PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts.
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Since it is becoming increasingly laborious to manually extract useful information embedded in the ever-growing volumes of literature, automated intelligent text analysis tools are becoming more and more essential to assist in this task. PubFinder (www.glycosciences.de/tools/PubFinder) is a publicly available web tool designed to improve the retrieval rate of scientific abstracts relevant for a specific scientific topic. Only the selection of a representative set of abstracts is required, which are central for a scientific topic. No special knowledge concerning the query-syntax is necessary. Based on the selected abstracts, a list of discriminating words is automatically calculated, which is subsequently used for scoring all defined PubMed abstracts for their probability of belonging to the defined scientific topic. This results in a hit-list of references in the descending order of their likelihood score. The algorithms and procedures implemented in PubFinder facilitate the perpetual task for every scientist of staying up-to-date with current publications dealing with a specific subject in biomedicine. (+info)
LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts.
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The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). Owing to the limitations (no direction, unverified automatic prediction) of the co-occurrence approach, the primary data in the LitMiner database represent postulated basic gene-gene relationships. The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modelling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. LitMiner (http://andromeda.gsf.de/litminer) and WikiGene (http://andromeda.gsf.de/wiki) can be used unrestricted with any Internet browser. (+info)
GoPubMed: exploring PubMed with the Gene Ontology.
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The biomedical literature grows at a tremendous rate and PubMed comprises already over 15 000 000 abstracts. Finding relevant literature is an important and difficult problem. We introduce GoPubMed, a web server which allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology. GoPubMed provides the following benefits: first, it gives an overview of the literature abstracts by categorizing abstracts according to the GO and thus allowing users to quickly navigate through the abstracts by category. Second, it automatically shows general ontology terms related to the original query, which often do not even appear directly in the abstract. Third, it enables users to verify its classification because GO terms are highlighted in the abstracts and as each term is labelled with an accuracy percentage. Fourth, exploring PubMed abstracts with GoPubMed is useful as it shows definitions of GO terms without the need for further look up. GoPubMed is online at www.gopubmed.org. Querying is currently limited to 100 papers per query. (+info)
Use of Internet audience measurement data to gauge market share for online health information services.
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BACKGROUND: The transition to a largely Internet and Web-based environment for dissemination of health information has changed the health information landscape and the framework for evaluation of such activities. A multidimensional evaluative approach is needed. OBJECTIVE: This paper discusses one important dimension of Web evaluation-usage data. In particular, we discuss the collection and analysis of external data on website usage in order to develop a better understanding of the health information (and related US government information) market space, and to estimate the market share or relative levels of usage for National Library of Medicine (NLM) and National Institutes of Health (NIH) websites compared to other health information providers. METHODS: The primary method presented is Internet audience measurement based on Web usage by external panels of users and assembled by private vendors-in this case, comScore. A secondary method discussed is Web usage based on Web log software data. The principle metrics for both methods are unique visitors and total pages downloaded per month. RESULTS: NLM websites (primarily MedlinePlus and PubMed) account for 55% to 80% of total NIH website usage depending on the metric used. In turn, NIH.gov top-level domain usage (inclusive of NLM) ranks second only behind WebMD in the US domestic home health information market and ranks first on a global basis. NIH.gov consistently ranks among the top three or four US government top-level domains based on global Web usage. On a site-specific basis, the top health information websites in terms of global usage appear to be WebMD, MSN Health, PubMed, Yahoo! Health, AOL Health, and MedlinePlus. Based on MedlinePlus Web log data and external Internet audience measurement data, the three most heavily used cancer-centric websites appear to be www.cancer.gov (National Cancer Institute), www.cancer.org (American Cancer Society), and www.breastcancer.org (non-profit organization). CONCLUSIONS: Internet audience measurement has proven useful to NLM, with significant advantages compared to sole reliance on usage data from Web log software. Internet audience data has helped NLM better understand the relative usage of NLM and NIH websites in the intersection of the health information and US government information market sectors, which is the primary market intersector for NLM and NIH. However important, Web usage is only one dimension of a complete Web evaluation framework, and other primary research methods, such as online user surveys, usability tests, and focus groups, are also important for comprehensive evaluation that includes qualitative elements, such as user satisfaction and user friendliness, as well as quantitative indicators of website usage. (+info)
A rare complication of pneumonectomy: diagnosis made by a literature search.
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This case describes platypnoea-orthodeoxia syndrome in a patient 2 months after a right pneumonectomy for adenocarcinoma of the lung. The patient complained of platypnoea (breathlessness in the upright position) and was noted to have orthodeoxia (arterial desaturation on standing) on clinical examination. This was due to anatomical changes after the pneumonectomy that resulted in direct blood flow from the inferior vena cava through a previously unrecognised atrial septal defect into the left atrium. The closure of this right to left shunt with an Amplatzer occluder produced immediate and striking symptomatic relief in the patient. The authors had no previous experience of this very rare complication of pneumonectomy. The diagnosis was made after a literature search using PubMed/Medline, underlining the direct clinical benefit provided by these databases. (+info)
PubMed perspective of family medicine research: where does it stand?
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OBJECTIVE: The aim of this study was to obtain a view of family medicine research by analyzing PubMed citations from 1960-2003. METHOD: Family practice (FP) citations in PubMed from 1960 to 2003 were downloaded in MEDLINE format. This was written into relation database using 'PubMed Grabber/Analyzer' software developed at University of Kelaniya, Sri Lanka. Search Query Language (SQL) and online PubMed queries were used for further analysis. RESULTS: There were 50288 FP citations from 80 countries. Of these, 33712 (67%) citations were from 15 FP journals. United Kingdom (18760), United States (13584), Australia (3262), Canada (1848), Germany-west (1340) were the five countries which had the most citations and 22 countries had less than 5 citations. Van Weel C (118), Geyman JP (116), Olesen F (87), Jones R (83) and Knottnerus JA (82) were numerically, the top five authors. Only 921 authors had more than 10 citations and the vast majority of authors had only one citation. Letters (5121), review (2715), editorial (2259), randomized controlled trials-RCT (1585) and Meta-analysis (44) were the top publication types. 40 citations found under 'qualitative research'. Discussion. The relatively few PubMed FP citations (50288) are by a small number of academics in developed countries. Citations showed an upsurge from the mid 1980s to the late 1990's but reached a plateau in the new millennium. Compared to PubMed citations from 1960-2003 in other specialties such as 2737655 for public health, 1151194 for cardiology & cardiovascular diseases and 318538 for medical informatics, the 50288 FP citations were paltry. Paucity of RCT (1585) and meta-analysis (44) was noted. The low 'qualitative research' citations (44) could have been due to the late introduction of the MeSH concept in 2003. CONCLUSIONS: Priority should be given to increase FP research and also to ensure the indexing of FP journals that are not currently indexed in PubMed. Efforts to increase citations in Medline may not give the desired results because of low priority given primary care specialties such as family medicine in the USA. Alternative solution of a separate bibliographic database for FP similar to PsycInfo may be too costly. (+info)
PubMed, the New York Times and the Chicago Tribune as tools for teaching genetics.
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An elementary course in human heredity for students not planning to major in the sciences can be based on current scientific literature and on the popular media. Examinations are constructed from questions on recent abstracts obtained from PubMed. The course is designed to promote writing skills in the sciences, and students write two papers in the course of a quarter. In the first paper, students trace the primary source of media reports on genetics and attempt to evaluate the reporter's translation. In a second paper, students write popular articles on the basis of current primary sources. (+info)
Predictors and risk factors for recurrent scleroderma renal crisis in the kidney allograft: case report and review of the literature.
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Scleroderma renal crisis (SRC) can lead to end-stage renal disease (ESRD) and subsequent need for dialysis and/or renal transplantation. We review all reported cases of renal transplantations in scleroderma patients from PubMed search, present UNOS data on transplant outcomes, and identify predictors for allograft SRC. Of the five cases with recurrent SRC, all developed ESRD within a year of onset of native kidney SRC, whereas none of those who developed ESRD more than 1-2 years after the onset of SRC developed recurrence. Anemia preceded allograft SRC in two cases, pericardial effusion in one, and skin tightening in two others. UNOS data (October 1987-July 2004) documented 260 transplants performed for the renal diagnosis of scleroderma, with a 5-year graft survival rate of 56.7%. The risk for allograft SRC recurrence appears to correlate with early native renal function loss following the onset of SRC. Recurrent SRC in the allograft may be heralded by multiple clinical markers known to be predictive of severe scleroderma, including progression of diffuse skin thickening, new-onset anemia and cardiac complications. (+info)