CiteULike: Gaetan's library [305 articles]

Content of Weblogs Written by Health Professionals

Tara Lagu — 2008-07-25T06:43:11-00:00

Journal of General Internal Medicine

Background Medical weblogs (?blogs?) have emerged as a new connection between health professionals and the public. Objective To examine the scope and content of medical blogs and approximate how often blog authors commented about patients, violated patient privacy, or displayed a lack of professionalism. Design We defined medical blogs as those that contain some medical content and were apparently written by physicians or nurses. We used the Google search term ?medical blog? to begin a modified snowball sampling method to identify sites posting entries from 1/1/06 through 12/14/06. We reviewed five entries per blog, categorizing content and characteristics. Results We identified 271 medical blogs. Over half (56.8%) of blog authors provided sufficient information in text or image to reveal their identities. Individual patients were described in 114 (42.1%) blogs. Patients were portrayed positively in 43 blogs (15.9%) and negatively in 48 blogs (17.7%). Of blogs that described interactions with individual patients, 45 (16.6%) included sufficient information for patients to identify their doctors or themselves. Three blogs showed recognizable photographic images of patients. Healthcare products were promoted, either by images or descriptions, in 31 (11.4%) blogs. Conclusions Blogs are a growing part of the public face of the health professions. They offer physicians and nurses the opportunity to share their narratives. They also risk revealing confidential information or, in their tone or content, risk reflecting poorly on the blog authors and their professions. The health professions should assume some responsibility for helping authors and readers negotiate these challenges.

Using the Internet to search for cancer clinical trials: A comparative audit of clinical trial search tools.

Nancy L Atkinson — 2008-03-20T08:29:12-00:00

Contemp Clin Trials (7 February 2008)

Advancing the clinical trial research process to improve cancer treatment necessitates helping people with cancer identify and enroll in studies, and researchers are using the power of the Internet to facilitate this process. This study used a content analysis of online cancer clinical trial search tools to understand what people with cancer might encounter. The content analysis revealed that clinical trial search tools were easy to identify using a popular search engine, but their functionality and content varied greatly. Most required that users be fairly knowledgeable about their medical condition and sophisticated in their web navigation skills. The ability to search by a specific health condition or type of cancer was the most common search strategy. The more complex tools required that users input detailed information about their personal medical history and have knowledge of specific clinical trial terminology. Search tools, however, only occasionally advised users to consult their doctors regarding clinical trial decision-making. This, along with the complexity of the tools suggests that online search tools may not adequately facilitate the clinical trial recruitment process. Findings from this analysis can be used as a framework from which to systematically examine actual consumer experience with online clinical trial search tools.

Long-Term Patterns of Online Evidence Retrieval Use in General Practice: A 12-Month Study

Farah Magrabi — 2008-03-20T08:27:13-00:00

J Med Internet Res, Vol. 10, No. 1. (Mar 2008)

Background: Provision of online evidence at the point of care is one strategy that could provide clinicians with easy access to up-to-date evidence in clinical settings in order to support evidence-based decision making. Objective: The aim was to determine long-term use of an online evidence system in routine clinical practice. Methods: This was a prospective cohort study. 59 clinicians who had a computer with Internet access in their consulting room participated in a 12-month trial of Quick Clinical, an online evidence system specifically designed around the needs of general practitioners (GPs). Patterns of use were determined by examination of computer logs and survey analysis. Results: On average, 9.9 searches were conducted by each GP in the first 2 months of the study. After this, usage dropped to 4.4 searches per GP in the third month and then levelled off to between 0.4 and 2.6 searches per GP per month. The majority of searches (79.2%, 2013/2543) were conducted during practice hours (between 9 am and 5 pm) and on weekdays (90.7%, 2315/2543). The most frequent searches related to diagnosis (33.6%, 821/2291) and treatment (34.5%, 844/2291). Conclusion: GPs will use an online evidence retrieval system in routine practice; however, usage rates drop significantly after initial introduction of the system. Long-term studies are required to determine the extent to which GPs will integrate the use of such technologies into their everyday clinical practice and how this will affect the satisfaction and health outcomes of their patients.

Medical librarian 2.0 : use of Web 2.0 technologies in reference services

M Wood — 2007-10-11T11:53:55-00:00

(2007)

How the internet is changing health care.

M Cross — 2008-07-24T07:37:18-00:00

BMJ (Clinical research ed.), Vol. 337 (2008)

How We Surveyed Doctors to Learn What They Want from Computers and Technology

Tania Bardyn — 2008-02-15T07:56:11-00:00

Computers in Libraries, Vol. 28, No. 1. (0 January 2008), pp. 7-11.

Librarians at New York City's Bellevue Hospital Center needed to write a 3-year strategic plan that included technology data. In this article, they describe how they surveyed doctors and residents about their technology and internet use to determine what the Bellevue Medical Library needed to do in order to support those who deliver medical care. Specifically, they needed to know where doctors use computers, why and where they use the internet, and where they search for information. They explain how they chose survey questions, reveal what they learned from the doctors' completed surveys, and describe how that data was used to plan services. The results helped them write their plan and justify a big budget increase to purchase more computers. Five tips are presented for writing survey questions about technology and internet use.

Bibliographie sur Medline-PubMed. Chercher l'information pertinente ou comment bien utiliser une base de données

D Ollat — 2007-12-11T14:26:59-00:00

Rev Chir Orthop Reparatrice Appar Mot, Vol. 93, No. 6. (October 2007), pp. 619-626.

La littérature scientifique a pris une place croissante dans notre pratique quotidienne. L'abondance de cette littérature a rendu incontournable l'utilisation d'outils tels que les bases de données pour obtenir des résultats de recherche pertinents. Force est de constater que nous sommes peu préparés à l'utilisation de tels outils... Medline est la base de donnée la plus répandue et nous proposons de détailler son fonctionnement. Après une brève définition, nous détaillons son mode d'organisation et de mise à jour. Nous expliquons comment élaborer une recherche efficace notamment par l'emploi des mots-clés et des opérateurs booléens. Un choix précis conditionne la pertinence du résultat de la recherche. À cet effet, nous détaillons l'utilisation du répertoire MESH pour choisir un mot-clé ainsi que ses diverses options accessoires. Les fonctions annexes et services associés de la base de données Medline sont également passés en revue. Enfin la gestion des résultats, leur affichage et leur exploitation sont détaillés.

Web 2.0 technologies for undergraduate and postgraduate medical education: an online survey

J Sandars — 2007-12-06T15:01:40-00:00

Postgrad Med J, Vol. 83, No. 986. (1 December 2007), pp. 759-762.

ObjectivesTo identify the current familiarity and use of Web 2.0 technologies by medical students and qualified medical practitioners, and to identify the barriers to its use for medical education. MethodsA semi-structured online questionnaire survey of 3000 medical students and 3000 qualified medical practitioners (consultants, general practitioners and doctors in training) on the British Medical Association's membership database. ResultsAll groups had high familiarity, but low use, of podcasts. Ownership of digital media players was higher among medical students. There was high familiarity, but low use, of other Web 2.0 technologies except for high use of instant messaging and social networking by medical students. All groups stated that they were interested in using Web 2.0 technologies for education but there was lack of knowledge and skills in how to use these new technologies. ConclusionsThere is an overall high awareness of a range of new Web 2.0 technologies by both medical students and qualified medical practitioners and high interest in its use for medical education. However, the potential of Web 2.0 technologies for undergraduate and postgraduate medical education will only be achieved if there is increased training in how to use this new approach. 10.1136/pgmj.2007.063123

The medical digital library landscape

Kathleen Ismond — 2007-11-29T11:48:45-00:00

Online Information Review, Vol. 31, No. 6. (2007), pp. 744-758.

Purpose – The purpose of this paper is to identify two medical digital libraries from each of the following three countries: Canada, the USA and the UK. It aims to discuss strengths and weaknesses in system design in an effort to provide a basis on which to improve both the organisation of, and the access to, electronic, scholarly information. Design/methodology/approach – Inclusion criteria for identifying the medical digital libraries were, those who: had primarily text-based collections, intended for use by researchers or healthcare professionals; were freely accessible, and fulfilled the author's definition of a digital library as opposed to an online database. (Medical digital libraries with either a historical focus or that had primarily image/video collections were excluded.) To identify suitable medical digital libraries, the following resources were used: scholarly databases, online search engines, government and national library web sites, lists of online medical resources, and university web sites. Selection preference was given to those libraries with the most recent launch dates and service features. Each library was systematically evaluated, qualitatively and quantitatively, from the user's perspective in six distinct areas: administrative overview and site architecture, knowledge organisation, results management, interaction with the collection, additional information services, usability, and personalisation. Findings – The study finds that each digital library had a unique set of strengths and weaknesses. Each offered different services to help users identify relevant material and to quickly understand and assess their contents. However, this required that each library have a team of experts to obtain, assess, catalogue, and annotate the information. Where available, user comments were supportive of each effort and very positive. Research limitations/implications – Medical digital libraries are an excellent conduit between authors and practitioners. However, they require intensive resources for establishment and maintenance. For these libraries to realise their full potential, emphasis must be placed on the currency and quality of their collections, maintaining pace with the technology employed by their users, providing services that facilitate the access and digestion of complex, scholarly information, and ensuring that online users are aware of the existence of these libraries. Practical implications – This paper contributes to the overall improvement of existing and future medical digital libraries. Originality/value – This is the first ever evaluation and comparison of freely available medical digital libraries from three countries.

Basic rules for a "resource rich" internet site.

M Orsini — 2007-10-25T07:07:56-00:00

Caring, Vol. 26, No. 9. (September 2007), pp. 58-59.

EBM metadata based on Dublin Core better presenting validity of clinical trials.

W Xu — 2007-10-11T11:14:03-00:00

J Med Syst, Vol. 31, No. 5. (October 2007), pp. 337-343.

To help clinicians find better evidence, a metadata schema for Evidence Based Medicine (EBM) is developed. Dublin Core metadata standard (DC) was adopted to help build a metadata schema. An experimental system was developed to test the validity of the metadata and full text papers of clinical therapy on stomach ulcer extracted using PubMed. An EBM metadata schema was developed. Citations were created from original papers using the metadata schema. Three clinicians evaluated papers by utilizing metadata and full texts respectively. Agreement of evaluation was analyzed, and the result on weighted kappa was 0.55 (95% CI, 0.42-0.67). It reveals that there is moderate agreement between evaluation of metadata citations and full texts. It is possible to use the metadata to select papers before reading the full texts. A further study should be made to prove the applicability of the metadata in the real world setting.

Introducing Web 2.0: RSS trends for health librarians

Eugene Barsky — 2006-05-16T21:46:12-00:00

JCHLA / JABSC, Vol. 27, No. 1. (Winter 2006), pp. 7-8.

The Primary Care Electronic Library: RSS feeds using SNOMED-CT indexing for dynamic content delivery.

J Robinson — 2007-09-10T08:44:36-00:00

Inform Prim Care, Vol. 14, No. 4. (2006), pp. 247-252.

BACKGROUND: Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. OBJECTIVE: To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. METHOD: Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. RESULTS: Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. CONCLUSION: The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.

DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing.

C Taswell — 2008-03-20T13:11:29-00:00

IEEE Trans Inf Technol Biomed, Vol. 12, No. 2. (March 2008), pp. 191-204.

The semantic web remains in the early stages of development. It has not yet achieved the goals envisioned by its founders as a pervasive web of distributed knowledge and intelligence. Success will be attained when a dynamic synergism can be created between people and a sufficient number of infrastructure systems and tools for the semantic web in analogy with those for the original web. The domain name system (DNS), web browsers, and the benefits of publishing web pages motivated many people to register domain names and publish web sites on the original web. An analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks will motivate people to register resource labels and publish resource descriptions on the semantic web. The Domain Ontology Oriented Resource System (DOORS) and Problem Oriented Registry of Tags and Labels (PORTAL) are proposed as infrastructure systems for resource metadata within a paradigm that can serve as a bridge between the original web and the semantic web. Registers domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, PORTAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. BioPORT is proposed as a prototype PORTAL registry specific for the problem domain of biomedical computing.

Ontology-Based MEDLINE Document Classification

Fabrice Camous — 2008-01-10T20:14:29-00:00

Vol. 4414 (2007), pp. 439-452.

Indicateurs bibliométriques : réalités, mythes et prospective

Lesya Baudoin — 2008-01-10T08:33:09-00:00

Médecine/Sciences, Vol. 20, No. 10. (October 2004)

Le facteur d’impact, établi par l’Institute for Scientific Information (ISI), est fréquemment utilisé pour évaluer les chercheurs et leurs programmes. Sur la base d’exemples, cet article propose quelques clés pour analyser les conditions et les limites d’interprétation d’indicateurs qui, à l’origine, n’ont pas été conçus pour l’évaluation individuelle. Il présente aussi les conséquences prévisibles des nouvelles technologies d’information, en particulier l’avènement de journaux électroniques, sur la production, la publication et l’évaluation des résultats de la recherche dans les sciences biomédicales.

Deja vu A Study of Duplicate Citations in Medline

Mounir Errami — 2007-12-03T07:40:20-00:00

Bioinformatics (1 December 2007), btm574.

Motivation: Duplicate publication impacts the quality of the scientific corpus, has been difficult to detect, and studies this far have been limited in scope and size .Using text similarity searches, we were able to identify signatures of duplicate citations among a body of abstracts. Results: A sample of 62,213 Medline citations was examined and a database of manually verified duplicate citations was created to study author publication behavior. We found that 0.04% of the citations with no shared authors were highly similar and are thus potential cases of plagiarism. 1.35% with shared authors were sufficiently similar to be considered a duplicate. Extrapolating, this would correspond to 3,500 and 117,500 duplicate citations in total, respectively. Availability: eTBLAST, an automated citation matching tool, and Deja vu, the duplicate citation database, are freely available at http://invention.swmed.edu/ and http:/spore.swmed.edu/dejavu. Contact: Harold.Garner@utsouthwestern.edu 10.1093/bioinformatics/btm574

Blogs, wikis and podcasts: the 'evaluation bypass' in action?

Andrew Booth — 2007-11-19T07:55:54-00:00

Health Info Libr J, Vol. 24, No. 4. (December 2007), pp. 298-302.

A really simple guide to a powerful tool: RSS

Adel Abdellaoui — 2007-09-17T11:26:37-00:00

BMJ Career Focus, Vol. 332, No. 7555. (17 June 2006), 244.

The sensitivity and precision of search terms in Phases I, II and III of the Cochrane Highly Sensitive Search Strategy for identifying reports of randomized trials inmedlinein a specific area of health careHIV/AIDS prevention and treatment interventions

Eisinga — 2007-06-24T00:09:22-00:00

Health Information and Libraries Journal, Vol. 24, No. 2. (June 2007), pp. 103-109.

Electronic Publication and the Narrowing of Science and Scholarship

James Evans — 2008-07-18T07:21:32-00:00

Science, Vol. 321, No. 5887. (18 July 2008), pp. 395-399.

Online journals promise to serve more information to more dispersed audiences and are more efficiently searched and recalled. But because they are used differently than print--scientists and scholars tend to search electronically and follow hyperlinks rather than browse or peruse--electronically available journals may portend an ironic change for science. Using a database of 34 million articles, their citations (1945 to 2005), and online availability (1998 to 2005), I show that as more journal issues came online, the articles referenced tended to be more recent, fewer journals and articles were cited, and more of those citations were to fewer journals and articles. The forced browsing of print archives may have stretched scientists and scholars to anchor findings deeply into past and present scholarship. Searching online is more efficient and following hyperlinks quickly puts researchers in touch with prevailing opinion, but this may accelerate consensus and narrow the range of findings and ideas built upon. 10.1126/science.1150473

More than just a mouse click: research into work practices behind the assignment of medical trust marks on the World Wide Web.

SA Adams — 2008-07-24T14:32:55-00:00

International journal of medical informatics, Vol. 76 Suppl 1 (June 2007)

Hyperlinked web trust marks have been a popular topic of discussion during the past 10 years. However, the discussion has focused mostly on what these trust marks are not doing in terms of helping patients (or other lay end users) find reliable medical information on the web. In this paper, we discuss how this focus on patients and their actions with respect to trust marks, has overshadowed, if not rendered invisible, what trust marks are doing to educate medical site/information providers. We draw on data from ethnographic research conducted at the Health on the Net Foundation in 2002 and 2003 in order to explore an alternate definition of what it means to be a 'user' of a trust mark and the importance of the review process in educating site providers. We argue that understanding the work involved in the process of assigning a seal is crucial to understanding the role that the seal plays as part of the medical internet.

Blog/web log - a new easy and interactive website building tool for a non-net savvy radiologist.

SK Sethi — 2007-10-10T14:38:12-00:00

J Thorac Imaging, Vol. 22, No. 2. (May 2007), pp. 115-119.

Recently, there has been no escaping the mention of blogs in the media. Blogging has emerged as a social phenomenon, which has impacted politics, business, and communication. Blogging software has enabled people with limited knowledge of the Internet to publish their thoughts online and participate in a global conversation; whereas the Blogosphere has hyperaccelerated the spread of information. Technorati, a blog search engine is now tracking over 7.8 million Weblogs, and 937 million links, and reports that there are about 30,000 to 40,000 new blogs created a day. The majority of people who blog do so as a hobby, using blogs to publish their thoughts, feelings, and viewpoints on whatever topics interest them. Blogging software also enables people to post pictures, music, and more recently videos. For many people blogs are used as online journals or diaries; other people use blogs to communicate with their family and friends. Whether people generate revenue with their blogs or use them as a hobby the one thing they all have in common is that they are part of the Blogosphere, or network of blogs that gives people a voice and allows them to spread information at an unprecedented rate. Although searching PubMed produces few results for "blog" (6 relevant articles of 24), "weblog" (1 article), web log (8 entries of varying relevance), and "blogging" (4 articles) (none of which were in Radiology, RadioGraphics, AJR, or JVIR), blogging might well become an important means of information transfer in Radiology also. As radiology is an image-based science, a blog is a satisfying endeavor in that you can share your experiences with others instantaneously In this context, I would like to submit my experience with easy method for building a Web site known as blogging (maintaining a Web log). As a radiologist, I use my blog (http://www.sumerdoc.blogspot.com/; or http://www.indianradiology.com/) to post interesting cases from my routine practice along with any interesting abstracts I come across during my day-to-day work. The success of this project can be measured by the fact that in the last full year of "rad-blogging," more than 30,000 visitors came to the site from all over the world, with thousands of queries from patients, colleagues, and many interested students. Rad-blogging might well become a new easy method of information exchange and opinion building in Radiology.

Navigating information spaces: A case study of related article search in PubMed

Jimmy Lin — 2008-07-23T10:14:16-00:00

Information Processing & Management, Vol. 44, No. 5. (September 2008), pp. 1771-1783.

The concept of an "information space" provides a powerful metaphor for guiding the design of interactive retrieval systems. We present a case study of related article search, a browsing tool designed to help users navigate the information space defined by results of the PubMed® search engine. This feature leverages content-similarity links that tie MEDLINE® citations together in a vast document network. We examine the effectiveness of related article search from two perspectives: a topological analysis of networks generated from information needs represented in the TREC 2005 genomics track and a query log analysis of real PubMed users. Together, data suggest that related article search is a useful feature and that browsing related articles has become an integral part of how users interact with PubMed.

["Méta-analyse": a web-based tool for research and analysis of radiology papers.]

N Garcelon — 2008-07-22T13:25:16-00:00

Journal de radiologie, Vol. 89, No. 6. (June 2008), pp. 817-820.

Finding articles providing answers to specific clinical questions is greatly facilitated by the availability of indexed Medline abstracts using the Pubmed search engine. Nonetheless, the large number of references sometimes requires a time-consuming review of multiple abstracts. In order to streamline the search process, we have created a tool facilitating the search and review of these abstracts. We present here this tool named "Méta-analyse".

Application of Web 2.0 tools in Medical Librarianship to Support Medicine 2.0

Vahideh Gavgani — 2008-07-21T11:02:23-00:00

Webology, Vol. 5, No. 1. (March 2008)

It is almost a decade that social networking technology along with its tools such as blogs, wikis, slidesharing/videosharing and photosharing softwares, podcasts, RSS feeds, mashups, folksonomies, and bookmarks has developed its influence on all human fields of study/activity. It is obvious that these tools are increasingly growing, in different languages, regions and fields, due to social dynamic and liberal characteristic of Web 2.0 technologies. Medical sciences and library science also are not exception to this influence. Consequently, library 2.0 and newly coined concepts of Medicine 2.0, and Health 2.0 have become the buzzwords in the Internet culture. In spite of proliferation of such social tools listed above, there is no aggregation and harmony for the utilization of the potential of these technologies in specific subject areas and the sources of information on the Web is almost proliferating and uncontrolled. This gives rise to the problem of webliographic control due to which the information seekers find difficulties in information retrieval. The paper presents application of Web 2.0 in medical libraries to support Medicine 2.0 emphasizing the above-mentioned problems. Considering the nature of an original article the experience of the authors, as a medical librarian and a faculty member in Library and Information Science, through observation of the needs, problems and prospects, played an important role in forming the idea and presentation. The study also used secondary data collected from related literatures. Standardization and webliographic control would solve the problem. In addition, governmental support and creating awareness at the management level in the organizations is also crucial.

An update on Uniform Resource Locator (URL) decay in MEDLINE abstracts and measures for its mitigation.

Erick Ducut — 2008-06-12T08:03:34-00:00

BMC Medical Informatics and Decision Making, Vol. 8 (11 June 2008), 23.

Using Seminar Blogs To Enhance Student Participation and Learning in Public Health School Classes

Rose Goldman — 2008-07-21T07:14:06-00:00

Am J Public Health (16 July 2008), AJPH.2008.133694.

Objectives. We evaluated whether "seminar blogs" enhanced learning in a large graduate-level introductory public health school class.Methods. Sixty students were divided into 6 online blog groups. Students posted their assignments (case analyses, news commentaries), prompting comments from other students. Anonymous poll surveys of students were conducted at midpoint and at the end of the course.Results. Sixty percent reported that blog participation enriched their learning quite a bit, 34% a small amount, and 6% not at all; 54% said that the blogs provided opportunities to learn from classmates. When comparing writing on the blog to speaking in class, 60% found it easier, 30% about the same, and 10% harder. About 65% said that skills attained by participating in blogs were useful for current or future work. Major criticisms involved time issues.Conclusions. Small seminar blogs offer opportunities for increased student participation, interaction, and learning. To be most effective and appealing, assignments for postings need to allow sufficient time for commentary. This educational technology has potential to expand the classroom experience and is worthy of further development and testing. 10.2105/AJPH.2008.133694

Transdab wiki: the interactive transglutaminase substrate database on web 2.0 surface.

Eva Csősz — 2008-07-03T13:15:04-00:00

Amino acids (2 July 2008)

TRANSDAB wiki is a database of transglutaminase substrate proteins. This wiki is designed to provide quality content of all the details (including synonyms, structures, references) about transglutaminase substrate proteins and interaction partners. Currently TRANSDAB contains 243 articles about substrate proteins for 6 transglutaminase types in a user-friendly, editable format. Our aim was to collect structural information about substrate proteins and this information is provided in form of images, videos and links. The scientific community is invited to edit the database and besides providing up-to-date information, this wiki should serve as a platform for valuable discussions.

Combining Semantic Web technologies with Multi-Agent Systems for integrated access to biological resources.

Francisco García-Sánchez — 2008-07-01T14:14:57-00:00

Journal of biomedical informatics (23 May 2008)

The increasing volume and diversity of information in biomedical research is demanding new approaches for data integration in this domain. Semantic Web technologies and applications can leverage the potential of biomedical information integration and discovery, facing the problem of semantic heterogeneity of biomedical information sources. In such an environment, agent technology can assist users in discovering and invoking the services available on the Internet. In this paper we present SEMMAS, an ontology-based, domain-independent framework for seamlessly integrating Intelligent Agents and Semantic Web Services. Our approach is backed with a proof-of-concept implementation where the breakthrough and efficiency of integrating disparate biomedical information sources have been tested.

PuReD-MCL: a graph-based PubMed document clustering methodology

T Theodosiou — 2008-07-01T14:26:39-00:00

Bioinformatics (1 July 2008), btn318.

Motivation: Biomedical literature is the principal repository of biomedical knowledge, with PubMed being the most complete database collecting, organising, and analysing such textual knowledge. There are numerous efforts that attempt to exploit this information by using text mining and machine learning techniques. We developed a novel approach, called PuReD-MCL (Pubmed Related Documents-MCL), which is based on the graph clustering algorithm MCL and relevant resources from PubMed. Methods: PuReD-MCL avoids using natural language processing (NLP) techniques directly; instead, it takes advantage of existing resources, available from PubMed. PuReD-MCL then clusters documents efficiently using the MCL graph clustering algorithm, which is based on graph flow simulation. This process allows users to analyse the results by highlighting important clues, and finally to visualise the clusters and all relevant information using an interactive graph layout algorithm, for instance BioLayout Express 3D. Results: The methodology was applied to two different datasets, previously used for the validation of the document clustering tool TextQuest. The first dataset involves the organisms E. coli and yeast, whereas the second is related to Drosophila development. PuReD-MCL successfully reproduces the annotated results obtained from TextQuest, while at the same time provides additional insights into the clusters and the corresponding documents. Availability: Source code in perl and R are available from http://tartara.csd.auth.gr/~theodos/ 10.1093/bioinformatics/btn318

Developing a Web 2.0 Telemedical Education System: the AJAX-Cocoon Portal.

S Mohammed — 2008-06-30T08:32:04-00:00

International journal of electronic healthcare, Vol. 4, No. 1. (2008), pp. 24-42.

Web 2.0 technologies such as wikis, podcasts/vodcasting, blogs and semantic portals could be quite effective tools in e-learning for health professionals. If effectively deployed, such tools can offer a way to enhance students', clinicians' and patients' learning experiences, and deepens levels of learners' engagement and collaboration within medical learning environments. However, Web 2.0 requires simplicity of use as well as integration with modern web technologies. This article presents a Web 2.0 telemedical portal, which provides a social community-learning paradigm from the desk of the physician, the student, the hospital administrator, or the insurer. The presented portal utilises RESTful web services and techniques like content syndication, mushups and Asynchronous JavaScript API and XML (AJAX). The designed portal is based on the Apache Cocoon RESTful framework for sharing Digital Imaging and Communications in Medicine (DICOM) medical case studies. Central to this article is the integration between Cocoon and AJAX. The proposed AJAX-Cocoon portal utilises a JSP portlet architecture, which manages the interaction dynamics and overcomes the shortcomings of the JSR 168 and WSRP 1.0 standards.

GAPscreener: An Automatic Tool for Screening Human Genetic Association Literature in PubMed Using the Support Vector Machine Technique

Wei Yu — 2008-04-23T07:16:11-00:00

BMC Bioinformatics, Vol. 9 (22 April 2008), 205.

Searching Additional Databases Except PubMed Are Necessary for a Systematic Review.

Ming-Hua Zheng — 2008-06-30T08:09:42-00:00

Stroke; a journal of cerebral circulation (26 June 2008)

Internet-based dissemination of educational video presentations: a primer in video podcasting.

FM Corl — 2008-06-20T14:21:16-00:00

AJR. American journal of roentgenology, Vol. 191, No. 1. (July 2008)

OBJECTIVE: Video "podcasting" is an Internet-based publication and syndication technology that is defined as the process of capturing, editing, distributing, and downloading audio, video, and general multimedia productions. The expanded capacity for visual components allows radiologists to view still and animated media. CONCLUSION: These image-viewing characteristics and the ease of widespread delivery are well suited for radiologic education. This article presents detailed information about how to generate and distribute a video podcast using a Macintosh platform.

Anni 2.0: a multipurpose text-mining tool for the life sciences

Rob Jelier — 2008-06-13T04:46:41-00:00

Genome Biology, Vol. 9, No. 6. (2008)

Anni 2.0 is an online tool (http://biosemantics.org/anni/) to aid the biomedical researcher with a broad range of information needs. Anni provides an ontology-based interface to Medline and retrieves documents and associations for several classes of biomedical concepts, including genes, drugs and diseases, with established text-mining technology. In this article we illustrate Anni's usability by applying the tool to two use cases: interpretation of a set differentially expressed genes, and literature-based knowledge discovery.

The emerging Web 2.0 social software: an enabling suite of sociable technologies in health and health care education

Kamel Boulos — 2007-03-02T15:22:57-00:00

Health Information and Libraries Journal, Vol. 24, No. 1. (March 2007), pp. 2-23.

"Blogs" and "Wikis" Are Valuable Software Tools for Communication Within Research Groups

Igor Sauer — 2004-12-28T18:27:42-00:00

Artificial Organs, Vol. 29, No. 1., 82.

Pure: a pubmed article recommendation system based on content-based filtering.

T Yoneya — 2008-06-12T14:20:23-00:00

Genome informatics. International Conference on Genome Informatics, Vol. 18 (2007), pp. 267-276.

We have developed a PubMed article recommendation system, PURE, which is based on content-based filtering. PURE has a web interface by which users can add/delete their preferred articles. Once articles are registered, PURE then performs model-based clustering of the preferred articles and recommends the highly-rated articles by the prediction using the trained model. PURE updates the PubMed articles and reports the recommendation by email on daily-base. This system will be helpful for biologists to reduce the time required for gathering information from PubMed. PURE is downloadable under GPL license, via http://www.bic.kyoto-u.ac.jp/pathway/mami/out/PURE.tar.gz.

Blogging in an online health information technology class.

X Zeng — 2008-06-12T08:16:34-00:00

Perspectives in health information management / AHIMA, American Health Information Management Association, Vol. 2 (2005)

In this article we introduce blogs, including their brief history, their current status, and motivations for blogging. We describe how we created a course blog in one online Health information management (HIM) baccalaureate course. We describe three pedagogical purposes (online discussion, digital drop box, and class project management tool) of the course blog. We report the results of our after-class survey on using the blog as a learning tool. Survey results illustrated that 55 percent of the students agree that the blog can be a tool for facilitating learning, 50 percent agree it can be used as a tool for student activities, 60 percent agree it can serve as a medium for reflective thinking and writing, and 60 percent want to see its application in other courses.

PageRank without hyperlinks: reranking with PubMed related article networks for biomedical text retrieval

Jimmy Lin — 2008-06-06T18:39:41-00:00

BMC Bioinformatics, Vol. 9, No. 1. (2008)

BACKGROUND:Graph analysis algorithms such as PageRank and HITS have been successful in Web environments because they are able to extract important inter-document relationships from manually-created hyperlinks. We consider the application of these techniques to biomedical text retrieval. In the current PubMed search interface, a MEDLINE citation is connected to a number of related citations, which are in turn connected to other citations. Thus, a MEDLINE record represents a node in a vast content-similarity network. This article explores the hypothesis that these networks can be exploited for text retrieval, in the same manner as hyperlink graphs on the Web.RESULTS:We conducted a number of reranking experiments using the TREC 2005 genomics track test collection in which scores extracted from PageRank and HITS analysis were combined with scores returned by an off-the-shelf retrieval engine. Experiments demonstrate that incorporating PageRank scores yields significant improvements in terms of standard ranked-retrieval metrics.CONCLUSIONS:The link structure of content-similarity networks can be exploited to improve the effectiveness of information retrieval systems. These results generalize the applicability of graph analysis algorithms to text retrieval in the biomedical domain.

Nursing education 2.0: Twitter & tweets. Can you post a nugget of knowledge in 140 characters or less?

DJ Skiba — 2008-06-06T14:05:04-00:00

Nursing education perspectives, Vol. 29, No. 2. (r 2008), pp. 110-112.

Health 2.0. Will its promise be realized?

N Versel — 2008-06-06T07:12:37-00:00

Managed care (Langhorne, Pa.), Vol. 17, No. 3. (March 2008), pp. 49-52.

Office 2.0: a web 2.0 tool for international collaborative research.

P Gambadauro — 2008-06-04T07:02:35-00:00

Lancet, Vol. 371, No. 9627. (31 May 2008), pp. 1837-1838.

Evaluation of a Blog Used in a Dental Terminology Course for First-Year Dental Students

El — 2008-06-03T14:33:50-00:00

J Dent Educ., Vol. 72, No. 6. (1 June 2008), pp. 725-735.

This article reports the findings of a study conducted to evaluate a blog used in a dental terminology course. The blog was established using free online software to provide more learning exercises for students and to collect feedback about course proceedings. The instructor posted exercises such as multiple choice and true/false questions and invited students to publish answers. Students were also encouraged to post comments about difficult parts of the course that needed clarification. Students contributed 149 comments, mostly as answers in response to thirteen posts of exercises over three months. All users of the blog who responded to a questionnaire considered it useful, and most of them expressed the opinion that blogs should be used in other courses. The main reason that students reported for not using the blog was lack of time. Statistically significant differences in examination performance existed between students who used the blog and those who did not. Based on these findings, the blog achieved its purposes, which were to enhance instructor communication with students and provide students with practice exercises to improve their understanding of dental terminology. Further research about the application of blogging and its potential to enhance dental education is needed.

Web 2.0: what a health care manager needs to know.

X Zeng — 2008-06-02T08:08:42-00:00

The health care manager, Vol. 27, No. 1. (r 2008), pp. 58-70.

Web 2.0 is one of the latest buzzwords for an assortment of emerging technologies on the Web. Health care managers need to know the benefits and drawbacks of these technologies before integrating them into organizational operations. In this article, we first illustrate the differences in health care management style and workflow between the Web 1.0 and Web 2.0 technologies. After defining and explaining some of the representative technologies, we discuss the benefits of Web 2.0 in general and the reasons why a health care manager should know these trends. And lastly, we list some caveats that a health care manager should know before fully embracing the technologies. The keys are to align the technologies with the culture and workflow of the organization and have a clear policy on their usages.

Social Uses of Personal Health Information Within PatientsLikeMe, an Online Patient Community: What Can Happen When Patients Have Access to One Another's Data

Jeana Frost — 2008-05-27T11:19:31-00:00

J Med Internet Res, Vol. 10, No. 3. (May 2008)

Background: This project investigates the ways in which patients respond to the shared use of what is often considered private information: personal health data. There is a growing demand for patient access to personal health records. The predominant model for this record is a repository of all clinically relevant health information kept securely and viewed privately by patients and their health care providers. While this type of record does seem to have beneficial effects for the patient--physician relationship, the complexity and novelty of these data coupled with the lack of research in this area means the utility of personal health information for the primary stakeholders---the patients---is not well documented or understood. Objective: PatientsLikeMe is an online community built to support information exchange between patients. The site provides customized disease-specific outcome and visualization tools to help patients understand and share information about their condition. We begin this paper by describing the components and design of the online community. We then identify and analyze how users of this platform reference personal health information within patient-to-patient dialogues. Methods: Patients diagnosed with amyotrophic lateral sclerosis (ALS) post data on their current treatments, symptoms, and outcomes. These data are displayed graphically within personal health profiles and are reflected in composite community-level symptom and treatment reports. Users review and discuss these data within the Forum, private messaging, and comments posted on each other's profiles. We analyzed member communications that referenced individual-level personal health data to determine how patient peers use personal health information within patient-to-patient exchanges. Results: Qualitative analysis of a sample of 123 comments (about 2% of the total) posted within the community revealed a variety of commenting and questioning behaviors by patient members. Members referenced data to locate others with particular experiences to answer specific health-related questions, to proffer personally acquired disease-management knowledge to those most likely to benefit from it, and to foster and solidify relationships based on shared concerns. Conclusions: Few studies examine the use of personal health information by patients themselves. This project suggests how patients who choose to explicitly share health data within a community may benefit from the process, helping them engage in dialogues that may inform disease self-management. We recommend that future designs make each patient's health information as clear as possible, automate matching of people with similar conditions and using similar treatments, and integrate data into online platforms for health conversations.

Natural Language Processing in aid of FlyBase curators

Nikiforos Karamanis — 2008-04-15T11:11:07-00:00

BMC Bioinformatics, Vol. 9, No. 1. (2008)

BACKGROUND:Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear.RESULTS:PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article.CONCLUSIONS:We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully.

Synonym set extraction from the biomedical literature by lexical pattern discovery

John Mccrae — 2008-03-25T17:55:58-00:00

BMC Bioinformatics, Vol. 9 (24 March 2008), 159.

HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0.

Kei-Hoi Cheung — 2008-05-20T13:16:16-00:00

Journal of biomedical informatics (11 April 2008)

We describe the potential of current Web 2.0 technologies to achieve data mashup in the health care and life sciences (HCLS) domains, and compare that potential to the nascent trend of performing semantic mashup. After providing an overview of Web 2.0, we demonstrate two scenarios of data mashup, facilitated by the following Web 2.0 tools and sites: Yahoo! Pipes, Dapper, Google Maps and GeoCommons. In the first scenario, we exploited Dapper and Yahoo! Pipes to implement a challenging data integration task in the context of DNA microarray research. In the second scenario, we exploited Yahoo! Pipes, Google Maps, and GeoCommons to create a geographic information system (GIS) interface that allows visualization and integration of diverse categories of public health data, including cancer incidence and pollution prevalence data. Based on these two scenarios, we discuss the strengths and weaknesses of these Web 2.0 mashup technologies. We then describe Semantic Web, the mainstream Web 3.0 technology that enables more powerful data integration over the Web. We discuss the areas of intersection of Web 2.0 and Semantic Web, and describe the potential benefits that can be brought to HCLS research by combining these two sets of technologies.