Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

BACKGROUND: The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. RESULTS: PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. CONCLUSION: PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications

SLIM: an alternative Web interface for MEDLINE/PubMed searches – a preliminary study

BACKGROUND: With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded. RESULTS: Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features. CONCLUSION: SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine

Alcohol consumption and its correlation with medical conditions: a UK Biobank study

BackgroundAlcohol consumption has been associated with the occurrence of many health conditions. We analyzed UK Biobank data to explore associations of various conditions to type and amount of alcohol consumed. UK Biobank is a large biomedical database providing information from UK participants, including lifestyle questionnaires and diagnosis data.MethodsUsing UK Biobank, we examined the relationship between weekly alcohol consumption, alcohol type and the incidence of eight select conditions. We calculated counts of individuals consuming each type diagnosed with these conditions. To assess the effect of alcohol consumption on each condition’s prevalence, we used log-logistic regression models to generate dose–response models for each alcohol type.ResultsThe alcohol consumed included: red wine (228,439 participants), white wine (188811), beer (182648), spirits (129418), and fortified wine (34598). We observed increased condition prevalence with increasing amounts of alcohol. This was especially seen for chronic obstructive lung disease, cirrhosis of liver, hypertension, gastritis, and type 2 diabetes. Beer consumers showed higher prevalence for most conditions while fortified wine had the largest increases in incidence rates. Only white wine showed decreased incidence for acute myocardial infarction. In general, the prevalence of many conditions was higher among alcohol consumers, particularly for hypertension, 33.8%, compared to 28.6% for non-drinkers.ConclusionAlthough many conditions were already prevalent among non-drinkers, participants consuming increasing amounts of alcohol had increased incidence rates for many of the studied conditions. This was especially true for consumers of beer and fortified wine, but also true to a lesser extent for consumers of spirits, red and white wine

Evaluation of txt2MEDLINE and Development of Short Messaging Service–Optimized, Clinical Practice Guidelines in Botswana

Objective: Currently clinicians in sub-Saharan Africa have limited access to the Internet, whereas mobile phone access and use is extensive. The University of Pennsylvania in collaboration with the National Library of Medicine launched txt2MEDLINE, a short messaging service (SMS) query of PubMed/MEDLINE, and SMS-optimized clinical guidelines in Botswana. The objective of this project was to establish and evaluate the utility of these tools for clinicians in Botswana. Materials and Methods: A local server was established at the University of Botswana that allowed clinicians to send queries and receive results via local (in-country) SMS text messaging on any type of cellular phone. The queries sent via txt2MEDLINE were returned as abbreviated “the bottom line” summaries of abstracts. The 2007 Botswana Treatment Guide was converted into a format that can be queried by SMS. Various types of healthcare workers were recruited to use and evaluate these services. Results: Seventy-six healthcare workers attended training sessions for these services. In the preusage survey, most said they would use the services daily or weekly. During a 4-week trial period, use of these services dropped off dramatically. Participant feedback was collected and indicated that improvements in ease of use would increase the usage. Conclusions: This pilot project enables clinicians to query and receive PubMed abstract summaries and country-specific clinical guidelines using mobile phones. Feedback offers insight on how to improve this technology so that it can be adopted for long-term use. With further adjustments, these resources may provide an effective working model for other countries where limited Internet access impedes upon patient care

Evidence-based medicine among internal medicine residents in a community hospital program using smart phones

BACKGROUND: This study implemented and evaluated a point-of-care, wireless Internet access using smart phones for information retrieval during daily clinical rounds and academic activities of internal medicine residents in a community hospital. We did the project to assess the feasibility of using smart phones as an alternative to reach online medical resources because we were unable to find previous studies of this type. In addition, we wanted to learn what Web-based information resources internal medicine residents were using and whether providing bedside, real-time access to medical information would be perceived useful for patient care and academic activities. METHODS: We equipped the medical teams in the hospital wards with smart phones (mobile phone/PDA hybrid devices) to provide immediate access to evidence-based resources developed at the National Library of Medicine as well as to other medical Websites. The emphasis of this project was to measure the convenience and feasibility of real-time access to current medical literature using smart phones. RESULTS: The smart phones provided real-time mobile access to medical literature during daily rounds and clinical activities in the hospital. Physicians found these devices easy to use. A post-study survey showed that the information retrieved was perceived to be useful for patient care and academic activities. CONCLUSION: In community hospitals and ambulatory clinics without wireless networks where the majority of physicians work, real-time access to current medical literature may be achieved through smart phones. Immediate availability of reliable and updated information obtained from authoritative sources on the Web makes evidence-based practice in a community hospital a reality

Utilization of the PICO framework to improve searching PubMed for clinical questions

Research articl

A UMLS-based spell checker for natural language processing in vaccine safety

BACKGROUND: The Institute of Medicine has identified patient safety as a key goal for health care in the United States. Detecting vaccine adverse events is an important public health activity that contributes to patient safety. Reports about adverse events following immunization (AEFI) from surveillance systems contain free-text components that can be analyzed using natural language processing. To extract Unified Medical Language System (UMLS) concepts from free text and classify AEFI reports based on concepts they contain, we first needed to clean the text by expanding abbreviations and shortcuts and correcting spelling errors. Our objective in this paper was to create a UMLS-based spelling error correction tool as a first step in the natural language processing (NLP) pipeline for AEFI reports. METHODS: We developed spell checking algorithms using open source tools. We used de-identified AEFI surveillance reports to create free-text data sets for analysis. After expansion of abbreviated clinical terms and shortcuts, we performed spelling correction in four steps: (1) error detection, (2) word list generation, (3) word list disambiguation and (4) error correction. We then measured the performance of the resulting spell checker by comparing it to manual correction. RESULTS: We used 12,056 words to train the spell checker and tested its performance on 8,131 words. During testing, sensitivity, specificity, and positive predictive value (PPV) for the spell checker were 74% (95% CI: 74–75), 100% (95% CI: 100–100), and 47% (95% CI: 46%–48%), respectively. CONCLUSION: We created a prototype spell checker that can be used to process AEFI reports. We used the UMLS Specialist Lexicon as the primary source of dictionary terms and the WordNet lexicon as a secondary source. We used the UMLS as a domain-specific source of dictionary terms to compare potentially misspelled words in the corpus. The prototype sensitivity was comparable to currently available tools, but the specificity was much superior. The slow processing speed may be improved by trimming it down to the most useful component algorithms. Other investigators may find the methods we developed useful for cleaning text using lexicons specific to their area of interest