The theses which were published in journals indexed either in PubMed or SCI-E were considered as international publications.
Results:
Our search yielded a total of 538 theses (243 PHDT, 295 PHST). It was found that the overall publication rate in Turkish national journals was 18%. The overall publication rate in international journals was 11.9%. Overall the most common research area was occupational health.
Conclusion:
Publication rates of Turkish PHDT and PHST are low. A better understanding of factors affecting this publication rate is important for public health issues where national data is vital for better intervention programs and develop better public health policies.
PMCID: PMC3494212  PMID: 23193503
Bibliometrics; Mentor; Publishing; Research; Scientometrics; Turkey
19.  Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results 
Background
PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic. However, because PubMed does not organize the search output further, it is difficult for users to grasp an overview of the retrieved literature according to non-topical dimensions, to drill-down to find individual articles relevant to a particular individual's need, or to browse the collection.
Results
In this paper, we present Anne O'Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories such as the "most important" words found in titles or abstracts; topics; journals; authors; publication years; and affiliations. Clicking on a given item opens a new window that displays all papers that contain that item. One can navigate by drilling down through the categories progressively, e.g., one can first restrict the articles according to author name and then restrict that subset by affiliation. Alternatively, one can expand small sets of articles to display the most closely related articles. We also implemented a novel cluster-by-topic method that generates a concise set of topics covering most of the retrieved articles.
Conclusion
Anne O'Tate is an integrated, generic tool for summarization, drill-down and browsing of PubMed search results that accommodates a wide range of biomedical users and needs. It can be accessed at [4]. Peer review and editorial matters for this article were handled by Aaron Cohen.
doi:10.1186/1747-5333-3-2
PMCID: PMC2276193  PMID: 18279519
20.  GeneView: a comprehensive semantic search engine for PubMed 
Nucleic Acids Research  2012;40(Web Server issue):W585-W591.
Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein–protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ∼21 million citations with 271 000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/.
doi:10.1093/nar/gks563
PMCID: PMC3394277  PMID: 22693219
21.  PubMed QUEST: The PubMed Query Search Tool. An informatics tool to aid cancer centers and cancer investigators in searching the PubMed databases 
Cancer Informatics  2007;2:79-82.
Searching PubMed for citations related to a specific cancer center or group of authors can be labor-intensive. We have created a tool, PubMed QUEST, to aid in the rapid searching of PubMed for publications of interest. It was designed by taking into account the needs of entire cancer centers as well as individual investigators. The experience of using the tool by our institution’s cancer center administration and investigators has been favorable and we believe it could easily be adapted to other institutions. Use of the tool has identified limitations of automated searches for publications based on an author’s name, especially for common names. These limitations could likely be solved if the PubMed database assigned a unique identifier to each author.
PMCID: PMC2675510  PMID: 19458759
PubMed Databases; Bibliographic Medical Informatics Applications; Information Storage and Retrieval
22.  Do Students Eventually Get to Publish their Research Findings? The Case of Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome Research in Cameroon 
Background:
Scientific publication is commonly used to communicate research findings and in most academic/research settings, to evaluate the potential of a researcher and for recruitment and promotion. It has also been said that researchers have the duty to make public, the findings of their research. As a result, researchers are encouraged to share their research findings with the scientific world through peer review publications. In this study, we looked at the characteristics and publication rate of theses that documented studies on human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome in Cameroon.
Materials and Methods:
To check if a thesis resulted in a publication, we searched: A database of publications on HIV in Cameroon, African Journals Online, PubMed and Google scholar. For each publication we recorded if the student was an author, the position of the student in the author listing, the journal and where the journal was indexed. We also looked at the impact factor of the journals.
Results:
One hundred and thirty theses/dissertations were included in the study, 74.6% (97/130) were written as part of a medical degree (MD), 23.8% (31/130) a postgraduate (PG) degree and 1.5% (2/130) for a Doctorate/PhD. On a whole, 13.9% (18/130) of the theses resulted in at least one publication in a scientific journal with a total of 22 journal articles, giving a mean publication rate of 0.17 article/thesis, 86.4% (11/22) were indexed on PubMed, 9.1% (2/22) on African Journals Online and 4.6% (1/22) on Google scholar. One PG thesis led to two book chapters. The student was the first author in 22.7% (5/22) of the articles and not an author in 9.1% (2/22) of the articles. Student supervisor was an author in all the articles.
Conclusion:
This study reveals that most students in Cameroon failed to transform their theses/dissertations to scientific publications. This indicates an urgent need to sensitize students on the importance of presenting their research findings in scientific meetings and peer reviewed journals. There is also a great necessity to build capacity in scientific writing among university students in Cameroon.
doi:10.4103/2141-9248.133474
PMCID: PMC4071747  PMID: 24971222
Cameroon; Graduate and medical students; Human immunodeficiency virus/acquired immunodeficiency syndrome; Publication rates
23.  Recall and bias of retrieving gene expression microarray datasets through PubMed identifiers 
Background
The ability to locate publicly available gene expression microarray datasets effectively and efficiently facilitates the reuse of these potentially valuable resources. Centralized biomedical databases allow users to query dataset metadata descriptions, but these annotations are often too sparse and diverse to allow complex and accurate queries. In this study we examined the ability of PubMed article identifiers to locate publicly available gene expression microarray datasets, and investigated whether the retrieved datasets were representative of publicly available datasets found through statements of data sharing in the associated research articles.
Results
In a recent article, Ochsner and colleagues identified 397 studies that had generated gene expression microarray data. Their search of the full text of each publication for statements of data sharing revealed 203 publicly available datasets, including 179 in the Gene Expression Omnibus (GEO) or ArrayExpress databases. Our scripted search of GEO and ArrayExpress for PubMed identifiers of the same 397 studies returned 160 datasets, including six not found by the original search for data sharing statements. As a proportion of datasets found by either method, the search for data sharing statements identified 91.4% of the 209 publicly available datasets, compared to 76.6% found by our search for PubMed identifiers. Searching GEO or ArrayExpress alone retrieved 63.2% and 46.9% of all available datasets, respectively. Studies retrieved through PubMed identifiers were representative of all datasets in terms of research theme, technology, size, and impact, though the recall was highest for datasets published by the highest-impact journals.
Conclusions
Searching database entries using PubMed identifiers can identify the majority of publicly available datasets. We urge authors of all datasets to complete the citation fields for their dataset submissions once publication details are known, thereby ensuring their work has maximum visibility and can contribute to subsequent studies.
PMCID: PMC2990274  PMID: 20349403
information retrieval; data sharing; databases; bioinformatics; PubMed; gene expression microarrays
24.  NetiNeti: discovery of scientific names from text using machine learning methods 
BMC Bioinformatics  2012;13:211.
Background
A scientific name for an organism can be associated with almost all biological data. Name identification is an important step in many text mining tasks aiming to extract useful information from biological, biomedical and biodiversity text sources. A scientific name acts as an important metadata element to link biological information.
Results
We present NetiNeti (Name Extraction from Textual Information-Name Extraction for Taxonomic Indexing), a machine learning based approach for recognition of scientific names including the discovery of new species names from text that will also handle misspellings, OCR errors and other variations in names. The system generates candidate names using rules for scientific names and applies probabilistic machine learning methods to classify names based on structural features of candidate names and features derived from their contexts. NetiNeti can also disambiguate scientific names from other names using the contextual information. We evaluated NetiNeti on legacy biodiversity texts and biomedical literature (MEDLINE). NetiNeti performs better (precision = 98.9% and recall = 70.5%) compared to a popular dictionary based approach (precision = 97.5% and recall = 54.3%) on a 600-page biodiversity book that was manually marked by an annotator. On a small set of PubMed Central’s full text articles annotated with scientific names, the precision and recall values are 98.5% and 96.2% respectively. NetiNeti found more than 190,000 unique binomial and trinomial names in more than 1,880,000 PubMed records when used on the full MEDLINE database. NetiNeti also successfully identifies almost all of the new species names mentioned within web pages.
Conclusions
We present NetiNeti, a machine learning based approach for identification and discovery of scientific names. The system implementing the approach can be accessed at http://namefinding.ubio.org.
doi:10.1186/1471-2105-13-211
PMCID: PMC3542245  PMID: 22913485
25.  BioDEAL: community generation of biological annotations 
Background
Publication databases in biomedicine (e.g., PubMed, MEDLINE) are growing rapidly in size every year, as are public databases of experimental biological data and annotations derived from the data. Publications often contain evidence that confirm or disprove annotations, such as putative protein functions, however, it is increasingly difficult for biologists to identify and process published evidence due to the volume of papers and the lack of a systematic approach to associate published evidence with experimental data and annotations. Natural Language Processing (NLP) tools can help address the growing divide by providing automatic high-throughput detection of simple terms in publication text. However, NLP tools are not mature enough to identify complex terms, relationships, or events.
Results
In this paper we present and extend BioDEAL, a community evidence annotation system that introduces a feedback loop into the database-publication cycle to allow scientists to connect data-driven biological concepts to publications.
Conclusion
BioDEAL may change the way biologists relate published evidence with experimental data. Instead of biologists or research groups searching and managing evidence independently, the community can collectively build and share this knowledge.
doi:10.1186/1472-6947-9-S1-S5
PMCID: PMC2773920  PMID: 19891799

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