The structural and content aspects of abstracts versus bodies of full text journal articles are different

<p>Abstract</p> <p>Background</p> <p>An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there has been no comprehensive characterization of how the bodies of full text journal articles differ from the abstracts that until now have been the subject of most biomedical text mining research.</p> <p>Results</p> <p>We examined the structural and linguistic aspects of abstracts and bodies of full text articles, the performance of text mining tools on both, and the distribution of a variety of semantic classes of named entities between them. We found marked structural differences, with longer sentences in the article bodies and much heavier use of parenthesized material in the bodies than in the abstracts. We found content differences with respect to linguistic features. Three out of four of the linguistic features that we examined were statistically significantly differently distributed between the two genres. We also found content differences with respect to the distribution of semantic features. There were significantly different densities per thousand words for three out of four semantic classes, and clear differences in the extent to which they appeared in the two genres. With respect to the performance of text mining tools, we found that a mutation finder performed equally well in both genres, but that a wide variety of gene mention systems performed much worse on article bodies than they did on abstracts. POS tagging was also more accurate in abstracts than in article bodies.</p> <p>Conclusions</p> <p>Aspects of structure and content differ markedly between article abstracts and article bodies. A number of these differences may pose problems as the text mining field moves more into the area of processing full-text articles. However, these differences also present a number of opportunities for the extraction of data types, particularly that found in parenthesized text, that is present in article bodies but not in article abstracts.</p

Do peers see more in a paper than its authors?

Recent years have shown a gradual shift in the content of biomedical publications that is freely accessible, from titles and abstracts to full text. This has enabled new forms of automatic text analysis and has given rise to some interesting questions: How informative is the abstract compared to the full-text? What important information in the full-text is not present in the abstract? What should a good summary contain that is not already in the abstract? Do authors and peers see an article differently? We answer these questions by comparing the information content of the abstract to that in citances-sentences containing citations to that article. We contrast the important points of an article as judged by its authors versus as seen by peers. Focusing on the area of molecular interactions, we perform manual and automatic analysis, and we find that the set of all citances to a target article not only covers most information (entities, functions, experimental methods, and other biological concepts) found in its abstract, but also contains 20% more concepts. We further present a detailed summary of the differences across information types, and we examine the effects other citations and time have on the content of citances

Analysis of conference abstract-to-publication rate in UK orthopaedic research

Presentation of research at orthopaedic conferences is an important component for surgical evidence-based practice. However, there remains uncertainty as to how many conference abstracts proceed to achieve full-text publication for wider dissemination. This study aimed to determine the abstract-to-publication rate (APR) of research presented in the largest hip and knee orthopaedic meetings in the UK, and to identify predictive factors which influence the APR.All published abstracts (N=744) from the 2006, 2008, 2009 and 2010 British Hip Society (BHS) and the 2007, 2009, 2010, and 2011 British Association for Surgery of the Knee (BASK) annual conference meetings were examined by four researchers independently. To determine whether abstracts had been published in full-text form, Google Scholar, Medline and EMBASE evidence databases were used to verify full-text publication (FTP) status. Variables including: sample size, statistical significance, grade of the first author, research affiliated institution and research design were extracted and analysed to identify whether these were associated with FTP.176 out of 744 abstracts achieved FTP status (APR: 23.7%). Factors associated with FTP status included statistically significant results (p0.05).APR of the assessed BHS and BASK annual conference presentations are low in comparison to other scientific meetings. Encouragement should be provided to clinicians and academics to submit their work for publication to address this short-fall, thereby enhancing the potential for full-text research publications to inform evidence-based orthopaedics

Large-scale event extraction from literature with multi-level gene normalization

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license

Beyond the third dimension of BIM:A systematic review of literature and assessment of professional views

Across the world, the use of Building Information Modelling (BIM) and the three-dimensional (3D) model in projects are increasingly frequent for supporting design tasks. The digital data embodied in the BIM model is shared between the project stakeholders from the various disciplines. After giving an overview of the BIM 3D Model data used for planning (4D) and costing (5D), the study assesses the level of clarity or confusion on what the numbers of dimension refer to after the 5th dimension. A systematic review of the different BIM dimensions was conducted associated with an online questionnaire sent to various Architecture, Engineering and Construction stakeholders across Europe. The online questionnaire survey was limited to the 28 European Union (EU) countries. Each of the 28 EU countries was represented by at least one respondent. The research identified 52 papers considering BIM 4D Model, 15 considering 5D modelling, 6 considering the 6D Model and 2 considering the 7D. It was also identified a confusion between academics and practitioners for the 6D and 7D BIM dimensions. In fact, 86% of the professionals, actually using 6D, allocate Sustainability to 6D. Whereas 85% of the professionals using 7D allocate it to Facility Management.</p

Assessment of emergency medicine residents: a systematic review

Background: Competency-based medical education is becoming the new standard for residency programs, including Emergency Medicine (EM). To inform programmatic restructuring, guide resources and identify gaps in publication, we reviewed the published literature on types and frequency of resident assessment.Methods: We searched MEDLINE, EMBASE, PsycInfo and ERIC from Jan 2005 - June 2014. MeSH terms included “assessment,” “residency,” and “emergency medicine.” We included studies on EM residents reporting either of two primary outcomes: 1) assessment type and 2) assessment frequency per resident. Two reviewers screened abstracts, reviewed full text studies, and abstracted data. Reporting of assessment-related costs was a secondary outcome.Results: The search returned 879 articles; 137 articles were full-text reviewed; 73 met inclusion criteria. Half of the studies (54.8%) were pilot projects and one-quarter (26.0%) described fully implemented assessment tools/programs. Assessment tools (n=111) comprised 12 categories, most commonly: simulation-based assessments (28.8%), written exams (28.8%), and direct observation (26.0%). Median assessment frequency (n=39 studies) was twice per month/rotation (range: daily to once in residency). No studies thoroughly reported costs.Conclusion: EM resident assessment commonly uses simulation or direct observation, done once-per-rotation. Implemented assessment systems and assessment-associated costs are poorly reported. Moving forward, routine publication will facilitate transitioning to competency-based medical education