Tagging gene and protein names in full text articles

PubTator Central (https://www.ncbi.nlm.nih.gov/research/pubtator/) is a web service for viewing and retrieving bioconcept annotations in full text biomedical articles. PubTator Central (PTC) provides automated annotations from state-of-the-art text mining systems for genes/proteins, genetic variants, diseases, chemicals, species and cell lines, all available for immediate download. PTC annotates PubMed (29 million abstracts) and the PMC Text Mining subset (3 million full text articles). The new PTC web interface allows users to build full text document collections and visualize concept annotations in each document. Annotations are downloadable in multiple formats (XML, JSON and tab delimited) via the online interface, a RESTful web service and bulk FTP. Improved concept identification systems and a new disambiguation module based on deep learning increase annotation accuracy, and the new server-side architecture is significantly faster. PTC is synchronized with PubMed and PubMed Central, with new articles added daily. The original PubTator service has served annotated abstracts for ∼300 million requests, enabling third-party research in use cases such as biocuration support, gene prioritization, genetic disease analysis, and literature-based knowledge discovery. We demonstrate the full text results in PTC significantly increase biomedical concept coverage and anticipate this expansion will both enhance existing downstream applications and enable new use cases.

Full-text articles, manuscript tracking, and automated literature search lead new array of AJKD online features.

BackgroundWith the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the following question: is searching full text more effective than searching abstracts? This question is answered by comparing text retrieval algorithms on MEDLINE® abstracts, full-text articles, and spans (paragraphs) within full-text articles using data from the TREC 2007 genomics track evaluation. Two retrieval models are examined: bm25 and the ranking algorithm implemented in the open-source Lucene search engine.ResultsExperiments show that treating an entire article as an indexing unit does not consistently yield higher effectiveness compared to abstract-only search. However, retrieval based on spans, or paragraphs-sized segments of full-text articles, consistently outperforms abstract-only search. Results suggest that highest overall effectiveness may be achieved by combining evidence from spans and full articles.ConclusionUsers searching full text are more likely to find relevant articles than searching only abstracts. This finding affirms the value of full text collections for text retrieval and provides a starting point for future work in exploring algorithms that take advantage of rapidly-growing digital archives. Experimental results also highlight the need to develop distributed text retrieval algorithms, since full-text articles are significantly longer than abstracts and may require the computational resources of multiple machines in a cluster. The MapReduce programming model provides a convenient framework for organizing such computations.

BackgroundComputational methods have been used to find duplicate biomedical publications in MEDLINE. Full text articles are becoming increasingly available, yet the similarities among them have not been systematically studied. Here, we quantitatively investigated the full text similarity of biomedical publications in PubMed Central.Methodology/Principal Findings72,011 full text articles from PubMed Central (PMC) were parsed to generate three different datasets: full texts, sections, and paragraphs. Text similarity comparisons were performed on these datasets using the text similarity algorithm eTBLAST. We measured the frequency of similar text pairs and compared it among different datasets. We found that high abstract similarity can be used to predict high full text similarity with a specificity of 20.1% (95% CI [17.3%, 23.1%]) and sensitivity of 99.999%. similarity and full text similarity have a moderate correlation (Pearson correlation coefficient: −0.423) when the similarity ratio is above 0.4. Among pairs of articles in PMC, method sections are found to be the most repetitive (frequency of similar pairs, methods: 0.029, introduction: 0.0076, results: 0.0043). In contrast, among a set of manually verified duplicate articles, results are the most repetitive sections (frequency of similar pairs, results: 0.94, methods: 0.89, introduction: 0.82). Repetition of introduction and methods sections is more likely to be committed by the same authors (odds of a highly similar pair having at least one shared author, introduction: 2.31, methods: 1.83, results: 1.03). There is also significantly more similarity in pairs of review articles than in pairs containing one review and one nonreview paper (frequency of similar pairs: 0.0167 and 0.0023, respectively).Conclusion/SignificanceWhile quantifying abstract similarity is an effective approach for finding duplicate citations, a comprehensive full text analysis is necessary to uncover all potential duplicate citations in the scientific literature and is helpful when establishing ethical guidelines for scientific publications.

This paper details the development and implementation of CiteGraph, a system for constructing large-scale citation and co-authorship networks from full-text biomedical articles. CiteGraph represents articles and authors by uniquely identified nodes, and connects those nodes through citation and co-authorship relations. CiteGraph network encompasses over 1.65 million full-text articles and 6.35 million citations by 1.37 million unique authors from the Elsevier full-text articles. Our evaluation shows 98% 99% F1-score for mapping a citation to the corresponding article and identifying MEDLINE articles. We further analyzed the characteristics of CiteGraph and found that they are consistent with assumptions made using small-scale bibliometric analysis. We also developed several novel network-based methods for analyzing publication, citation and collaboration patterns. This is the first work to develop a completely automated system for the creation of a large-scale citation network in the biomedical domain, and also to introduce novel findings in researcher publication histories. CiteGraph can be a useful resource to both the biomedical community, and bibliometric research.

PurposeStudy findings can reach a worldwide audience only after a paper is published in the peer‐reviewed literature; this is regarded by many as the definitive contribution to global exchange of knowledge. The abstract to publication (A:P) rates for free papers presented at an emergency medicine meeting in Asia has not been investigated before. The purpose of this study was to determine the full publication rate of abstracts presented as oral presentations at the Third Asian Conference on Emergency Medicine (ACEM) in Hong Kong in 2004.MethodsA detailed literature search of the MEDLINE database was performed using first and last authors' names and appropriate key words up to January 2008.ResultsA total of 54 free paper abstracts were presented at this conference as oral presentations. Ten (18.5%) abstracts had subsequently been published as full articles by the end of January 2008. The full‐text articles were published in eight different journals.ConclusionsThe A:P ratio of abstracts for oral presentations at ACEM 2004 was 18.5%, lower than that of similar meetings in the US and Australasia. It is normal for less than half of the abstracts presented at meetings to be published as full papers in refereed journals, largely due to the inability to overcome the barriers that present at each stage towards publication. Lack of researcher time due to pressure of clinical work and English language skills may play an important role in Asia.

A high proportion of life science researches are gene-oriented, in which scientists aim to investigate the roles that genes play in biological processes, and their involvement in biological mechanisms. As a result, gene names and their related information turn out to be one of the main objects of interest in biomedical literatures. While the capability of recognizing gene mentions has made significant progress, the results of recognition are still insufficient for direct use due to the ambiguity of gene names. Gene normalization (GN) goes beyond the recognition task by linking a gene mention to a database ID. Unlike most previous works, we approach GN on the instance-level and evaluate its overall performance on the recognition and normalization steps in abstracts and full texts. We release the first instance-level gene normalization (IGN) corpus in the BioC format, which includes annotations for the boundaries of all gene mentions and the corresponding IDs for human gene mentions. Species information, along with existing co-reference chains and full name/abbreviation pairs are also provided for each gene mention. Using the released corpus, we have designed a collective instance-level GN approach using not only the contextual information of each individual instance, but also the relations among instances and the inherent characteristics of full-text sections. Our experimental results show that our collective approach can achieve an F-score of 0.743. The proposed approach that exploits section characteristics in full-text articles can improve the F-scores of information lacking sections by up to 1.8%. In addition, using the proposed refinement process improved the F-score of gene mention recognition by 0.125 and that of GN by 0.03. Whereas current experimental results are limited to the human species, we seek to continue updating the annotations of the IGN corpus and observe how the proposed approach can be extended to other species.

Introduction: In recent years, the use of portfolios as learning and assessment tools has become more widespread across the range of health professions. Whilst a growing body of literature has accompanied these trends, there is no clear collated summary of the evidence for the educational effects of the use of portfolios in undergraduate education. This systematic review is the result of our work to provide such a summary.Methods: We developed a protocol based on the recommendations of the Best Evidence Medical Education (BEME) collaboration. Citations retrieved by electronic searches of 10 databases were assessed against pre-defined inclusion/exclusion criteria by two independent reviewers and full texts of potentially relevant articles were obtained. Studies were identified for inclusion in the review by examination of full text articles by two independent reviewers. At all stages, discrepancies were resolved by consensus. Data relating to characteristics of the student population, intervention, outcome...

Editor's Response to Letters about Rappaport et al.

Introduction: The availability of prescription drugs as OTC medications is also becoming more common. However, self-medication carries risks such as misdiagnosis, use of excessive drug doses, prolonged use, and drug interactions. This review aimed to collect evidence about the impact of self-medications on health outcomes. Methods: The systematic review in this study involved several steps to identify and assess relevant research. The search phase involved finding potentially relevant studies in various databases such as PubMed, PsychInfo, EBSCO Medline, BioMed central, and Science Direct. The screening phase involved applying predetermined inclusion and exclusion criteria to determine which studies were appropriate for the review. To conclude the selection process, the full text of the articles was reviewed to determine whether they met the inclusion criteria. Additionally, the full text of review articles was reviewed to identify any additional articles that might be relevant and included in the review. Results: A total of 17 studies were found that met the inclusion criteria. The majority (11/17) of these studies were cross-sectional and relied on self-report. The combined sample size of the 17 studies was 28,628 (ranging from 5 to 5,426), and the average response rate was 66%. In 76% of the studies, reported self-treatment was 50% (ranging from 12% to 99%). Overall, only one or two respondents were registered with a general practitioner (GP) or primary care physician (mean of 56%, ranging from 21% to 96%). In the 13 studies that provided information on self-prescription, the mean percentage of physicians reporting self-prescription was 61% with a standard deviation of 25% and a range of 9% to 99%. Conclusions: Although many patients view over-the-counter (OTC) medications as completely safe, their use always carries some degree of risk for the consumer. This is especially true for patients who do not follow the instructions on the label or package insert.

INTRODUCTION: Nonrelaxing pelvic floor dysfunction (PFD) is a condition characterized by tension of the pelvic floor musculature, often resulting in pelvic pain. The objective of this study was to review patient-reported pain outcomes following treatment of nonrelaxing pelvic floor dysfunction to identify gaps in current evidence. METHODS: A systematic review of the following databases from inception to July 2020 was performed: Ovid MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Scopus. Two authors reviewed titles and abstracts for relevance, and full articles were obtained and evaluated for inclusion. Studies were included if they assess interventions for nonrelaxing PFD characterized by pelvic pain. The third author was consulted in instances of disagreement. RESULTS: Of the 1,184 abstracts identified and reviewed, 36 full text articles were reviewed. Treatments for nonrelaxing PFD included biofeedback, botulinum toxin injections, electrical stimulation, intravaginal diazepam, massage, osteopathy, psychiatric interview, physical therapy, sacral nerve stimulation, trigger point injection, and combined therapies. Nineteen studies assessed the effectiveness of treatment based on patient reported pain outcomes. All studies demonstrated an improvement in pelvic pain. Several limitations were identified including varied pre-treatment diagnostic evaluation, small sample size, retrospective and single arm design, heterogeneity in treatment administration within and between studies, lack of standardized pain assessments, and limited long term outcome data. CONCLUSION: Nonrelaxing PFD is a debilitating condition. There is a paucity of high-quality clinical trials evaluating the effectiveness of pelvic floor muscle dysfunction treatments. Although preliminary studies support multi-modal treatment options, robust trials assessing patient-centered outcomes are necessary.

The aim of DTV’s Article Database Service (DADS) is to offer our end users a whole new generation of library services with integrated search and browse facilities, a common user interface and direct electronic document delivery - all accessible from their own desks. The system should handle bibliographic data, including abstracts as well as articles in full text and table-of-contents data.Using an electronic article database service users can access a particular article or journal within seconds rather than hours or days typical for paper based collections. Large collections of material can be searched simultaneously and retrieved instantly. There is also the possibility for active dissemination of information based on “interest profiles” of users, ie current awareness services.Technical design considerations of the DADS system include: Integration of data (full text documents, bibliographic records and table-of-contents data) from different vendors and information sources Common user interface for searching and browsing Simultaneous searching in multiple heterogeneous databases Integrated ordering and delivery of documents Accessibility 24 hours a day, 7 days a week, 365 days a year The system should be based on open standards, wherever possible Support of multiple hardware platforms and operating environments. Organizing, indexing and providing access to material from different information providers becomes a major task.

Systematic Review of the Literature. The purpose of this study was to perform a systematic review describing fusion rates for anterior cervical discectomy and fusion (ACDF) using autograft vs various interbody devices augmented with different osteobiologic materials. A systematic review limited to the English language was performed in Medline, Embase and Cochrane library using Medical Subject Heading (MeSH) terms. Studies that evaluated fusion after ACDF using autografts and osteobiologics combined with PEEK, carbon fibre, or metal cages were searched for. Articles in full text that met the criteria were included in the review. The main outcomes evaluated were the time taken to merge, the definition of the fusion assessment, and the modality of the fusion assessment. The risk of bias of each article was assessed by the MINORS score or ROB 2.0 depending on the randomisation process. The total number of references reviewed was six hundred and eighty-two. After applying the inclusion criteria, 54 were selected for the retrieval of the full text. Eight studies were selected and included for final analysis in this study. Fusion rates were reported between 83.3% and 100% for autograft groups compared to 46.5% and 100% for various interbody device/osteobiological combinations. The overall quality of the evidence in all radiographic fusion studies was considered insufficient due to a serious risk of bias. Mechanical interbody devices augmented with osteobiologics performed similarly to autografts in terms of reliability and efficacy. Their time to fusion and fusion rate were comparable to autografts at the end of the final follow-up.

Open Access Journal (OAJ) is a journal publication that contains articles in full text and user’s can be accessed and used free of charge. The purpose of this study was to determine the extent to which open access was used in the Borneo Administrator Journal (JBA) by measuring reader satisfaction. The research method used was a descriptive quantitative approach. The data collection used a survey method and a data analysis technique used a simple descriptive statistical method. This research has eight research questions, namely the level of user’s satisfaction with access and download facilities, Kemenristek/Dikti accreditation, language, benefit for the profession and career advancement, number of articles and columns, overall format and content, issued quarterly (3x a year), and services provided by JBA managers. The research data analysis has the three highest indicators were published every quarter (3x a year), the format and content as a whole, and were beneficial for professional and career advancement. The lowest score indicators but still in the satisfied category were download facilities, language, and the number of articles and columns. In conclusion, the overall level of reader satisfaction is in the satisfied category. The implementation of open access in the Borneo Administrator Journal is basically to support the development and dissemination of knowledge.

FisheriesVolume 25, Issue 12 p. 1-48 Article Full Issue Article Volume 25, Issue 12 First published: 09 January 2011 https://doi.org/10.1577/1548-8446-25-12Citations: 1AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume25, Issue12December 2000Pages 1-48 RelatedInformation