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1.  Scientific meeting abstracts: significance, access, and trends. 
Abstracts of scientific papers and posters that are presented at annual scientific meetings of professional societies are part of the broader category of conference literature. They are an important avenue for the dissemination of current data. While timely and succinct, these abstracts present problems such as an abbreviated peer review and incomplete bibliographic access. METHODS: Seventy societies of health sciences professionals were surveyed about the publication of abstracts from their annual meetings. Nineteen frequently cited journals also were contacted about their policies on the citation of meeting abstracts. Ten databases were searched for the presence of meetings abstracts. RESULTS: Ninety percent of the seventy societies publish their abstracts, with nearly half appearing in the society's journal. Seventy-seven percent of the societies supply meeting attendees with a copy of each abstract, and 43% make their abstracts available in an electronic format. Most of the journals surveyed allow meeting abstracts to be cited. Bibliographic access to these abstracts does not appear to be widespread. CONCLUSIONS: Meeting abstracts play an important role in the dissemination of scientific knowledge. Bibliographic access to meeting abstracts is very limited. The trend toward making meeting abstracts available via the Internet has the potential to give a broader audience access to the information they contain.
PMCID: PMC226328  PMID: 9549015
2.  PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts 
Nucleic Acids Research  2005;33(Web Server issue):W774-W778.
Since it is becoming increasingly laborious to manually extract useful information embedded in the ever-growing volumes of literature, automated intelligent text analysis tools are becoming more and more essential to assist in this task. PubFinder () is a publicly available web tool designed to improve the retrieval rate of scientific abstracts relevant for a specific scientific topic. Only the selection of a representative set of abstracts is required, which are central for a scientific topic. No special knowledge concerning the query-syntax is necessary. Based on the selected abstracts, a list of discriminating words is automatically calculated, which is subsequently used for scoring all defined PubMed abstracts for their probability of belonging to the defined scientific topic. This results in a hit-list of references in the descending order of their likelihood score. The algorithms and procedures implemented in PubFinder facilitate the perpetual task for every scientist of staying up-to-date with current publications dealing with a specific subject in biomedicine.
PMCID: PMC1160190  PMID: 15980583
3.  Study of the comprehension of the scientific method by members of a university health research laboratory 
In Brazil, scientific research is carried out mainly at universities, where professors coordinate research projects with the active participation of undergraduate and graduate students. However, there is no formal program for the teaching/learning of the scientific method. The objective of the present study was to evaluate the comprehension of the scientific method by students of health sciences who participate in scientific projects in an academic research laboratory. An observational descriptive cross-sectional study was conducted using Edgar Morin complexity as theoretical reference. In a semi-structured interview, students were asked to solve an abstract logical puzzle - TanGram. The collected data were analyzed using the hermeneutic-dialectic analysis method proposed by Minayo and discussed in terms of the theoretical reference of complexity. The students' concept of the scientific method is limited to participation in projects, stressing the execution of practical procedures as opposed to scientific thinking. The solving of the TanGram puzzle revealed that the students had difficulties in understanding questions and activities focused on subjects and their processes. Objective answers, even when dealing with personal issues, were also reflected on the students' opinions about the characteristics of a successful researcher. Students' difficulties concerning these issues may affect their scientific performance and result in poorly designed experiments. This is a preliminary study that should be extended to other centers of scientific research.
PMCID: PMC3854260  PMID: 22249427
Scientific method; Complexity; Academic scientific research
4.  Males Are Overrepresented among Life Science Researchers Committing Scientific Misconduct 
mBio  2013;4(1):e00640-12.
A review of the United States Office of Research Integrity annual reports identified 228 individuals who have committed misconduct, of which 94% involved fraud. Analysis of the data by career stage and gender revealed that misconduct occurred across the entire career spectrum from trainee to senior scientist and that two-thirds of the individuals found to have committed misconduct were male. This exceeds the overall proportion of males among life science trainees and faculty. These observations underscore the need for additional efforts to understand scientific misconduct and to ensure the responsible conduct of research.
As many of humanity’s greatest problems require scientific solutions, it is critical for the scientific enterprise to function optimally. Misconduct threatens the scientific enterprise by undermining trust in the validity of scientific findings. We have examined specific demographic characteristics of individuals found to have committed research misconduct in the life sciences. Our finding that misconduct occurs across all stages of career development suggests that attention to ethical aspects of the conduct of science should not be limited to those in training. The observation that males are overrepresented among those who commit misconduct implies a gender difference that needs to be better understood in any effort to promote research integrity.
PMCID: PMC3551552  PMID: 23341553
5.  Art of reading a journal article: Methodically and effectively 
Reading scientific literature is mandatory for researchers and clinicians. With an overflow of medical and dental journals, it is essential to develop a method to choose and read the right articles.
To outline a logical and orderly approach to reading a scientific manuscript. By breaking down the task into smaller, step-by-step components, one should be able to attain the skills to read a scientific article with ease.
The reader should begin by reading the title, abstract and conclusions first. If a decision is made to read the entire article, the key elements of the article can be perused in a systematic manner effectively and efficiently. A cogent and organized method is presented to read articles published in scientific journals.
One can read and appreciate a scientific manuscript if a systematic approach is followed in a simple and logical manner.
PMCID: PMC3687192  PMID: 23798833
Articles; journal; reading; research; systematic
6.  Abstract‐to‐publication ratio for papers presented at scientific meetings: a quality marker for UK emergency medicine research 
Emergency Medicine Journal : EMJ  2007;24(6):425-426.
To determine the publication rate of abstracts presented by UK emergency physicians at major emergency medicine meetings, and to identify the site of publication of papers.
All abstracts presented to the annual scientific meetings of both the British Association of Emergency Medicine and the Faculty of Accident and Emergency Medicine between 2001 and 2002 were identified retrospectively from conference programmes. To identify whether the work relating to the abstract had been published in a peer‐reviewed journal, the Medline database (Ovid interface) was searched using the first and last authors as well as key words from the abstract.
Of the 404 abstracts identified, 124 (30%) had been published as full articles. For abstracts presented in the oral sessions, 83 (57%) resulted in publication. A range of journals accepted papers for publication.
The abstract‐to‐publication ratio for UK emergency medicine is lower than for other specialties, but broadly similar to emergency medicine in the US and Australia.
PMCID: PMC2658283  PMID: 17513542
7.  Publication rates of abstracts presented at the 2007 and 2010 Canadian Association of Radiation Oncology meetings 
Current Oncology  2014;21(2):e250-e254.
We set out to determine the rate, time-trend, and defining factors associated with publication of abstracts presented at two annual scientific meetings of the Canadian Association of Radiation Oncology (caro).
All abstracts accepted for oral presentation in 2007 and 2010 were obtained from the caro program archives and searched using the PubMed database. Variables in the dataset included the year of presentation at caro and of publication in a scientific journal, time to publication (in months), publishing journal, impact factor of publishing journal, abstract research type (clinical, technical, or basic science) and disease site, country of origin, and university of the first author.
Overall, 88 of 172 abstracts from the 2007 (n = 102) and 2010 (n = 70) caro meetings were published in peer-reviewed journals (publication rate: 51.2%). Mean time to publication was 18.5 months. Among research types, clinical research (62.5%) and, among disease sites, prostate cancer (40.4%) were most likely to be published. Of all the abstracts, 50.1% were contributed by only 2 universities, a proportion that resembles the overall abstract publication rate of 51.2%. The conversion rate for those 2 universities (51.1%) is very similar to that for all abstracts presented at the two meetings.
Half the abstracts presented at the 2007 and 2010 caro meetings were ultimately published in journals indexed in PubMed by about 1.5 years after presentation. Half the abstracts and publications came from just 2 universities; more must to be done to close the gap.
PMCID: PMC3997458  PMID: 24764710
Abstracts; annual meetings; Canada; conversion rate; radiation oncology
8.  How to prepare and submit abstracts for scientific meetings 
The presentation of study results is a key step in scientific research, and submitting an abstract to a meeting is often the first form of public communication. Meeting abstracts have a defined structure that is similar to abstracts for scientific articles, with an introduction, the objective, methods, results and conclusions. However, abstracts for meetings are not presented as part of a full article and, therefore, must contain the necessary and most relevant data. In this article, we detail their structure and include tips to make them technically correct.
PMCID: PMC4031836  PMID: 23917970
Abstracts and indexing as topic; Meetings as topic; Publishing/standards
9.  Reviewer agreement trends from four years of electronic submissions of conference abstract 
The purpose of this study was to determine the inter-rater agreement between reviewers on the quality of abstract submissions to an annual national scientific meeting (Canadian Association of Emergency Physicians; CAEP) to identify factors associated with low agreement.
All abstracts were submitted using an on-line system and assessed by three volunteer CAEP reviewers blinded to the abstracts' source. Reviewers used an on-line form specific for each type of study design to score abstracts based on nine criteria, each contributing from two to six points toward the total (maximum 24). The final score was determined to be the mean of the three reviewers' scores using Intraclass Correlation Coefficient (ICC).
495 Abstracts were received electronically during the four-year period, 2001 – 2004, increasing from 94 abstracts in 2001 to 165 in 2004. The mean score for submitted abstracts over the four years was 14.4 (95% CI: 14.1–14.6). While there was no significant difference between mean total scores over the four years (p = 0.23), the ICC increased from fair (0.36; 95% CI: 0.24–0.49) to moderate (0.59; 95% CI: 0.50–0.68). Reviewers agreed less on individual criteria than on the total score in general, and less on subjective than objective criteria.
The correlation between reviewers' total scores suggests general recognition of "high quality" and "low quality" abstracts. Criteria based on the presence/absence of objective methodological parameters (i.e., blinding in a controlled clinical trial) resulted in higher inter-rater agreement than the more subjective and opinion-based criteria. In future abstract competitions, defining criteria more objectively so that reviewers can base their responses on empirical evidence may lead to increased consistency of scoring and, presumably, increased fairness to submitters.
PMCID: PMC1473196  PMID: 16545143
10.  Publication of Surgical Abstracts in Full Text: A Retrospective Cohort Study 
Abstracts presented at national and international scientific meetings are an important educational resource. However, the work is not peer reviewed and little is known about the quality or validity of the presented results and the fate of such abstracts.
This is a retrospective cohort study of abstracts presented to the 1997 annual meeting of the Association of Surgeons of Great Britain and Ireland. We examined the rates of full-text publication, time to publication, factors influencing publication, inconsistencies between presented and subsequently published manuscripts, and reasons for non-publication of abstracts.
Of the 241 abstracts presented, 136 (56.4%) were published at a median duration of 18 months. Multicentre studies had a greater tendency to subsequent publication and studies involving academic centres predicted publication in a high impact factor journal. Inconsistencies between presented and published abstracts were common and were significantly associated with delayed publication. Oral and poster presentations were equally likely to be published. Reasons for non-submission of presented abstracts included lack of time, low priority to publish, perceived methodological limitations, lack of novelty of findings and co-investigators leaving the organisation.
More than half of the work presented at a national surgical meeting in the UK has been subsequently published. Various factors that influence the process of publication and remediable causes for non-publication have been identified.
PMCID: PMC1963619  PMID: 16482660
Abstracts; Peer-reviewed publication
11.  Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search™ 
With the increasing volume of scientific papers and heterogeneous nomenclature in the biomedical literature, it is apparent that an improvement over standard pattern matching available in existing search engines is required. Cognition Search Information Retrieval (CSIR) is a natural language processing (NLP) technology that possesses a large dictionary (lexicon) and large semantic databases, such that search can be based on meaning. Encoded synonymy, ontological relationships, phrases, and seeds for word sense disambiguation offer significant improvement over pattern matching. Thus, the CSIR has the right architecture to form the basis for a scientific search engine.
Here we have augmented CSIR to improve access to the MEDLINE database of scientific abstracts. New biochemical, molecular biological and medical language and acronyms were introduced from curated web-based sources. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym, ontology, phrases and sense seeds have been encoded. The present implementation can be found at
PMCID: PMC3041583  PMID: 21347167
12.  Stability and Validity of an Automated Measure of Vocal Development From Day-Long Samples in Children With and Without Autism Spectrum Disorder 
Lay Abstract
Measuring the degree to which young children’s vocalizations, many of which are non-words, have acoustic characteristics similar to speech may eventually help us match expectations and treatment methods to individual needs and abilities. To accomplish this goal, we need vocal measures that have scientific utility. The current study indicates that a single all-day recording and subsequent computer-analysis of its acoustic characteristics produces a measure of vocal development that is highly related to expressive language in children with ASD and in children who are typically developing. These findings provide the needed basis for future use of this measure for clinical and scientific purposes.
Scientific Abstract
Individual difference measures of vocal development may eventually aid our understanding of the variability in spoken language acquisition in children with autism spectrum disorder (ASD). Large samples of child vocalizations may be needed to maximize the stability of vocal development estimates. Day-long vocal samples can now be automatically analyzed based on acoustic characteristics of speech-likeness identified in theoretically-driven and empirically cross-validated quantitative models of typical vocal development. This report indicates that a single day-long recording can produce a stable estimate for a measure of vocal development that is highly related to expressive spoken language in a group of young children with ASD and in a group that is typically developing.
PMCID: PMC3664259  PMID: 23436778
13.  Selected Abstracts presented at the 18th International Congress of the International Society of Cardiovascular Pharmacotherapy (ISCP), Rome, Italy, 28--30 June 2013 
JRSM Cardiovascular Disease  2013;2:2048004013506452.
ROME, 28–30 JUNE 2013
The following scientific abstracts were presented at the latest Annual Scientific Meeting of ISCP this year in Rome. They summarise the work of young investigators from different geographical regions worldwide. ISCP supports the scientific work of researchers round the Globe and offers a forum where the results of their investigations can be presented and discussed in the context of the annual meetings and other regional activities. This activity represents not only a possibility for young investigators to showcase their work but also an opportunity to have their results assessed and discussed by world experts in the field. ISCP sees this as a useful contribution to the development of young scientists working in the field of cardiovascular pharmacotherapy.
PMCID: PMC3821785
14.  Redaction of Sensitive Data in the Publication of Dual Use Research of Concern 
mBio  2013;5(1):e00991-13.
The publication of scientific information that derives from dual use research of concern (DURC) poses major problems for journals because it brings into conflict the benefits of free access to data and the need to prevent misuse of that information by others. Recently, a group of authors and a major scientific journal addressed the issue of publishing information on a newly discovered, highly lethal toxin that can be delivered to large populations and for which there are no available countermeasures. The journal addressed this conflict by permitting the redaction of information that is normally considered essential for publication. This action establishes a precedent for redaction of sensitive data that also provides an example of responsible scientific publishing. However, this precedent leaves many questions unanswered and suggests a need for a discussion by all stakeholders of scientific information so as to derive normative standards for the publication of DURC.
PMCID: PMC3884058  PMID: 24381302
15.  Information extraction from full text scientific articles: Where are the keywords? 
BMC Bioinformatics  2003;4:20.
To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text articles in electronic version, which offer larger sources of data, are currently available. Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant.
In this work we addressed those questions showing that the keyword content of the different sections of a standard scientific article (abstract, introduction, methods, results, and discussion) is very heterogeneous.
Although the abstract contains the best ratio of keywords per total of words, other sections of the article may be a better source of biologically relevant data.
PMCID: PMC166134  PMID: 12775220
Information extraction; full text article; keyword; gene name; data mining; text mining
16.  An Analysis of the Abstracts Presented at the Annual Meetings of the Society for Neuroscience from 2001 to 2006 
PLoS ONE  2008;3(4):e2052.
Annual meeting abstracts published by scientific societies often contain rich arrays of information that can be computationally mined and distilled to elucidate the state and dynamics of the subject field. We extracted and processed abstract data from the Society for Neuroscience (SFN) annual meeting abstracts during the period 2001–2006 in order to gain an objective view of contemporary neuroscience. An important first step in the process was the application of data cleaning and disambiguation methods to construct a unified database, since the data were too noisy to be of full utility in the raw form initially available. Using natural language processing, text mining, and other data analysis techniques, we then examined the demographics and structure of the scientific collaboration network, the dynamics of the field over time, major research trends, and the structure of the sources of research funding. Some interesting findings include a high geographical concentration of neuroscience research in the north eastern United States, a surprisingly large transient population (66% of the authors appear in only one out of the six studied years), the central role played by the study of neurodegenerative disorders in the neuroscience community, and an apparent growth of behavioral/systems neuroscience with a corresponding shrinkage of cellular/molecular neuroscience over the six year period. The results from this work will prove useful for scientists, policy makers, and funding agencies seeking to gain a complete and unbiased picture of the community structure and body of knowledge encapsulated by a specific scientific domain.
PMCID: PMC2324197  PMID: 18446237
17.  Open access for the non-English-speaking world: overcoming the language barrier 
This editorial highlights the problem of language barrier in scientific communication in spite of the recent success of Open Access Movement. Four options for English-language journals to overcome the language barrier are suggested: 1) abstracts in alternative languages provided by authors, 2) Wiki open translation, 3) international board of translator-editors, and 4) alternative language version of the journal. The Emerging Themes in Epidemiology announces that with immediate effect, it will accept translations of abstracts or full texts by authors as Additional files.
Editorial note:
In an effort towards overcoming the language barrier in scientific publication, ETE will accept translations of abstracts or the full text of published articles. Each translation should be submitted separately as an Additional File in PDF format. ETE will only peer review English-language versions. Therefore, translations will not be scrutinized in the review-process and the responsibility for accurate translation rests with the authors.
PMCID: PMC2268932  PMID: 18173854
18.  Does direction of results of abstracts submitted to scientific conferences on drug addiction predict full publication? 
Data from scientific literature show that about 63% of abstracts presented at biomedical conferences will be published in full. Some studies have indicated that full publication is associated with the direction of results (publication bias). No study has looked into the occurrence of publication bias in the field of addiction.
To investigate whether the significance or direction of results of abstracts presented at the major international scientific conference on addiction is associated with full publication
The conference proceedings of the US Annual Meeting of the College on Problems of Drug Dependence (CPDD), were handsearched for abstracts of randomized controlled trials and controlled clinical trials that evaluated interventions for prevention, rehabilitation and treatment of drug addiction in humans (years searched 1993–2002). Data regarding the study designs and outcomes reported were extracted. Subsequent publication in peer reviewed journals was searched in MEDLINE and EMBASE databases, as of March 2006.
Out of 5919 abstracts presented, 581 met the inclusion criteria; 359 (62%) conference abstracts had been published in a broad variety of peer reviewed journals (average time of publication 2.6 years, SD +/- 1.78). The proportion of published studies was almost the same for randomized controlled trials (62.4%) and controlled clinical trials (59.5%) while studies that reported positive results were significantly more likely to be published (74.5%) than those that did not report statistical results (60.9%.), negative or null results (47.1%) and no results (38.6%), Abstracts reporting positive results had a significantly higher probability of being published in full, while abstracts reporting null or negative results were half as likely to be published compared with positive ones (HR = 0.48; 95%CI 0.30–0.74)
Clinical trials were the minority of abstracts presented at the CPDD; we found evidence of possible publication bias in the field of addiction, with negative or null results having half the likelihood of being published than positive ones.
PMCID: PMC2674061  PMID: 19356245
19.  Abstracts from the 32nd Annual Scientific Meeting of the Canadian Geriatrics Society Quebec City, April 2012 
The opinions expressed in the abstracts are those of the authors and are not to be construed as the opinion of the publisher (Canadian Geriatrics Society) or the organizers of the 32nd Annual Scientific Meeting of the Canadian Geriatrics Society. Although the publisher (Canadian Geriatrics Society) has made every effort to accurately reproduce the abstracts, the Canadian Geriatrics Society and the 32nd Annual Scientific Meeting of the Canadian Geriatrics Society assumes no responsibility and/or liability for any errors and/or omissions in any abstract as published.
PMCID: PMC3516242
20.  Development and evaluation of a quality score for abstracts 
The evaluation of abstracts for scientific meetings has been shown to suffer from poor inter observer reliability. A measure was developed to assess the formal quality of abstract submissions in a standardized way.
Item selection was based on scoring systems for full reports, taking into account published guidelines for structured abstracts. Interrater agreement was examined using a random sample of submissions to the American Gastroenterological Association, stratified for research type (n = 100, 1992–1995). For construct validity, the association of formal quality with acceptance for presentation was examined. A questionnaire to expert reviewers evaluated sensibility items, such as ease of use and comprehensiveness.
The index comprised 19 items. The summary quality scores showed good interrater agreement (intra class coefficient 0.60 – 0.81). Good abstract quality was associated with abstract acceptance for presentation at the meeting. The instrument was found to be acceptable by expert reviewers.
A quality index was developed for the evaluation of scientific meeting abstracts which was shown to be reliable, valid and useful.
PMCID: PMC149448  PMID: 12581457
21.  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.
PMCID: PMC2674152  PMID: 18769988
22.  Is gastroenterology research in decline? A comparison of abstract publication rates from The British Society of Gastroenterology meetings between 1995 and 2005 
F1000Research  2013;2:59.
Background: Reports have suggested that academic medicine may be in decline within the UK. Further evidence suggests that rates of subsequent full publication of abstracts presented at major scientific meetings are low and may be declining. We have compared the publication rates of abstracts presented at meetings of the British Society of Gastroenterology (BSG) between 1995 and 2005 and examined factors associated with full paper publication. 
Methods: Abstracts presented at BSG meetings in 1995 and 2005 were assessed by cross-referencing with multiple databases. Abstract characteristics associated with publication were analysed.
Results: There were no differences in overall publication rates, impact factors or time to publication between 1995 and 2005. Overall, basic-science abstracts were twice as likely to achieve full publication than non-basic science. There was a significant fall in the publication rates for case series and audits, and significantly increased rates for fundamental/basic-science abstracts over the study period. There were non-significant increases in publication rates for controlled trials and systematic reviews. In general, publication rates for all predominantly clinically orientated abstracts reduced between the two periods with the most notable fall occurring in nutrition. 
Conclusions: There was no evidence of a decline in overall abstract publication rates between 1995 and 2005. There seemed to be trend for increased publication rates of abstracts using perceived high-quality study methodologies with a corresponding decrease in those with lower quality methods. The proportion of basic-science abstracts is likely to be a determinant of overall full publication rates following scientific meetings.
PMCID: PMC3752733  PMID: 24327877
23.  A Statistical Analysis of Reviewer Agreement and Bias in Evaluating Medical Abstracts 1 
Observer variability affects virtually all aspects of clinical medicine and investigation. One important aspect, not previously examined, is the selection of abstracts for presentation at national medical meetings. In the present study, 109 abstracts, submitted to the American Association for the Study of Liver Disease, were evaluated by three “blind” reviewers for originality, design-execution, importance, and overall scientific merit. Of the 77 abstracts rated for all parameters by all observers, interobserver agreement ranged between 81 and 88%. However, corresponding intraclass correlations varied between 0.16 (approaching statistical significance) and 0.37 (p < 0.01). Specific tests of systematic differences in scoring revealed statistically significant levels of observer bias on most of the abstract components. Moreover, the mean differences in interobserver ratings were quite small compared to the standard deviations of these differences. These results emphasize the importance of evaluating the simple percentage of rater agreement within the broader context of observer variability and systematic bias.
PMCID: PMC2595507  PMID: 997596
24.  Automating document classification for the Immune Epitope Database 
BMC Bioinformatics  2007;8:269.
The Immune Epitope Database contains information on immune epitopes curated manually from the scientific literature. Like similar projects in other knowledge domains, significant effort is spent on identifying which articles are relevant for this purpose.
We here report our experience in automating this process using Naïve Bayes classifiers trained on 20,910 abstracts classified by domain experts. Improvements on the basic classifier performance were made by a) utilizing information stored in PubMed beyond the abstract itself b) applying standard feature selection criteria and c) extracting domain specific feature patterns that e.g. identify peptides sequences. We have implemented the classifier into the curation process determining if abstracts are clearly relevant, clearly irrelevant, or if no certain classification can be made, in which case the abstracts are manually classified. Testing this classification scheme on an independent dataset, we achieve 95% sensitivity and specificity in the 51.1% of abstracts that were automatically classified.
By implementing text classification, we have sped up the reference selection process without sacrificing sensitivity or specificity of the human expert classification. This study provides both practical recommendations for users of text classification tools, as well as a large dataset which can serve as a benchmark for tool developers.
PMCID: PMC1965490  PMID: 17655769
25.  Conflict of Interest in Spine Research Reporting 
PLoS ONE  2012;7(8):e44327.
Medical studies are more likely to report favorable findings when a conflict of interest is declared. We aim to quantify and determine the effect of author disclosure of conflict of interest on scientific reporting.
Abstracts from an international spine research meeting (North American Spine Society 2010) were selected that specifically evaluated a device, biologic, or proprietary procedure. They were then made anonymous to reviewers. An item of interest was established in each of the abstracts in order to standardize evaluation. Next, three blinded reviewers independently rated the abstracts as favorable, neutral, or unfavorable with regard to the item of interest. Additionally, the blinded reviewers attempted to predict whether a related disclosure was made. The meeting disclosure index was used to tabulate the minimum US dollar value attributable to disclosures.
Of the 344 total abstracts, 76 met inclusion criteria. In 79%, a related conflict of interest was reported. The amount of the disclosure was incompletely reported in 30% of cases. Where available, it averaged a cumulative minimum of $219,634 USD per abstract. The results of the abstracts were judged to be favorable, neutral, and unfavorable in 63%, 32% and 5% of abstracts, respectively. There was no correlation between the presence of a related disclosure and the findings of the studies (p = 0.81), although interpretation of this is limited by a small sample size and an overall apparent bias to report favorable studies. Additionally, the blinded reviewers were unable to predict whether a related disclosure was made (p = 0.40).
No association existed between the presence of a related disclosure and the results of the studies. While the actual compliance with reporting a potential conflict of interest is unable to be determined, the value amount related to the disclosures made was inadequately reported according to meeting guidelines.
PMCID: PMC3432133  PMID: 22952956

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