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Sample records for biomedical information searching

  1. Searching for biomedical information on the World Wide Web.

    PubMed

    Rodgers, R P

    2000-01-01

    The rapid growth of biomedical information available via the Internet and its most popular retrieval system, the World Wide Web, has fostered active research and development directed toward locating resources that are appropriate for answering specific queries. The goal is to create tools that optimize information retrieval (as measured by two quantities, precision and recall) while minimizing the effort required by the user. Existing Web retrieval tools can be divided into the following groups: manually maintained topical lists; automatically generated word-based indices; software agents and multi-index searching aids; network cataloging methods; and miscellaneous hybrid and newer approaches. Improvements in current methods should arise from further research into: methods of describing objects on the Web; improved ways of searching for (and within) collections of documents as opposed to single documents; the ability to search for fielded documents; and ways to describe resources that span intra- and interdisciplinary as well as cross-cultural linguistic differences. For this last problem, the U.S. National Library of Medicine's Unified Medical Language System (UMLS) will be of great help. As online information retrieval improves, efforts are underway to improve the online information itself; quality control over content is being addressed as the peer-review systems of traditional printed journals migrate into the realm of electronic publication. PMID:11183455

  2. [Biomedical information on the internet using search engines. A one-year trial].

    PubMed

    Corrao, Salvatore; Leone, Francesco; Arnone, Sabrina

    2004-01-01

    The internet is a communication medium and content distributor that provide information in the general sense but it could be of great utility regarding as the search and retrieval of biomedical information. Search engines represent a great deal to rapidly find information on the net. However, we do not know whether general search engines and meta-search ones are reliable in order to find useful and validated biomedical information. The aim of our study was to verify the reproducibility of a search by key-words (pediatric or evidence) using 9 international search engines and 1 meta-search engine at the baseline and after a one year period. We analysed the first 20 citations as output of each searching. We evaluated the formal quality of Web-sites and their domain extensions. Moreover, we compared the output of each search at the start of this study and after a one year period and we considered as a criterion of reliability the number of Web-sites cited again. We found some interesting results that are reported throughout the text. Our findings point out an extreme dynamicity of the information on the Web and, for this reason, we advice a great caution when someone want to use search and meta-search engines as a tool for searching and retrieve reliable biomedical information. On the other hand, some search and meta-search engines could be very useful as a first step searching for defining better a search and, moreover, for finding institutional Web-sites too. This paper allows to know a more conscious approach to the internet biomedical information universe. PMID:15032337

  3. Ethics and biomedical information.

    PubMed

    France, F H

    1998-03-01

    Ethical rules are similar for physicians in most countries that follow the Hippocratic oath. They have no formal legal force, but can be used as a reference to provide answers to solve individual cases. It appears erroneous to believe that privacy is about information. It is about relationship. In medicine, there is a contract between a patient and a physician, where health care personnel has to respect secrecy, while integrity and availability of information should be obtained for continuity of care. These somewhat contradictory objectives have to be applied very carefully to computerised biomedical information. Ethical principles have to be made clear to everyone, and society should take the necessary steps to organise their enforcement. Several examples are given in the delivery of health care, telediagnosis, patient follow-up. clinical research as well as possible breakthroughs that could jeopardise privacy, using biomedical information. PMID:9723809

  4. Biomedical information retrieval across languages.

    PubMed

    Daumke, Philipp; Markü, Kornél; Poprat, Michael; Schulz, Stefan; Klar, Rüdiger

    2007-06-01

    This work presents a new dictionary-based approach to biomedical cross-language information retrieval (CLIR) that addresses many of the general and domain-specific challenges in current CLIR research. Our method is based on a multilingual lexicon that was generated partly manually and partly automatically, and currently covers six European languages. It contains morphologically meaningful word fragments, termed subwords. Using subwords instead of entire words significantly reduces the number of lexical entries necessary to sufficiently cover a specific language and domain. Mediation between queries and documents is based on these subwords as well as on lists of word-n-grams that are generated from large monolingual corpora and constitute possible translation units. The translations are then sent to a standard Internet search engine. This process makes our approach an effective tool for searching the biomedical content of the World Wide Web in different languages. We evaluate this approach using the OHSUMED corpus, a large medical document collection, within a cross-language retrieval setting. PMID:17541863

  5. Rising Expectations: Access to Biomedical Information

    PubMed Central

    Lindberg, D. A. B.; Humphreys, B. L.

    2008-01-01

    Summary Objective To provide an overview of the expansion in public access to electronic biomedical information over the past two decades, with an emphasis on developments to which the U.S. National Library of Medicine contributed. Methods Review of the increasingly broad spectrum of web-accessible genomic data, biomedical literature, consumer health information, clinical trials data, and images. Results The amount of publicly available electronic biomedical information has increased dramatically over the past twenty years. Rising expectations regarding access to biomedical information were stimulated by the spread of the Internet, the World Wide Web, advanced searching and linking techniques. These informatics advances simplified and improved access to electronic information and reduced costs, which enabled inter-organizational collaborations to build and maintain large international information resources and also aided outreach and education efforts The demonstrated benefits of free access to electronic biomedical information encouraged the development of public policies that further increase the amount of information available. Conclusions Continuing rapid growth of publicly accessible electronic biomedical information presents tremendous opportunities and challenges, including the need to ensure uninterrupted access during disasters or emergencies and to manage digital resources so they remain available for future generations. PMID:18587496

  6. search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information

    PubMed Central

    2013-01-01

    Background Due to the growing number of biomedical entries in data repositories of the National Center for Biotechnology Information (NCBI), it is difficult to collect, manage and process all of these entries in one place by third-party software developers without significant investment in hardware and software infrastructure, its maintenance and administration. Web services allow development of software applications that integrate in one place the functionality and processing logic of distributed software components, without integrating the components themselves and without integrating the resources to which they have access. This is achieved by appropriate orchestration or choreography of available Web services and their shared functions. After the successful application of Web services in the business sector, this technology can now be used to build composite software tools that are oriented towards biomedical data processing. Results We have developed a new tool for efficient and dynamic data exploration in GenBank and other NCBI databases. A dedicated search GenBank system makes use of NCBI Web services and a package of Entrez Programming Utilities (eUtils) in order to provide extended searching capabilities in NCBI data repositories. In search GenBank users can use one of the three exploration paths: simple data searching based on the specified user’s query, advanced data searching based on the specified user’s query, and advanced data exploration with the use of macros. search GenBank orchestrates calls of particular tools available through the NCBI Web service providing requested functionality, while users interactively browse selected records in search GenBank and traverse between NCBI databases using available links. On the other hand, by building macros in the advanced data exploration mode, users create choreographies of eUtils calls, which can lead to the automatic discovery of related data in the specified databases. Conclusions search Gen

  7. Use of controlled vocabularies to improve biomedical information retrieval tasks.

    PubMed

    Pasche, Emilie; Gobeill, Julien; Vishnyakova, Dina; Ruch, Patrick; Lovis, Christian

    2013-01-01

    The high heterogeneity of biomedical vocabulary is a major obstacle for information retrieval in large biomedical collections. Therefore, using biomedical controlled vocabularies is crucial for managing these contents. We investigate the impact of query expansion based on controlled vocabularies to improve the effectiveness of two search engines. Our strategy relies on the enrichment of users' queries with additional terms, directly derived from such vocabularies applied to infectious diseases and chemical patents. We observed that query expansion based on pathogen names resulted in improvements of the top-precision of our first search engine, while the normalization of diseases degraded the top-precision. The expansion of chemical entities, which was performed on the second search engine, positively affected the mean average precision. We have shown that query expansion of some types of biomedical entities has a great potential to improve search effectiveness; therefore a fine-tuning of query expansion strategies could help improving the performances of search engines. PMID:23920842

  8. Electronic Biomedical Literature Search for Budding Researcher

    PubMed Central

    Thakre, Subhash B.; Thakre S, Sushama S.; Thakre, Amol D.

    2013-01-01

    Search for specific and well defined literature related to subject of interest is the foremost step in research. When we are familiar with topic or subject then we can frame appropriate research question. Appropriate research question is the basis for study objectives and hypothesis. The Internet provides a quick access to an overabundance of the medical literature, in the form of primary, secondary and tertiary literature. It is accessible through journals, databases, dictionaries, textbooks, indexes, and e-journals, thereby allowing access to more varied, individualised, and systematic educational opportunities. Web search engine is a tool designed to search for information on the World Wide Web, which may be in the form of web pages, images, information, and other types of files. Search engines for internet-based search of medical literature include Google, Google scholar, Scirus, Yahoo search engine, etc., and databases include MEDLINE, PubMed, MEDLARS, etc. Several web-libraries (National library Medicine, Cochrane, Web of Science, Medical matrix, Emory libraries) have been developed as meta-sites, providing useful links to health resources globally. A researcher must keep in mind the strengths and limitations of a particular search engine/database while searching for a particular type of data. Knowledge about types of literature, levels of evidence, and detail about features of search engine as available, user interface, ease of access, reputable content, and period of time covered allow their optimal use and maximal utility in the field of medicine. Literature search is a dynamic and interactive process; there is no one way to conduct a search and there are many variables involved. It is suggested that a systematic search of literature that uses available electronic resource effectively, is more likely to produce quality research. PMID:24179937

  9. ON-LINE BIOMEDICAL DATABASES–THE BEST SOURCE FOR QUICK SEARCH OF THE SCIENTIFIC INFORMATION IN THE BIOMEDICINE

    PubMed Central

    Masic, Izet; Milinovic, Katarina

    2012-01-01

    Most of medical journals now has it’s electronic version, available over public networks. Although there are parallel printed and electronic versions, and one other form need not to be simultaneously published. Electronic version of a journal can be published a few weeks before the printed form and must not has identical content. Electronic form of a journals may have an extension that does not contain a printed form, such as animation, 3D display, etc., or may have available fulltext, mostly in PDF or XML format, or just the contents or a summary. Access to a full text is usually not free and can be achieved only if the institution (library or host) enters into an agreement on access. Many medical journals, however, provide free access for some articles, or after a certain time (after 6 months or a year) to complete content. The search for such journals provide the network archive as High Wire Press, Free Medical Journals.com. It is necessary to allocate PubMed and PubMed Central, the first public digital archives unlimited collect journals of available medical literature, which operates in the system of the National Library of Medicine in Bethesda (USA). There are so called on- line medical journals published only in electronic form. It could be searched over on-line databases. In this paper authors shortly described about 30 data bases and short instructions how to make access and search the published papers in indexed medical journals. PMID:23322957

  10. Explorative search of distributed bio-data to answer complex biomedical questions

    PubMed Central

    2014-01-01

    Background The huge amount of biomedical-molecular data increasingly produced is providing scientists with potentially valuable information. Yet, such data quantity makes difficult to find and extract those data that are most reliable and most related to the biomedical questions to be answered, which are increasingly complex and often involve many different biomedical-molecular aspects. Such questions can be addressed only by comprehensively searching and exploring different types of data, which frequently are ordered and provided by different data sources. Search Computing has been proposed for the management and integration of ranked results from heterogeneous search services. Here, we present its novel application to the explorative search of distributed biomedical-molecular data and the integration of the search results to answer complex biomedical questions. Results A set of available bioinformatics search services has been modelled and registered in the Search Computing framework, and a Bioinformatics Search Computing application (Bio-SeCo) using such services has been created and made publicly available at http://www.bioinformatics.deib.polimi.it/bio-seco/seco/. It offers an integrated environment which eases search, exploration and ranking-aware combination of heterogeneous data provided by the available registered services, and supplies global results that can support answering complex multi-topic biomedical questions. Conclusions By using Bio-SeCo, scientists can explore the very large and very heterogeneous biomedical-molecular data available. They can easily make different explorative search attempts, inspect obtained results, select the most appropriate, expand or refine them and move forward and backward in the construction of a global complex biomedical query on multiple distributed sources that could eventually find the most relevant results. Thus, it provides an extremely useful automated support for exploratory integrated bio search, which is

  11. Evaluation of On-Line Searching in MEDLARS (AIM-TWX) by Biomedical Practitioners.

    ERIC Educational Resources Information Center

    Lancaster, F. Wilfrid

    The purpose of the investigation was to determine how effectively biomedical practitioners, with a minimum of introduction to the system, can conduct on-line searches to satisfy their own information needs. The searches were conducted on the Abridged Index Medicus data base as implemented on the on-line ELHILL system (AIM-TWX). ELHILL is the ORBIT…

  12. A Monte Carlo Approach to Biomedical Time Series Search

    PubMed Central

    Woodbridge, Jonathan; Mortazavi, Bobak; Sarrafzadeh, Majid; Bui, Alex A.T.

    2016-01-01

    Time series subsequence matching (or signal searching) has importance in a variety of areas in health care informatics. These areas include case-based diagnosis and treatment as well as the discovery of trends and correlations between data. Much of the traditional research in signal searching has focused on high dimensional R-NN matching. However, the results of R-NN are often small and yield minimal information gain; especially with higher dimensional data. This paper proposes a randomized Monte Carlo sampling method to broaden search criteria such that the query results are an accurate sampling of the complete result set. The proposed method is shown both theoretically and empirically to improve information gain. The number of query results are increased by several orders of magnitude over approximate exact matching schemes and fall within a Gaussian distribution. The proposed method also shows excellent performance as the majority of overhead added by sampling can be mitigated through parallelization. Experiments are run on both simulated and real-world biomedical datasets.

  13. Accessing biomedical literature in the current information landscape.

    PubMed

    Khare, Ritu; Leaman, Robert; Lu, Zhiyong

    2014-01-01

    Biomedical and life sciences literature is unique because of its exponentially increasing volume and interdisciplinary nature. Biomedical literature access is essential for several types of users including biomedical researchers, clinicians, database curators, and bibliometricians. In the past few decades, several online search tools and literature archives, generic as well as biomedicine specific, have been developed. We present this chapter in the light of three consecutive steps of literature access: searching for citations, retrieving full text, and viewing the article. The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar, Web of Science, Scopus, and Embase, and a study on biomedical literature archives such as PubMed Central. The next section describes current research and the state-of-the-art systems motivated by the challenges a user faces during query formulation and interpretation of search results. The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results. Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy. PMID:24788259

  14. Accessing Biomedical Literature in the Current Information Landscape

    PubMed Central

    Khare, Ritu; Leaman, Robert; Lu, Zhiyong

    2015-01-01

    i. Summary Biomedical and life sciences literature is unique because of its exponentially increasing volume and interdisciplinary nature. Biomedical literature access is essential for several types of users including biomedical researchers, clinicians, database curators, and bibliometricians. In the past few decades, several online search tools and literature archives, generic as well as biomedicine-specific, have been developed. We present this chapter in the light of three consecutive steps of literature access: searching for citations, retrieving full-text, and viewing the article. The first section presents the current state of practice of biomedical literature access, including an analysis of the search tools most frequently used by the users, including PubMed, Google Scholar, Web of Science, Scopus, and Embase, and a study on biomedical literature archives such as PubMed Central. The next section describes current research and the state-of-the-art systems motivated by the challenges a user faces during query formulation and interpretation of search results. The research solutions are classified into five key areas related to text and data mining, text similarity search, semantic search, query support, relevance ranking, and clustering results. Finally, the last section describes some predicted future trends for improving biomedical literature access, such as searching and reading articles on portable devices, and adoption of the open access policy. PMID:24788259

  15. A unified architecture for biomedical search engines based on semantic web technologies.

    PubMed

    Jalali, Vahid; Matash Borujerdi, Mohammad Reza

    2011-04-01

    There is a huge growth in the volume of published biomedical research in recent years. Many medical search engines are designed and developed to address the over growing information needs of biomedical experts and curators. Significant progress has been made in utilizing the knowledge embedded in medical ontologies and controlled vocabularies to assist these engines. However, the lack of common architecture for utilized ontologies and overall retrieval process, hampers evaluating different search engines and interoperability between them under unified conditions. In this paper, a unified architecture for medical search engines is introduced. Proposed model contains standard schemas declared in semantic web languages for ontologies and documents used by search engines. Unified models for annotation and retrieval processes are other parts of introduced architecture. A sample search engine is also designed and implemented based on the proposed architecture in this paper. The search engine is evaluated using two test collections and results are reported in terms of precision vs. recall and mean average precision for different approaches used by this search engine. PMID:20703566

  16. An overview of biomedical literature search on the World Wide Web in the third millennium.

    PubMed

    Kumar, Prince; Goel, Roshni; Jain, Chandni; Kumar, Ashish; Parashar, Abhishek; Gond, Ajay Ratan

    2012-06-01

    Complete access to the existing pool of biomedical literature and the ability to "hit" upon the exact information of the relevant specialty are becoming essential elements of academic and clinical expertise. With the rapid expansion of the literature database, it is almost impossible to keep up to date with every innovation. Using the Internet, however, most people can freely access this literature at any time, from almost anywhere. This paper highlights the use of the Internet in obtaining valuable biomedical research information, which is mostly available from journals, databases, textbooks and e-journals in the form of web pages, text materials, images, and so on. The authors present an overview of web-based resources for biomedical researchers, providing information about Internet search engines (e.g., Google), web-based bibliographic databases (e.g., PubMed, IndMed) and how to use them, and other online biomedical resources that can assist clinicians in reaching well-informed clinical decisions. PMID:22692275

  17. Task-Based Information Searching.

    ERIC Educational Resources Information Center

    Vakkari, Pertti

    2003-01-01

    Reviews studies on the relationship between task performance and information searching by end-users, focusing on information searching in electronic environments and information retrieval systems. Topics include task analysis; task characteristics; search goals; modeling information searching; modeling search goals; information seeking behavior;…

  18. BIOSMILE web search: a web application for annotating biomedical entities and relations.

    PubMed

    Dai, Hong-Jie; Huang, Chi-Hsin; Lin, Ryan T K; Tsai, Richard Tzong-Han; Hsu, Wen-Lian

    2008-07-01

    BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along with snippets by order of relevancy to protein-protein interaction. Users can then select articles for further analysis, and BWS will find and mark up biomedical relations in the text. The analysis results can be viewed in the abstract text or in table form. To date, BWS has been field tested by over 30 biologists and questionnaires have shown that subjects are highly satisfied with its capabilities and usability. BWS is accessible free of charge at http://bioservices.cse.yzu.edu.tw/BWS. PMID:18515840

  19. BIOSMILE web search: a web application for annotating biomedical entities and relations

    PubMed Central

    Dai, Hong-Jie; Huang, Chi-Hsin; Lin, Ryan T. K.; Tsai, Richard Tzong-Han; Hsu, Wen-Lian

    2008-01-01

    BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along with snippets by order of relevancy to protein–protein interaction. Users can then select articles for further analysis, and BWS will find and mark up biomedical relations in the text. The analysis results can be viewed in the abstract text or in table form. To date, BWS has been field tested by over 30 biologists and questionnaires have shown that subjects are highly satisfied with its capabilities and usability. BWS is accessible free of charge at http://bioservices.cse.yzu.edu.tw/BWS. PMID:18515840

  20. Job Search Information Guide.

    ERIC Educational Resources Information Center

    Alberta Dept. of Education, Edmonton. Special Educational Services Branch.

    This guide was developed to help classroom teachers in Alberta, Canada, assist high school students in preparing for employment. (It was originally designed to accompany Alberta Job Search information presentations.) The guide contains 11 units covering the following topics: introduction, career planning, personal fact sheets, the job search,…

  1. Sagace: A web-based search engine for biomedical databases in Japan

    PubMed Central

    2012-01-01

    Background In the big data era, biomedical research continues to generate a large amount of data, and the generated information is often stored in a database and made publicly available. Although combining data from multiple databases should accelerate further studies, the current number of life sciences databases is too large to grasp features and contents of each database. Findings We have developed Sagace, a web-based search engine that enables users to retrieve information from a range of biological databases (such as gene expression profiles and proteomics data) and biological resource banks (such as mouse models of disease and cell lines). With Sagace, users can search more than 300 databases in Japan. Sagace offers features tailored to biomedical research, including manually tuned ranking, a faceted navigation to refine search results, and rich snippets constructed with retrieved metadata for each database entry. Conclusions Sagace will be valuable for experts who are involved in biomedical research and drug development in both academia and industry. Sagace is freely available at http://sagace.nibio.go.jp/en/. PMID:23110816

  2. Mining biomedical images towards valuable information retrieval in biomedical and life sciences

    PubMed Central

    Ahmed, Zeeshan; Zeeshan, Saman; Dandekar, Thomas

    2016-01-01

    Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature. In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems. In this review, we summarize technologies related to data mining of figures. We describe and compare the potential of different approaches in terms of their developmental aspects, used methodologies, produced results, achieved accuracies and limitations. Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries. PMID:27538578

  3. Mining biomedical images towards valuable information retrieval in biomedical and life sciences.

    PubMed

    Ahmed, Zeeshan; Zeeshan, Saman; Dandekar, Thomas

    2016-01-01

    Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature. In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems. In this review, we summarize technologies related to data mining of figures. We describe and compare the potential of different approaches in terms of their developmental aspects, used methodologies, produced results, achieved accuracies and limitations. Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries. PMID:27538578

  4. search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles

    PubMed Central

    Iwema, Carrie L.; LaDue, John; Zack, Angela; Chattopadhyay, Ansuman

    2016-01-01

    The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing on any web site to be integrated with articles from preprint servers. This tool, search.bioPreprint, is publicly available at http://www.hsls.pitt.edu/resources/preprint. PMID:27508060

  5. search.bioPreprint: a discovery tool for cutting edge, preprint biomedical research articles.

    PubMed

    Iwema, Carrie L; LaDue, John; Zack, Angela; Chattopadhyay, Ansuman

    2016-01-01

    The time it takes for a completed manuscript to be published traditionally can be extremely lengthy. Article publication delay, which occurs in part due to constraints associated with peer review, can prevent the timely dissemination of critical and actionable data associated with new information on rare diseases or developing health concerns such as Zika virus. Preprint servers are open access online repositories housing preprint research articles that enable authors (1) to make their research immediately and freely available and (2) to receive commentary and peer review prior to journal submission. There is a growing movement of preprint advocates aiming to change the current journal publication and peer review system, proposing that preprints catalyze biomedical discovery, support career advancement, and improve scientific communication. While the number of articles submitted to and hosted by preprint servers are gradually increasing, there has been no simple way to identify biomedical research published in a preprint format, as they are not typically indexed and are only discoverable by directly searching the specific preprint server websites. To address this issue, we created a search engine that quickly compiles preprints from disparate host repositories and provides a one-stop search solution. Additionally, we developed a web application that bolsters the discovery of preprints by enabling each and every word or phrase appearing on any web site to be integrated with articles from preprint servers. This tool, search.bioPreprint, is publicly available at http://www.hsls.pitt.edu/resources/preprint. PMID:27508060

  6. Using a Search Engine-Based Mutually Reinforcing Approach to Assess the Semantic Relatedness of Biomedical Terms

    PubMed Central

    Hsu, Yi-Yu; Chen, Hung-Yu; Kao, Hung-Yu

    2013-01-01

    Background Determining the semantic relatedness of two biomedical terms is an important task for many text-mining applications in the biomedical field. Previous studies, such as those using ontology-based and corpus-based approaches, measured semantic relatedness by using information from the structure of biomedical literature, but these methods are limited by the small size of training resources. To increase the size of training datasets, the outputs of search engines have been used extensively to analyze the lexical patterns of biomedical terms. Methodology/Principal Findings In this work, we propose the Mutually Reinforcing Lexical Pattern Ranking (ReLPR) algorithm for learning and exploring the lexical patterns of synonym pairs in biomedical text. ReLPR employs lexical patterns and their pattern containers to assess the semantic relatedness of biomedical terms. By combining sentence structures and the linking activities between containers and lexical patterns, our algorithm can explore the correlation between two biomedical terms. Conclusions/Significance The average correlation coefficient of the ReLPR algorithm was 0.82 for various datasets. The results of the ReLPR algorithm were significantly superior to those of previous methods. PMID:24348899

  7. Crossing the Chasm: Information Technology to Biomedical Informatics

    PubMed Central

    Fahy, Brenda G.; Balke, C. William; Umberger, Gloria H.; Talbert, Jeffery; Canales, Denise Niles; Steltenkamp, Carol L.; Conigliaro, Joseph

    2011-01-01

    Accelerating the translation of new scientific discoveries to improve human health and disease management is the overall goal of a series of initiatives integrated in the National Institutes of Health (NIH) “Roadmap for Medical Research.” The Clinical and Translational Research Award (CTSA) program is, arguably, the most visible component of the NIH Roadmap providing resources to institutions to transform their clinical and translational research enterprises along the goals of the Roadmap. The CTSA program emphasizes biomedical informatics as a critical component for the accomplishment of the NIH’s translational objectives. To be optimally effective, emerging biomedical informatics programs must link with the information technology (IT) platforms of the enterprise clinical operations within academic health centers. This report details one academic health center’s transdisciplinary initiative to create an integrated academic discipline of biomedical informatics through the development of its infrastructure for clinical and translational science infrastructure and response to the CTSA mechanism. This approach required a detailed informatics strategy to accomplish these goals. This transdisciplinary initiative was the impetus for creation of a specialized biomedical informatics core, the Center for Biomedical Informatics (CBI). Development of the CBI codified the need to incorporate medical informatics including quality and safety informatics and enterprise clinical information systems within the CBI. This paper describes the steps taken to develop the biomedical informatics infrastructure, its integration with clinical systems at one academic health center, successes achieved, and barriers encountered during these efforts. PMID:21383632

  8. Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols

    PubMed Central

    Campagne, Fabien

    2008-01-01

    Background The evaluation of information retrieval techniques has traditionally relied on human judges to determine which documents are relevant to a query and which are not. This protocol is used in the Text Retrieval Evaluation Conference (TREC), organized annually for the past 15 years, to support the unbiased evaluation of novel information retrieval approaches. The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications. Results We describe two protocols for evaluating biomedical information retrieval techniques without human relevance judgments. We call these protocols No Title Evaluation (NT Evaluation). The first protocol measures performance for focused searches, where only one relevant document exists for each query. The second protocol measures performance for queries expected to have potentially many relevant documents per query (high-recall searches). Both protocols take advantage of the clear separation of titles and abstracts found in Medline. We compare the performance obtained with these evaluation protocols to results obtained by reusing the relevance judgments produced in the 2004 and 2005 TREC Genomics Track and observe significant correlations between performance rankings generated by our approach and TREC. Spearman's correlation coefficients in the range of 0.79–0.92 are observed comparing bpref measured with NT Evaluation or with TREC evaluations. For comparison, coefficients in the range 0.86–0.94 can be observed when evaluating the same set of methods with data from two independent TREC Genomics Track evaluations. We discuss the advantages of NT Evaluation over the TRels and the data fusion evaluation protocols introduced recently. Conclusion Our results suggest that the NT Evaluation protocols described here could be used to optimize some search engine parameters before human evaluation. Further research is needed to determine if NT Evaluation or variants of these

  9. An integrated biomedical knowledge extraction and analysis platform: using federated search and document clustering technology.

    PubMed

    Taylor, Donald P

    2007-01-01

    High content screening (HCS) requires time-consuming and often complex iterative information retrieval and assessment approaches to optimally conduct drug discovery programs and biomedical research. Pre- and post-HCS experimentation both require the retrieval of information from public as well as proprietary literature in addition to structured information assets such as compound libraries and projects databases. Unfortunately, this information is typically scattered across a plethora of proprietary bioinformatics tools and databases and public domain sources. Consequently, single search requests must be presented to each information repository, forcing the results to be manually integrated for a meaningful result set. Furthermore, these bioinformatics tools and data repositories are becoming increasingly complex to use; typically they fail to allow for more natural query interfaces. Vivisimo has developed an enterprise software platform to bridge disparate silos of information. The platform automatically categorizes search results into descriptive folders without the use of taxonomies to drive the categorization. A new approach to information retrieval for HCS experimentation is proposed. PMID:16988412

  10. Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature.

    PubMed

    Sutton, Victoria R; Hauser, Susan E

    2005-01-01

    MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information. PMID:16779415

  11. Preliminary comparison of the Essie and PubMed search engines for answering clinical questions using MD on Tap, a PDA-based program for accessing biomedical literature

    PubMed Central

    Sutton, Victoria R.; Hauser, Susan E.

    2005-01-01

    MD on Tap, a PDA application that searches and retrieves biomedical literature, is specifically designed for use by mobile healthcare professionals. With the goal of improving the usability of the application, a preliminary comparison was made of two search engines (PubMed and Essie) to determine which provided most efficient path to the desired clinically-relevant information. PMID:16779415

  12. Introducing meta-services for biomedical information extraction

    PubMed Central

    Leitner, Florian; Krallinger, Martin; Rodriguez-Penagos, Carlos; Hakenberg, Jörg; Plake, Conrad; Kuo, Cheng-Ju; Hsu, Chun-Nan; Tsai, Richard Tzong-Han; Hung, Hsi-Chuan; Lau, William W; Johnson, Calvin A; Sætre, Rune; Yoshida, Kazuhiro; Chen, Yan Hua; Kim, Sun; Shin, Soo-Yong; Zhang, Byoung-Tak; Baumgartner, William A; Hunter, Lawrence; Haddow, Barry; Matthews, Michael; Wang, Xinglong; Ruch, Patrick; Ehrler, Frédéric; Özgür, Arzucan; Erkan, Güneş; Radev, Dragomir R; Krauthammer, Michael; Luong, ThaiBinh; Hoffmann, Robert; Sander, Chris; Valencia, Alfonso

    2008-01-01

    We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; ). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations. PMID:18834497

  13. International biomedical law in search for its normative status.

    PubMed

    Krajewska, Atina

    2012-01-01

    The broad and multifaceted problem of global health law and global health governance has been attracting increasing attention in the last few decades. The global community has failed to establish international legal regime that deals comprehensively with the 'technological revolution'. The latter has posed complex questions to regions of the world with widely differing cultural perspectives. At the same time, an increasing number of governmental and non-state actors have become significantly involved in the sector. They use legal, political, and other forms of decision-making that result in regulatory instruments of contrasting normative status. Law created in this heterogeneous environment has been said to be fragmented, inconsistent, and exacerbating uncertainties. Therefore, claims have been made that a centralised and institutionalised system would help address the problems of transparency, legitimacy and efficiency. Nevertheless, little scholarly consideration is paid to the normative status of international biomedical law. This paper explores whether formalisation and "constitutionalisation" of biomedical law are indeed inevitable for its establishment as a separate regulatory regime. It does so by analysing the proliferation of biomedical law in light of two the theory of fragmentation and the theory of global legal pluralism. Investigating the problem in this way helps determine the theoretical framework and methodology of future studies of biomedical law at the international level. This in turn should help its future development in a more consistent and harmonised manner. PMID:23115826

  14. Development and evaluation of a biomedical search engine using a predicate-based vector space model.

    PubMed

    Kwak, Myungjae; Leroy, Gondy; Martinez, Jesse D; Harwell, Jeffrey

    2013-10-01

    Although biomedical information available in articles and patents is increasing exponentially, we continue to rely on the same information retrieval methods and use very few keywords to search millions of documents. We are developing a fundamentally different approach for finding much more precise and complete information with a single query using predicates instead of keywords for both query and document representation. Predicates are triples that are more complex datastructures than keywords and contain more structured information. To make optimal use of them, we developed a new predicate-based vector space model and query-document similarity function with adjusted tf-idf and boost function. Using a test bed of 107,367 PubMed abstracts, we evaluated the first essential function: retrieving information. Cancer researchers provided 20 realistic queries, for which the top 15 abstracts were retrieved using a predicate-based (new) and keyword-based (baseline) approach. Each abstract was evaluated, double-blind, by cancer researchers on a 0-5 point scale to calculate precision (0 versus higher) and relevance (0-5 score). Precision was significantly higher (p<.001) for the predicate-based (80%) than for the keyword-based (71%) approach. Relevance was almost doubled with the predicate-based approach-2.1 versus 1.6 without rank order adjustment (p<.001) and 1.34 versus 0.98 with rank order adjustment (p<.001) for predicate--versus keyword-based approach respectively. Predicates can support more precise searching than keywords, laying the foundation for rich and sophisticated information search. PMID:23892296

  15. Construction of an annotated corpus to support biomedical information extraction

    PubMed Central

    Thompson, Paul; Iqbal, Syed A; McNaught, John; Ananiadou, Sophia

    2009-01-01

    Background Information Extraction (IE) is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources. Results We have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs. For each event instance, all participants (arguments) in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology. To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified. Using the scheme, we have created the Gene Regulation Event Corpus (GREC), consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists. A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%. Conclusion The GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions. As such, it is specifically designed to support bio-specific tool and resource development. It has already been used to acquire semantic frames for inclusion within the BioLexicon (a lexical, terminological resource to aid biomedical text mining). Initial experiments have also shown that the corpus may viably be used to train IE

  16. Information Diversity in Web Search

    ERIC Educational Resources Information Center

    Liu, Jiahui

    2009-01-01

    The web is a rich and diverse information source with incredible amounts of information about all kinds of subjects in various forms. This information source affords great opportunity to build systems that support users in their work and everyday lives. To help users explore information on the web, web search systems should find information that…

  17. University Students' Online Information Searching Strategies in Different Search Contexts

    ERIC Educational Resources Information Center

    Tsai, Meng-Jung; Liang, Jyh-Chong; Hou, Huei-Tse; Tsai, Chin-Chung

    2012-01-01

    This study investigates the role of search context played in university students' online information searching strategies. A total of 304 university students in Taiwan were surveyed with questionnaires in which two search contexts were defined as searching for learning, and searching for daily life information. Students' online search strategies…

  18. PaperChase: a user-friendly program for searching the biomedical literature.

    PubMed

    Lawson, R

    1990-06-01

    PaperChase is a computer program which provides an efficient interface to the National Library of Medicine's MEDLINE database of references to the biomedical literature. The database includes references (citations) and abstracts compiled from Index Medicus, the International Nursing Index and the Index to Dental Literature. PaperChase may be accessed using any computer terminal or personal computer with modem. No special knowledge of computers or biomedical terms is necessary. Simple menus enable the novice to search the biomedical literature without training. A command language speeds searching for the experienced user. PaperChase does not require the user to know the database's indexing terminology, called Medical Subject Headings. Everyday language may be used and PaperChase will translate, or "map", the user's search term into the required Medical Subject Heading. PaperChase monitors a search in progress and suggests additional Medical Subject Headings which can be used to broaden or narrow a search. The searcher can order a full-text photocopy of any reference found in PaperChase. Support documentation and a subscriber newsletter are provided at no charge. Trained search specialists are available to offer assistance and to answer questions. PMID:2192743

  19. A concept-based interactive biomedical image retrieval approach using visualness and spatial information

    NASA Astrophysics Data System (ADS)

    Rahman, Md M.; Antani, Sameer K.; Demner-Fushman, Dina; Thoma, George R.

    2015-03-01

    This paper presents a novel approach to biomedical image retrieval by mapping image regions to local concepts and represent images in a weighted entropy-based concept feature space. The term concept refers to perceptually distinguishable visual patches that are identified locally in image regions and can be mapped to a glossary of imaging terms. Further, the visual significance (e.g., visualness) of concepts is measured as Shannon entropy of pixel values in image patches and is used to refine the feature vector. Moreover, the system can assist user in interactively select a Region-Of-Interest (ROI) and search for similar image ROIs. Further, a spatial verification step is used as a post-processing step to improve retrieval results based on location information. The hypothesis that such approaches would improve biomedical image retrieval, is validated through experiments on a data set of 450 lung CT images extracted from journal articles from four different collections.

  20. Evaluation methods for retrieving information from interferograms of biomedical objects

    NASA Astrophysics Data System (ADS)

    Podbielska, Halina; Rottenkolber, Matthias

    1996-04-01

    Interferograms in the form of fringe patterns can be produced in two-beam interferometers, holographic or speckle interferometers, in setups realizing moire techniques or in deflectometers. Optical metrology based on the principle of interference can be applied as a testing tool in biomedical research. By analyzing of the fringe pattern images, information about the shape or mechanical behavior of the object under study can be retrieved. Here, some of the techniques for creating fringe pattern images were presented along with methods of analysis. Intensity based analysis as well as methods of phase measurements, are mentioned. Applications of inteferometric methods, especially in the field of experimental orthopedics, endoscopy and ophthalmology are pointed out.

  1. Information bottleneck based incremental fuzzy clustering for large biomedical data.

    PubMed

    Liu, Yongli; Wan, Xing

    2016-08-01

    Incremental fuzzy clustering combines advantages of fuzzy clustering and incremental clustering, and therefore is important in classifying large biomedical literature. Conventional algorithms, suffering from data sparsity and high-dimensionality, often fail to produce reasonable results and may even assign all the objects to a single cluster. In this paper, we propose two incremental algorithms based on information bottleneck, Single-Pass fuzzy c-means (spFCM-IB) and Online fuzzy c-means (oFCM-IB). These two algorithms modify conventional algorithms by considering different weights for each centroid and object and scoring mutual information loss to measure the distance between centroids and objects. spFCM-IB and oFCM-IB are used to group a collection of biomedical text abstracts from Medline database. Experimental results show that clustering performances of our approaches are better than such prominent counterparts as spFCM, spHFCM, oFCM and oHFCM, in terms of accuracy. PMID:27260783

  2. Information Search Services for Educators.

    ERIC Educational Resources Information Center

    Adams, Sharon; And Others

    Based on information provided primarily by two existing state-based information services, this handbook presents a clear, practical look at possible activities, procedures, and requirements of search services for educators. Descriptions of the two services that serve as models--Oklahoma's Sooner Exchange for Educational Knowledge (SEEK) and Texas'…

  3. Twitter K-H networks in action: Advancing biomedical literature for drug search.

    PubMed

    Hamed, Ahmed Abdeen; Wu, Xindong; Erickson, Robert; Fandy, Tamer

    2015-08-01

    The importance of searching biomedical literature for drug interaction and side-effects is apparent. Current digital libraries (e.g., PubMed) suffer infrequent tagging and metadata annotation updates. Such limitations cause absence of linking literature to new scientific evidence. This demonstrates a great deal of challenges that stand in the way of scientists when searching biomedical repositories. In this paper, we present a network mining approach that provides a bridge for linking and searching drug-related literature. Our contributions here are two fold: (1) an efficient algorithm called HashPairMiner to address the run-time complexity issues demonstrated in its predecessor algorithm: HashnetMiner, and (2) a database of discoveries hosted on the web to facilitate literature search using the results produced by HashPairMiner. Though the K-H network model and the HashPairMiner algorithm are fairly young, their outcome is evidence of the considerable promise they offer to the biomedical science community in general and the drug research community in particular. PMID:26065982

  4. [Information sheet and informed consent in biomedical research with samples].

    PubMed

    Gil Membrado, Cristina

    2012-01-01

    This paper examines from a practical perspective, the content of the information sheet to the participant in a clinical trial in which pharmacogenetic studies are conducted and/or pharmacogenomics, and scope of informed consent. The text is accompanied by a guide of questions to assess the fit of a participant information sheet on the regulation of clinical trials, biological samples and protection of personal data. PMID:23115824

  5. Semantic similarity measures in the biomedical domain by leveraging a web search engine.

    PubMed

    Hsieh, Sheau-Ling; Chang, Wen-Yung; Chen, Chi-Huang; Weng, Yung-Ching

    2013-07-01

    Various researches in web related semantic similarity measures have been deployed. However, measuring semantic similarity between two terms remains a challenging task. The traditional ontology-based methodologies have a limitation that both concepts must be resided in the same ontology tree(s). Unfortunately, in practice, the assumption is not always applicable. On the other hand, if the corpus is sufficiently adequate, the corpus-based methodologies can overcome the limitation. Now, the web is a continuous and enormous growth corpus. Therefore, a method of estimating semantic similarity is proposed via exploiting the page counts of two biomedical concepts returned by Google AJAX web search engine. The features are extracted as the co-occurrence patterns of two given terms P and Q, by querying P, Q, as well as P AND Q, and the web search hit counts of the defined lexico-syntactic patterns. These similarity scores of different patterns are evaluated, by adapting support vector machines for classification, to leverage the robustness of semantic similarity measures. Experimental results validating against two datasets: dataset 1 provided by A. Hliaoutakis; dataset 2 provided by T. Pedersen, are presented and discussed. In dataset 1, the proposed approach achieves the best correlation coefficient (0.802) under SNOMED-CT. In dataset 2, the proposed method obtains the best correlation coefficient (SNOMED-CT: 0.705; MeSH: 0.723) with physician scores comparing with measures of other methods. However, the correlation coefficients (SNOMED-CT: 0.496; MeSH: 0.539) with coder scores received opposite outcomes. In conclusion, the semantic similarity findings of the proposed method are close to those of physicians' ratings. Furthermore, the study provides a cornerstone investigation for extracting fully relevant information from digitizing, free-text medical records in the National Taiwan University Hospital database. PMID:25055314

  6. HubMed: a web-based biomedical literature search interface

    PubMed Central

    Eaton, Alfred D.

    2006-01-01

    HubMed is an alternative search interface to the PubMed database of biomedical literature, incorporating external web services and providing functions to improve the efficiency of literature search, browsing and retrieval. Users can create and visualize clusters of related articles, export citation data in multiple formats, receive daily updates of publications in their areas of interest, navigate links to full text and other related resources, retrieve data from formatted bibliography lists, navigate citation links and store annotated metadata for articles of interest. HubMed is freely available at . PMID:16845111

  7. Reinforcement Learning in Information Searching

    ERIC Educational Resources Information Center

    Cen, Yonghua; Gan, Liren; Bai, Chen

    2013-01-01

    Introduction: The study seeks to answer two questions: How do university students learn to use correct strategies to conduct scholarly information searches without instructions? and, What are the differences in learning mechanisms between users at different cognitive levels? Method: Two groups of users, thirteen first year undergraduate students…

  8. Informed consent among nursing students participating in biomedical research.

    PubMed

    Nambiar, Anupama; Christopher, D J; Mammen, Joy; David, Thambu; Kang, Gagandeep; David, Shirley

    2012-01-01

    For consent in biomedical research, it is essential that research participants understand the need for research, the study protocol, the risk and benefits of participation, the freedom to participate or decline and the right to leave the study at any time. A structured questionnaire was used to assess understanding and knowledge among nursing trainees participating in a cohort study investigating exposure and latent tuberculosis at a tertiary care hospital. Data were collected for 138 participants. While 97% were aware of their enrollment into a research protocol, only 78% could state that it was a study on tuberculosis. Approximately two-thirds were aware of plans for blood collection, but not all of them knew the timings or number of samples. The majority (59%) participants had consulted others before making the decision to participate, and only 73% felt that their participation was completely voluntary. Even among healthcare trainees, emphasis needs to be placed on testing both the knowledge and understanding of participants to ensure the principle and practice of truly informed consent. PMID:22864079

  9. MIMI: multimodality, multiresource, information integration environment for biomedical core facilities.

    PubMed

    Szymanski, Jacek; Wilson, David L; Zhang, Guo-Qiang

    2009-10-01

    The rapid expansion of biomedical research has brought substantial scientific and administrative data management challenges to modern core facilities. Scientifically, a core facility must be able to manage experimental workflow and the corresponding set of large and complex scientific data. It must also disseminate experimental data to relevant researchers in a secure and expedient manner that facilitates collaboration and provides support for data interpretation and analysis. Administratively, a core facility must be able to manage the scheduling of its equipment and to maintain a flexible and effective billing system to track material, resource, and personnel costs and charge for services to sustain its operation. It must also have the ability to regularly monitor the usage and performance of its equipment and to provide summary statistics on resources spent on different categories of research. To address these informatics challenges, we introduce a comprehensive system called MIMI (multimodality, multiresource, information integration environment) that integrates the administrative and scientific support of a core facility into a single web-based environment. We report the design, development, and deployment experience of a baseline MIMI system at an imaging core facility and discuss the general applicability of such a system in other types of core facilities. These initial results suggest that MIMI will be a unique, cost-effective approach to addressing the informatics infrastructure needs of core facilities and similar research laboratories. PMID:17999114

  10. Multitasking Information Seeking and Searching Processes.

    ERIC Educational Resources Information Center

    Spink, Amanda; Ozmutlu, H. Cenk; Ozmutlu, Seda

    2002-01-01

    Presents findings from four studies of the prevalence of multitasking information seeking and searching by Web (via the Excite search engine), information retrieval system (mediated online database searching), and academic library users. Highlights include human information coordinating behavior (HICB); and implications for models of information…

  11. Modeling and mining term association for improving biomedical information retrieval performance

    PubMed Central

    2012-01-01

    Background The growth of the biomedical information requires most information retrieval systems to provide short and specific answers in response to complex user queries. Semantic information in the form of free text that is structured in a way makes it straightforward for humans to read but more difficult for computers to interpret automatically and search efficiently. One of the reasons is that most traditional information retrieval models assume terms are conditionally independent given a document/passage. Therefore, we are motivated to consider term associations within different contexts to help the models understand semantic information and use it for improving biomedical information retrieval performance. Results We propose a term association approach to discover term associations among the keywords from a query. The experiments are conducted on the TREC 2004-2007 Genomics data sets and the TREC 2004 HARD data set. The proposed approach is promising and achieves superiority over the baselines and the GSP results. The parameter settings and different indices are investigated that the sentence-based index produces the best results in terms of the document-level, the word-based index for the best results in terms of the passage-level and the paragraph-based index for the best results in terms of the passage2-level. Furthermore, the best term association results always come from the best baseline. The tuning number k in the proposed recursive re-ranking algorithm is discussed and locally optimized to be 10. Conclusions First, modelling term association for improving biomedical information retrieval using factor analysis, is one of the major contributions in our work. Second, the experiments confirm that term association considering co-occurrence and dependency among the keywords can produce better results than the baselines treating the keywords independently. Third, the baselines are re-ranked according to the importance and reliance of latent factors behind

  12. How to Search, Write, Prepare and Publish the Scientific Papers in the Biomedical Journals

    PubMed Central

    Masic, Izet

    2011-01-01

    This article describes the methodology of preparation, writing and publishing scientific papers in biomedical journals. given is a concise overview of the concept and structure of the System of biomedical scientific and technical information and the way of biomedical literature retreival from worldwide biomedical databases. Described are the scientific and professional medical journals that are currently published in Bosnia and Herzegovina. Also, given is the comparative review on the number and structure of papers published in indexed journals in Bosnia and Herzegovina, which are listed in the Medline database. Analyzed are three B&H journals indexed in MEDLINE database: Medical Archives (Medicinski Arhiv), Bosnian Journal of Basic Medical Sciences and Medical Gazette (Medicinki Glasnik) in 2010. The largest number of original papers was published in the Medical Archives. There is a statistically significant difference in the number of papers published by local authors in relation to international journals in favor of the Medical Archives. True, the Journal Bosnian Journal of Basic Medical Sciences does not categorize the articles and we could not make comparisons. Journal Medical Archives and Bosnian Journal of Basic Medical Sciences by percentage published the largest number of articles by authors from Sarajevo and Tuzla, the two oldest and largest university medical centers in Bosnia and Herzegovina. The author believes that it is necessary to make qualitative changes in the reception and reviewing of papers for publication in biomedical journals published in Bosnia and Herzegovina which should be the responsibility of the separate scientific authority/ committee composed of experts in the field of medicine at the state level. PMID:23572850

  13. How to search, write, prepare and publish the scientific papers in the biomedical journals.

    PubMed

    Masic, Izet

    2011-06-01

    This article describes the methodology of preparation, writing and publishing scientific papers in biomedical journals. given is a concise overview of the concept and structure of the System of biomedical scientific and technical information and the way of biomedical literature retreival from worldwide biomedical databases. Described are the scientific and professional medical journals that are currently published in Bosnia and Herzegovina. Also, given is the comparative review on the number and structure of papers published in indexed journals in Bosnia and Herzegovina, which are listed in the Medline database. Analyzed are three B&H journals indexed in MEDLINE database: Medical Archives (Medicinski Arhiv), Bosnian Journal of Basic Medical Sciences and Medical Gazette (Medicinki Glasnik) in 2010. The largest number of original papers was published in the Medical Archives. There is a statistically significant difference in the number of papers published by local authors in relation to international journals in favor of the Medical Archives. True, the Journal Bosnian Journal of Basic Medical Sciences does not categorize the articles and we could not make comparisons. Journal Medical Archives and Bosnian Journal of Basic Medical Sciences by percentage published the largest number of articles by authors from Sarajevo and Tuzla, the two oldest and largest university medical centers in Bosnia and Herzegovina. The author believes that it is necessary to make qualitative changes in the reception and reviewing of papers for publication in biomedical journals published in Bosnia and Herzegovina which should be the responsibility of the separate scientific authority/ committee composed of experts in the field of medicine at the state level. PMID:23572850

  14. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

    PubMed

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

  15. Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation

    PubMed Central

    Huang, Chung-Chi; Lu, Zhiyong

    2016-01-01

    Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as ‘CHEMICAL-1 compared to CHEMICAL-2.’ With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical–disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked

  16. The "Conflicted Dying": The Active Search for Life Extension in Advanced Cancer Through Biomedical Treatment.

    PubMed

    Mohammed, Shan; Peter, Elizabeth; Gastaldo, Denise; Howell, Doris

    2016-03-01

    Using a poststructural perspective, we examine the subjectivities that are produced when advanced cancer patients seek life extension through biomedical treatments. Seven case studies were developed that included 20 interviews with patients, family, nurses, and physicians recruited from a tertiary hospital in Canada, 30 documents, and 5 hours of participant observation. We identify seven types of subjectivity: (a) the Desperate Subject, (b) the Cancer Expert Subject, (c) the Proactive Subject, (d) the Productive Subject, (e) the Mistrusting Subject, (f) the Model Patient Subject, and (g) the Suffering Subject. We characterize the "conflicted dying," a contemporary figure who holds multiple perspectives about seeking curative treatment despite the acknowledgment of death. Using active strategies to gain access to treatment, this figure resists traditional arrangements of power/knowledge established by health care providers. We suggest that the search for life extension is a process of shaping the self to fit certain aesthetical traits associated with surviving cancer. PMID:25711844

  17. Down syndrome screening information in midwifery practices in the Netherlands: Strategies to integrate biomedical information.

    PubMed

    Rosman, Sophia

    2016-03-01

    The aim of this qualitative study was to analyse counselling with regard to prenatal screening in midwifery consultations in the Netherlands where a national prenatal screening programme has only existed since 2007, after years of social and political debates. The methodology is based on in situ observations of 25 counselling consultations in four midwifery practices in two main cities in the Netherlands. The results of this study show that, since midwives are obliged to offer information on Down syndrome screening to all pregnant women (2007), they have to deal with the communication of medical screening information using biostatistical concepts to explain risks, calculations, probabilities and chromosomal anomalies. In order to avoid the risk of medicalization of their consultation, midwives develop strategies that allow them to integrate this new biomedical discourse while maintaining their low medicalized approach of midwife-led care. One of their main strategies is to switch from 'alarming' biomedical messages to 'reassuring words' in order to manage the anxiety induced by the information and to keep the control over their low medicalized consultation. They also tend to distance themselves from the obligation to talk about screening. The way midwives handle these counselling consultations allows them to respect their obligation to propose information, and to remain faithful to their struggle to protect the natural process of pregnancy as well as their professional autonomy. PMID:25504473

  18. A Computer Based Biomedical Information System. I. Logic Foundation and Techniques

    ERIC Educational Resources Information Center

    Syner, James C.

    A digital computer based biomedical information system was designed to service the needs of physicians engaged in patient care and clinical research, and scientists engaged in laboratory research. The system embraces all functions of information processing which include information collection, storage, retrieval, analyses and display. The…

  19. Application of an automated natural language processing (NLP) workflow to enable federated search of external biomedical content in drug discovery and development.

    PubMed

    McEntire, Robin; Szalkowski, Debbie; Butler, James; Kuo, Michelle S; Chang, Meiping; Chang, Man; Freeman, Darren; McQuay, Sarah; Patel, Jagruti; McGlashen, Michael; Cornell, Wendy D; Xu, Jinghai James

    2016-05-01

    External content sources such as MEDLINE(®), National Institutes of Health (NIH) grants and conference websites provide access to the latest breaking biomedical information, which can inform pharmaceutical and biotechnology company pipeline decisions. The value of the sites for industry, however, is limited by the use of the public internet, the limited synonyms, the rarity of batch searching capability and the disconnected nature of the sites. Fortunately, many sites now offer their content for download and we have developed an automated internal workflow that uses text mining and tailored ontologies for programmatic search and knowledge extraction. We believe such an efficient and secure approach provides a competitive advantage to companies needing access to the latest information for a range of use cases and complements manually curated commercial sources. PMID:26979546

  20. Managing biomedical image metadata for search and retrieval of similar images.

    PubMed

    Korenblum, Daniel; Rubin, Daniel; Napel, Sandy; Rodriguez, Cesar; Beaulieu, Chris

    2011-08-01

    Radiology images are generally disconnected from the metadata describing their contents, such as imaging observations ("semantic" metadata), which are usually described in text reports that are not directly linked to the images. We developed a system, the Biomedical Image Metadata Manager (BIMM) to (1) address the problem of managing biomedical image metadata and (2) facilitate the retrieval of similar images using semantic feature metadata. Our approach allows radiologists, researchers, and students to take advantage of the vast and growing repositories of medical image data by explicitly linking images to their associated metadata in a relational database that is globally accessible through a Web application. BIMM receives input in the form of standard-based metadata files using Web service and parses and stores the metadata in a relational database allowing efficient data query and maintenance capabilities. Upon querying BIMM for images, 2D regions of interest (ROIs) stored as metadata are automatically rendered onto preview images included in search results. The system's "match observations" function retrieves images with similar ROIs based on specific semantic features describing imaging observation characteristics (IOCs). We demonstrate that the system, using IOCs alone, can accurately retrieve images with diagnoses matching the query images, and we evaluate its performance on a set of annotated liver lesion images. BIMM has several potential applications, e.g., computer-aided detection and diagnosis, content-based image retrieval, automating medical analysis protocols, and gathering population statistics like disease prevalences. The system provides a framework for decision support systems, potentially improving their diagnostic accuracy and selection of appropriate therapies. PMID:20844917

  1. Strategies for Disseminating Information on Biomedical Research on Autism to Hispanic Parents

    ERIC Educational Resources Information Center

    Lajonchere, Clara M.; Wheeler, Barbara Y.; Valente, Thomas W.; Kreutzer, Cary; Munson, Aron; Narayanan, Shrikanth; Kazemzadeh, Abe; Cruz, Roxana; Martinez, Irene; Schrager, Sheree M.; Schweitzer, Lisa; Chklovski, Tara; Hwang, Darryl

    2016-01-01

    Low income Hispanic families experience multiple barriers to accessing evidence-based information on Autism Spectrum Disorders (ASD). This study utilized a mixed-strategy intervention to create access to information in published bio-medical research articles on ASD by distilling the content into parent-friendly English- and Spanish-language ASD…

  2. Sexual information seeking on web search engines.

    PubMed

    Spink, Amanda; Koricich, Andrew; Jansen, B J; Cole, Charles

    2004-02-01

    Sexual information seeking is an important element within human information behavior. Seeking sexually related information on the Internet takes many forms and channels, including chat rooms discussions, accessing Websites or searching Web search engines for sexual materials. The study of sexual Web queries provides insight into sexually-related information-seeking behavior, of value to Web users and providers alike. We qualitatively analyzed queries from logs of 1,025,910 Alta Vista and AlltheWeb.com Web user queries from 2001. We compared the differences in sexually-related Web searching between Alta Vista and AlltheWeb.com users. Differences were found in session duration, query outcomes, and search term choices. Implications of the findings for sexual information seeking are discussed. PMID:15006171

  3. Growth Dynamics of Information Search Services.

    ERIC Educational Resources Information Center

    Lindqvist, Mats

    Computer based information search services, ISS's, of the type that provide on-line literature searches are analyzed from a system's viewpoint using a continuous simulation model. The analysis shows that the observed growth and stagnation of a typical ISS can be explained as a natural consequence of market responses to the service together with a…

  4. The Dynamics of Information Search Services.

    ERIC Educational Resources Information Center

    Lindquist, Mats G.

    Computer-based information search services (ISSs) of the type that provide online literature searches are analyzed from a systems viewpoint using a continuous simulation model. The methodology applied is "system dynamics," and the system language is DYNAMO. The analysis reveals that the observed growth and stagnation of a typical ISS can be…

  5. Information Science; Search for Identity.

    ERIC Educational Resources Information Center

    Debons, Anthony, Ed.

    At the 1972 NATO Advanced Study Institute in Information Science the plenary sessions covered four main areas: the nature of information, information technology and its implications, the impact of information technology on social institutions, and professional issues. In addition, working groups were formed which addressed themselves to specific…

  6. Biomedical image representation approach using visualness and spatial information in a concept feature space for interactive region-of-interest-based retrieval.

    PubMed

    Rahman, Md Mahmudur; Antani, Sameer K; Demner-Fushman, Dina; Thoma, George R

    2015-10-01

    This article presents an approach to biomedical image retrieval by mapping image regions to local concepts where images are represented in a weighted entropy-based concept feature space. The term "concept" refers to perceptually distinguishable visual patches that are identified locally in image regions and can be mapped to a glossary of imaging terms. Further, the visual significance (e.g., visualness) of concepts is measured as the Shannon entropy of pixel values in image patches and is used to refine the feature vector. Moreover, the system can assist the user in interactively selecting a region-of-interest (ROI) and searching for similar image ROIs. Further, a spatial verification step is used as a postprocessing step to improve retrieval results based on location information. The hypothesis that such approaches would improve biomedical image retrieval is validated through experiments on two different data sets, which are collected from open access biomedical literature. PMID:26730398

  7. Access to Biomedical Information: The Unified Medical Language System.

    ERIC Educational Resources Information Center

    Squires, Steven J.

    1993-01-01

    Describes the development of a Unified Medical Language System (UMLS) by the National Library of Medicine that will retrieve and integrate information from a variety of information resources. Highlights include the metathesaurus; the UMLS semantic network; semantic locality; information sources map; evaluation of the metathesaurus; future…

  8. Information sources in biomedical science and medical journalism: methodological approaches and assessment.

    PubMed

    Miranda, Giovanna F; Vercellesi, Luisa; Bruno, Flavia

    2004-09-01

    Throughout the world the public is showing increasing interest in medical and scientific subjects and journalists largely spread this information, with an important impact on knowledge and health. Clearly, therefore, the relationship between the journalist and his sources is delicate: freedom and independence of information depend on the independence and truthfulness of the sources. The new "precision journalism" holds that scientific methods should be applied to journalism, so authoritative sources are a common need for journalists and scientists. We therefore compared the individual classifications and methods of assessing of sources in biomedical science and medical journalism to try to extrapolate scientific methods of evaluation to journalism. In journalism and science terms used to classify sources of information show some similarities, but their meanings are different. In science primary and secondary classes of information, for instance, refer to the levels of processing, but in journalism to the official nature of the source itself. Scientists and journalists must both always consult as many sources as possible and check their authoritativeness, reliability, completeness, up-to-dateness and balance. In journalism, however, there are some important differences and limits: too many sources can sometimes diminish the quality of the information. The sources serve a first filter between the event and the journalist, who is not providing the reader with the fact, but with its projection. Journalists have time constraints and lack the objective criteria for searching, the specific background knowledge, and the expertise to fully assess sources. To assist in understanding the wealth of sources of information in journalism, we have prepared a checklist of items and questions. There are at least four fundamental points that a good journalist, like any scientist, should know: how to find the latest information (the sources), how to assess it (the quality and

  9. An Improved Forensic Science Information Search.

    PubMed

    Teitelbaum, J

    2015-01-01

    Although thousands of search engines and databases are available online, finding answers to specific forensic science questions can be a challenge even to experienced Internet users. Because there is no central repository for forensic science information, and because of the sheer number of disciplines under the forensic science umbrella, forensic scientists are often unable to locate material that is relevant to their needs. The author contends that using six publicly accessible search engines and databases can produce high-quality search results. The six resources are Google, PubMed, Google Scholar, Google Books, WorldCat, and the National Criminal Justice Reference Service. Carefully selected keywords and keyword combinations, designating a keyword phrase so that the search engine will search on the phrase and not individual keywords, and prompting search engines to retrieve PDF files are among the techniques discussed. PMID:26227137

  10. Biomedical Computing Technology Information Center (BCTIC). Progress report, October 1, 1979-September 30, 1980

    SciTech Connect

    Gurney, Jane

    1980-07-30

    The operations and activities of the Biomedical Computing Technology Information Center (BCTIC) for the period 8 April 1980 to 30 July 1980 are summarized. These include mailing list update, software package preparation, software implementation, quality control of software, and Society of Nuclear Medicine support. (ACR)

  11. Recognizing names in biomedical texts using mutual information independence model and SVM plus sigmoid.

    PubMed

    Zhou, G D

    2006-06-01

    In this paper, we present a biomedical name recognition system, called PowerBioNE. In order to deal with the special phenomena in the biomedical domain, various evidential features are proposed and integrated through a mutual information independence model (MIIM). In addition, a support vector machine (SVM) plus sigmoid is proposed to resolve the data sparseness problem in the MIIM. In this way, the data sparseness problem in MIIM-based biomedical name recognition can be resolved effectively and a biomedical name recognition system with better performance and better portability can be achieved. Finally, we present two post-processing modules to deal with the nested entity name and abbreviation phenomena in the biomedical domain to further improve the performance. Evaluation shows that our system achieves F-measures of 69.1 and 71.2 on the 23 classes of GENIA V1.1 and V3.0, respectively. In particular, our system achieves an F-measure of 77.8 on the "protein" class of GENIA V3.0. It also shows that our system outperforms the best-reported system on GENIA V1.1 and V3.0. PMID:16112894

  12. In Search of Integrated Information

    ERIC Educational Resources Information Center

    Giannakopoulos, Georgios A.

    2008-01-01

    This article examines, from the viewpoint of archival science, the possibility of creating a common framework for information science in the academic and professional fields alike. Information management, both as an academic platform and as an occupation, makes it necessary for library studies and archival science to co-exist in the curricula of…

  13. Interaction in Information Searching and Retrieval.

    ERIC Educational Resources Information Center

    Beaulieu, Micheline

    2000-01-01

    Explores the concepts of interaction and interactivity presented in different theoretical models in the fields of human-computer interaction (HCI) and information-seeking/searching behavior, and relates these to information retrieval (IR) research. Suggests that interaction in HCI is primarily concerned with establishing a user/system dialogue at…

  14. Searching LOGIN, the Local Government Information Network.

    ERIC Educational Resources Information Center

    Jack, Robert F.

    1984-01-01

    Describes a computer-based information retrieval and electronic messaging system produced by Control Data Corporation now being used by government agencies and other organizations. Background of Local Government Information Network (LOGIN), database structure, types of LOGIN units, searching LOGIN (intersect, display, and list commands), and how…

  15. Strategies for Disseminating Information on Biomedical Research on Autism to Hispanic Parents.

    PubMed

    Lajonchere, Clara M; Wheeler, Barbara Y; Valente, Thomas W; Kreutzer, Cary; Munson, Aron; Narayanan, Shrikanth; Kazemzadeh, Abe; Cruz, Roxana; Martinez, Irene; Schrager, Sheree M; Schweitzer, Lisa; Chklovski, Tara; Hwang, Darryl

    2016-03-01

    Low income Hispanic families experience multiple barriers to accessing evidence-based information on Autism Spectrum Disorders (ASD). This study utilized a mixed-strategy intervention to create access to information in published bio-medical research articles on ASD by distilling the content into parent-friendly English- and Spanish-language ASD Science Briefs and presenting them to participants using two socially-oriented dissemination methods. There was a main effect for short-term knowledge gains associated with the Science Briefs but no effect for the dissemination method. After 5 months, participants reported utilizing the information learned and 90% wanted to read more Science Briefs. These preliminary findings highlight the potential benefits of distilling biomedical research articles on ASD into parent-friendly educational products for currently underserved Hispanic parents. PMID:26563948

  16. Cheap talk communication with dynamic information searching.

    PubMed

    Zhang, Yongjie; Liu, Yuechen; Feng, Xu

    2016-01-01

    We build an agent-based cheap talk communication model with dynamic information searching behavior. In this model, agent communicates with its neighbors freely to get true or false information. Moreover, the uninformed receivers has ability to break up one link of his neighbor who is considered as a dishonest sender and searches for a new neighbor in the market. We study the impacts of the accuracy of information, the number of neighbors and the percentage of relinking neighbors on the information identification of uninformed receivers. The results suggest that the effect of the accuracy of information and the number of neighbors on information identification is linear, but the effect of the percentage of relinking neighbors presents a first increasing and then decreasing trend. PMID:27375976

  17. Organization of Biomedical Data for Collaborative Scientific Research: A Research Information Management System

    PubMed Central

    Myneni, Sahiti; Patel, Vimla L.

    2010-01-01

    Biomedical researchers often work with massive, detailed and heterogeneous datasets. These datasets raise new challenges of information organization and management for scientific interpretation, as they demand much of the researchers’ time and attention. The current study investigated the nature of the problems that researchers face when dealing with such data. Four major problems identified with existing biomedical scientific information management methods were related to data organization, data sharing, collaboration, and publications. Therefore, there is a compelling need to develop an efficient and user-friendly information management system to handle the biomedical research data. This study evaluated the implementation of an information management system, which was introduced as part of the collaborative research to increase scientific productivity in a research laboratory. Laboratory members seemed to exhibit frustration during the implementation process. However, empirical findings revealed that they gained new knowledge and completed specified tasks while working together with the new system. Hence, researchers are urged to persist and persevere when dealing with any new technology, including an information management system in a research laboratory environment. PMID:20543892

  18. A System for Information Management in BioMedical Studies—SIMBioMS

    PubMed Central

    Krestyaninova, Maria; Zarins, Andris; Viksna, Juris; Kurbatova, Natalja; Rucevskis, Peteris; Neogi, Sudeshna Guha; Gostev, Mike; Perheentupa, Teemu; Knuuttila, Juha; Barrett, Amy; Lappalainen, Ilkka; Rung, Johan; Podnieks, Karlis; Sarkans, Ugis; McCarthy, Mark I; Brazma, Alvis

    2009-01-01

    Summary: SIMBioMS is a web-based open source software system for managing data and information in biomedical studies. It provides a solution for the collection, storage, management and retrieval of information about research subjects and biomedical samples, as well as experimental data obtained using a range of high-throughput technologies, including gene expression, genotyping, proteomics and metabonomics. The system can easily be customized and has proven to be successful in several large-scale multi-site collaborative projects. It is compatible with emerging functional genomics data standards and provides data import and export in accepted standard formats. Protocols for transferring data to durable archives at the European Bioinformatics Institute have been implemented. Availability: The source code, documentation and initialization scripts are available at http://simbioms.org. Contact: support@simbioms.org; mariak@ebi.ac.uk PMID:19633095

  19. Enabling clinicians, researchers, and educators to build custom web-based biomedical information systems.

    PubMed

    Jakobovits, R; Brinkley, J F; Rosse, C; Weinberger, E

    2001-01-01

    We describe an open-source toolkit that enables clinicians, researchers, and educators to build their own web-based biomedical information systems. The Web Interfacing Repository Manager (Wirm) is a high-level application server aimed at medical professionals, allowing them to create individually tailored systems for managing their multimedia data and knowledge. We provide an overview of the features of Wirm, explaining how they meet the requirements for supporting biomedical information management, and describe four applications that are currently being developed with Wirm: MyPACS, a teaching file authoring system for radiologists, Fathom, an experiment management system for natural language processing, the Digital Anatomist Repository, an image archiving tool for medical schools, and Ontolog, a browser for medical vocabularies. PMID:11825195

  20. Method for Detecting Core Malware Sites Related to Biomedical Information Systems

    PubMed Central

    Kim, Dohoon; Choi, Donghee; Jin, Jonghyun

    2015-01-01

    Most advanced persistent threat attacks target web users through malicious code within landing (exploit) or distribution sites. There is an urgent need to block the affected websites. Attacks on biomedical information systems are no exception to this issue. In this paper, we present a method for locating malicious websites that attempt to attack biomedical information systems. Our approach uses malicious code crawling to rearrange websites in the order of their risk index by analyzing the centrality between malware sites and proactively eliminates the root of these sites by finding the core-hub node, thereby reducing unnecessary security policies. In particular, we dynamically estimate the risk index of the affected websites by analyzing various centrality measures and converting them into a single quantified vector. On average, the proactive elimination of core malicious websites results in an average improvement in zero-day attack detection of more than 20%. PMID:25821511

  1. Method for detecting core malware sites related to biomedical information systems.

    PubMed

    Kim, Dohoon; Choi, Donghee; Jin, Jonghyun

    2015-01-01

    Most advanced persistent threat attacks target web users through malicious code within landing (exploit) or distribution sites. There is an urgent need to block the affected websites. Attacks on biomedical information systems are no exception to this issue. In this paper, we present a method for locating malicious websites that attempt to attack biomedical information systems. Our approach uses malicious code crawling to rearrange websites in the order of their risk index by analyzing the centrality between malware sites and proactively eliminates the root of these sites by finding the core-hub node, thereby reducing unnecessary security policies. In particular, we dynamically estimate the risk index of the affected websites by analyzing various centrality measures and converting them into a single quantified vector. On average, the proactive elimination of core malicious websites results in an average improvement in zero-day attack detection of more than 20%. PMID:25821511

  2. BioInfer: a corpus for information extraction in the biomedical domain

    PubMed Central

    Pyysalo, Sampo; Ginter, Filip; Heimonen, Juho; Björne, Jari; Boberg, Jorma; Järvinen, Jouni; Salakoski, Tapio

    2007-01-01

    Background Lately, there has been a great interest in the application of information extraction methods to the biomedical domain, in particular, to the extraction of relationships of genes, proteins, and RNA from scientific publications. The development and evaluation of such methods requires annotated domain corpora. Results We present BioInfer (Bio Information Extraction Resource), a new public resource providing an annotated corpus of biomedical English. We describe an annotation scheme capturing named entities and their relationships along with a dependency analysis of sentence syntax. We further present ontologies defining the types of entities and relationships annotated in the corpus. Currently, the corpus contains 1100 sentences from abstracts of biomedical research articles annotated for relationships, named entities, as well as syntactic dependencies. Supporting software is provided with the corpus. The corpus is unique in the domain in combining these annotation types for a single set of sentences, and in the level of detail of the relationship annotation. Conclusion We introduce a corpus targeted at protein, gene, and RNA relationships which serves as a resource for the development of information extraction systems and their components such as parsers and domain analyzers. The corpus will be maintained and further developed with a current version being available at . PMID:17291334

  3. Improving Validity of Informed Consent for Biomedical Research in Zambia Using a Laboratory Exposure Intervention

    PubMed Central

    Zulu, Joseph Mumba; Lisulo, Mpala Mwanza; Besa, Ellen; Kaonga, Patrick; Chisenga, Caroline C.; Chomba, Mumba; Simuyandi, Michelo; Banda, Rosemary; Kelly, Paul

    2014-01-01

    Background Complex biomedical research can lead to disquiet in communities with limited exposure to scientific discussions, leading to rumours or to high drop-out rates. We set out to test an intervention designed to address apprehensions commonly encountered in a community where literacy is uncommon, and where complex biomedical research has been conducted for over a decade. We aimed to determine if it could improve the validity of consent. Methods Data were collected using focus group discussions, key informant interviews and observations. We designed an intervention that exposed participants to a detailed demonstration of laboratory processes. Each group was interviewed twice in a day, before and after exposure to the intervention in order to assess changes in their views. Results Factors that motivated people to participate in invasive biomedical research included a desire to stay healthy because of the screening during the recruitment process, regular advice from doctors, free medical services, and trust in the researchers. Inhibiting factors were limited knowledge about samples taken from their bodies during endoscopic procedures, the impact of endoscopy on the function of internal organs, and concerns about the use of biomedical samples. The belief that blood can be used for Satanic practices also created insecurities about drawing of blood samples. Further inhibiting factors included a fear of being labelled as HIV positive if known to consult heath workers repeatedly, and gender inequality. Concerns about the use and storage of blood and tissue samples were overcome by a laboratory exposure intervention. Conclusion Selecting a group of members from target community and engaging them in a laboratory exposure intervention could be a useful tool for enhancing specific aspects of consent for biomedical research. Further work is needed to determine the extent to which improved understanding permeates beyond the immediate group participating in the intervention

  4. ReVeaLD: a user-driven domain-specific interactive search platform for biomedical research.

    PubMed

    Kamdar, Maulik R; Zeginis, Dimitris; Hasnain, Ali; Decker, Stefan; Deus, Helena F

    2014-02-01

    Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical datasets available through standardized interfaces, has created opportunities towards new methods in biomedical discovery. Despite the popularity of semantic web technologies in tackling the integrative bioinformatics challenge, there are many obstacles towards its usage by non-technical research audiences. In particular, the ability to fully exploit integrated information needs using improved interactive methods intuitive to the biomedical experts. In this report we present ReVeaLD (a Real-time Visual Explorer and Aggregator of Linked Data), a user-centered visual analytics platform devised to increase intuitive interaction with data from distributed sources. ReVeaLD facilitates query formulation using a domain-specific language (DSL) identified by biomedical experts and mapped to a self-updated catalogue of elements from external sources. ReVeaLD was implemented in a cancer research setting; queries included retrieving data from in silico experiments, protein modeling and gene expression. ReVeaLD was developed using Scalable Vector Graphics and JavaScript and a demo with explanatory video is available at http://www.srvgal78.deri.ie:8080/explorer. A set of user-defined graphic rules controls the display of information through media-rich user interfaces. Evaluation of ReVeaLD was carried out as a game: biomedical researchers were asked to assemble a set of 5 challenge questions and time and interactions with the platform were recorded. Preliminary results indicate that complex queries could be formulated under less than two minutes by unskilled researchers. The results also indicate that supporting the identification of the elements of a DSL significantly increased intuitiveness of the platform and usability of semantic web technologies by domain users

  5. Chasing information to search in random environments

    NASA Astrophysics Data System (ADS)

    Masson, J.-B.; Bailly Bechet, M.; Vergassola, M.

    2009-10-01

    We discuss search strategies for finding sources of particles transported in a random environment and detected by the searcher(s). The mixing of the particles in the environment is supposed to be strong, so that strategies based on concentration-gradient ascent are not viable. These dilute conditions are common in natural environments typical of searches performed by insects and birds. The sparseness of the detections constitutes the major stumbling block in developing efficient olfactory robots to detect mines, chemical leaks, etc. We first discuss a search strategy, 'infotaxis', recently introduced for the search of a single source by a single robot. Decisions are made by locally maximizing the rate of acquisition of information on the location of the source and they balance exploration and exploitation. We present numerical simulations demonstrating the efficiency of the method and, most importantly, its robustness to lack of detailed modeling of the transport of particles in the random environment. We then introduce a novel formulation of infotaxis for collective searches where a swarm of robots is available and must be coordinated. Gains in the search time are impressive and the method can be further generalized to deal with conflicts arising in the identification of multiple sources.

  6. Implementation and management of a biomedical observation dictionary in a large healthcare information system

    PubMed Central

    Vandenbussche, Pierre-Yves; Cormont, Sylvie; André, Christophe; Daniel, Christel; Delahousse, Jean; Charlet, Jean; Lepage, Eric

    2013-01-01

    Objective This study shows the evolution of a biomedical observation dictionary within the Assistance Publique Hôpitaux Paris (AP-HP), the largest European university hospital group. The different steps are detailed as follows: the dictionary creation, the mapping to logical observation identifier names and codes (LOINC), the integration into a multiterminological management platform and, finally, the implementation in the health information system. Methods AP-HP decided to create a biomedical observation dictionary named AnaBio, to map it to LOINC and to maintain the mapping. A management platform based on methods used for knowledge engineering has been put in place. It aims at integrating AnaBio within the health information system and improving both the quality and stability of the dictionary. Results This new management platform is now active in AP-HP. The AnaBio dictionary is shared by 120 laboratories and currently includes 50 000 codes. The mapping implementation to LOINC reaches 40% of the AnaBio entries and uses 26% of LOINC records. The results of our work validate the choice made to develop a local dictionary aligned with LOINC. Discussion and Conclusions This work constitutes a first step towards a wider use of the platform. The next step will support the entire biomedical production chain, from the clinician prescription, through laboratory tests tracking in the laboratory information system to the communication of results and the use for decision support and biomedical research. In addition, the increase in the mapping implementation to LOINC ensures the interoperability allowing communication with other international health institutions. PMID:23635601

  7. Battling the biomedical information explosion: a plan for implementing a quality filtered database.

    PubMed

    Moore, M

    1989-01-01

    In 1980 an article appeared in the Archives of Internal Medicine stating that two-thirds of the studies appearing in the best medical journals contain unwarranted conclusions. In order to deal with the ever increasing mass of biomedical information (termed a "journalistic blastoma" by one editor), IAIMS has extolled the use of quality filters, devices to sort through the literature and sift the good from the bad. The complexity of the task is staggering. Quality is obviously subjective, and its nature raises the question of whether our users can be taught the necessary skills to systematically evaluate the literature. This report is based on a research project that grew into an elective course for medical students at Texas Tech University School of Medicine on "Critical Appraisal of the Biomedical Literature." PMID:10303951

  8. Mediator infrastructure for information integration and semantic data integration environment for biomedical research.

    PubMed

    Grethe, Jeffrey S; Ross, Edward; Little, David; Sanders, Brian; Gupta, Amarnath; Astakhov, Vadim

    2009-01-01

    This paper presents current progress in the development of semantic data integration environment which is a part of the Biomedical Informatics Research Network (BIRN; http://www.nbirn.net) project. BIRN is sponsored by the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH). A goal is the development of a cyberinfrastructure for biomedical research that supports advance data acquisition, data storage, data management, data integration, data mining, data visualization, and other computing and information processing services over the Internet. Each participating institution maintains storage of their experimental or computationally derived data. Mediator-based data integration system performs semantic integration over the databases to enable researchers to perform analyses based on larger and broader datasets than would be available from any single institution's data. This paper describes recent revision of the system architecture, implementation, and capabilities of the semantically based data integration environment for BIRN. PMID:19623485

  9. Chemical Information in Scirus and BASE (Bielefeld Academic Search Engine)

    ERIC Educational Resources Information Center

    Bendig, Regina B.

    2009-01-01

    The author sought to determine to what extent the two search engines, Scirus and BASE (Bielefeld Academic Search Engines), would be useful to first-year university students as the first point of searching for chemical information. Five topics were searched and the first ten records of each search result were evaluated with regard to the type of…

  10. Children's Search Engines from an Information Search Process Perspective.

    ERIC Educational Resources Information Center

    Broch, Elana

    2000-01-01

    Describes cognitive and affective characteristics of children and teenagers that may affect their Web searching behavior. Reviews literature on children's searching in online public access catalogs (OPACs) and using digital libraries. Profiles two Web search engines. Discusses some of the difficulties children have searching the Web, in the…

  11. The Use of Web Search Engines in Information Science Research.

    ERIC Educational Resources Information Center

    Bar-Ilan, Judit

    2004-01-01

    Reviews the literature on the use of Web search engines in information science research, including: ways users interact with Web search engines; social aspects of searching; structure and dynamic nature of the Web; link analysis; other bibliometric applications; characterizing information on the Web; search engine evaluation and improvement; and…

  12. Informed consent document improvement does not increase patients' comprehension in biomedical research

    PubMed Central

    Paris, Adeline; Brandt, Christian; Cornu, Catherine; Maison, Patrick; Thalamas, Claire; Cracowski, Jean-Luc

    2010-01-01

    AIMS International guidelines on ethics in biomedical research require that the informed consent of all enrolled participants is obtained. A written document describing the research, the informed consent (IC) document, must be given to all participants by the investigator. Most IC documents are long, containing much information. The aim of the present study was to determine whether the modification of the IC document by a working group or systematic improvement in its lexicosyntactic readability can improve comprehension of the written information given to patients participating in biomedical research. METHODS One hundred and fifty-nine patients were randomized to read one of the three versions of the IC document: unchanged document, document modified using systematic improvement of lexicosyntactic readability and document modified by a working group. RESULTS Neither the improvement in the lexicosyntactic readability, nor the intervention of the working group significantly improved the score of objective comprehension for the subjects included in this study: it was 66.6 (95% confidence interval 64.0, 69.2) for the control group, 68.8 (66.2, 71.4) for the group with the document improved for lexicosyntactic readability and 69.2 (66.0, 72.4) for the group who read the document improved by the working group (P= 0.38). CONCLUSIONS We failed to show that improving IC document comprehension through a lexicosyntactic approach or by a working group leads to better comprehension. PMID:20233193

  13. Visualization of the Meridian System Based on Biomedical Information about Acupuncture Treatment

    PubMed Central

    Lee, In-Seon; Lee, Soon-Ho; Kim, Song-Yi; Lee, Hyejung; Park, Hi-Joon; Chae, Younbyoung

    2013-01-01

    The origin of the concept of the meridian system is closely connected with the treatment effects of acupuncture, and it serves as an empirical reference system in the clinical setting. Understanding the meridian channels would be a first step in enhancing the clinical efficacy of acupuncture treatment. To understand the relationship between the location of the disease and the sites of relevant acupoints, we investigated acupuncture treatment regimens for low-back pain in 37 clinical studies. We found that the most frequently used acupoints in the treatment of low-back pain were BL23 (51%), BL25 (43%), BL24 (32%), BL40 (32%), BL60 (32%), GB30 (32%), BL26 (28%), BL32 (28%), and GB34 (21%). For the example of low-back pain, we visualized the biomedical information (frequency rates) about acupuncture treatment on the meridians of a three-dimensional (3D) model of the human body. We found that both local and distal acupoints were used to treat low-back pain in clinical trials based on the meridian theory. We suggest a new model for the visualization of a data-driven 3D meridian system of biomedical information about the meridians and acupoints. These findings may be helpful in understanding the meridian system and revealing the effectiveness of acupuncture treatment. PMID:23781270

  14. BioTCM-SE: a semantic search engine for the information retrieval of modern biology and traditional Chinese medicine.

    PubMed

    Chen, Xi; Chen, Huajun; Bi, Xuan; Gu, Peiqin; Chen, Jiaoyan; Wu, Zhaohui

    2014-01-01

    Understanding the functional mechanisms of the complex biological system as a whole is drawing more and more attention in global health care management. Traditional Chinese Medicine (TCM), essentially different from Western Medicine (WM), is gaining increasing attention due to its emphasis on individual wellness and natural herbal medicine, which satisfies the goal of integrative medicine. However, with the explosive growth of biomedical data on the Web, biomedical researchers are now confronted with the problem of large-scale data analysis and data query. Besides that, biomedical data also has a wide coverage which usually comes from multiple heterogeneous data sources and has different taxonomies, making it hard to integrate and query the big biomedical data. Embedded with domain knowledge from different disciplines all regarding human biological systems, the heterogeneous data repositories are implicitly connected by human expert knowledge. Traditional search engines cannot provide accurate and comprehensive search results for the semantically associated knowledge since they only support keywords-based searches. In this paper, we present BioTCM-SE, a semantic search engine for the information retrieval of modern biology and TCM, which provides biologists with a comprehensive and accurate associated knowledge query platform to greatly facilitate the implicit knowledge discovery between WM and TCM. PMID:24772189

  15. Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.

    PubMed

    Groza, Tudor; Verspoor, Karin

    2015-01-01

    Concept recognition (CR) is a foundational task in the biomedical domain. It supports the important process of transforming unstructured resources into structured knowledge. To date, several CR approaches have been proposed, most of which focus on a particular set of biomedical ontologies. Their underlying mechanisms vary from shallow natural language processing and dictionary lookup to specialized machine learning modules. However, no prior approach considers the case sensitivity characteristics and the term distribution of the underlying ontology on the CR process. This article proposes a framework that models the CR process as an information retrieval task in which both case sensitivity and the information gain associated with tokens in lexical representations (e.g., term labels, synonyms) are central components of a strategy for generating term variants. The case sensitivity of a given ontology is assessed based on the distribution of so-called case sensitive tokens in its terms, while information gain is modelled using a combination of divergence from randomness and mutual information. An extensive evaluation has been carried out using the CRAFT corpus. Experimental results show that case sensitivity awareness leads to an increase of up to 0.07 F1 against a non-case sensitive baseline on the Protein Ontology and GO Cellular Component. Similarly, the use of information gain leads to an increase of up to 0.06 F1 against a standard baseline in the case of GO Biological Process and Molecular Function and GO Cellular Component. Overall, subject to the underlying token distribution, these methods lead to valid complementary strategies for augmenting term label sets to improve concept recognition. PMID:25790125

  16. Assessing the Impact of Case Sensitivity and Term Information Gain on Biomedical Concept Recognition

    PubMed Central

    Groza, Tudor; Verspoor, Karin

    2015-01-01

    Concept recognition (CR) is a foundational task in the biomedical domain. It supports the important process of transforming unstructured resources into structured knowledge. To date, several CR approaches have been proposed, most of which focus on a particular set of biomedical ontologies. Their underlying mechanisms vary from shallow natural language processing and dictionary lookup to specialized machine learning modules. However, no prior approach considers the case sensitivity characteristics and the term distribution of the underlying ontology on the CR process. This article proposes a framework that models the CR process as an information retrieval task in which both case sensitivity and the information gain associated with tokens in lexical representations (e.g., term labels, synonyms) are central components of a strategy for generating term variants. The case sensitivity of a given ontology is assessed based on the distribution of so-called case sensitive tokens in its terms, while information gain is modelled using a combination of divergence from randomness and mutual information. An extensive evaluation has been carried out using the CRAFT corpus. Experimental results show that case sensitivity awareness leads to an increase of up to 0.07 F1 against a non-case sensitive baseline on the Protein Ontology and GO Cellular Component. Similarly, the use of information gain leads to an increase of up to 0.06 F1 against a standard baseline in the case of GO Biological Process and Molecular Function and GO Cellular Component. Overall, subject to the underlying token distribution, these methods lead to valid complementary strategies for augmenting term label sets to improve concept recognition. PMID:25790125

  17. Knowledge-based Method for Determining the Meaning of Ambiguous Biomedical Terms Using Information Content Measures of Similarity

    PubMed Central

    McInnes, Bridget T.; Pedersen, Ted; Liu, Ying; Melton, Genevieve B.; Pakhomov, Serguei V.

    2011-01-01

    In this paper, we introduce a novel knowledge-based word sense disambiguation method that determines the sense of an ambiguous word in biomedical text using semantic similarity or relatedness measures. These measures quantify the degree of similarity between concepts in the Unified Medical Language System (UMLS). The objective of this work was to develop a method that can disambiguate terms in biomedical text by exploiting similarity information extracted from the UMLS and to evaluate the efficacy of information content-based semantic similarity measures, which augment path-based information with probabilities derived from biomedical corpora. We show that information content-based measures obtain a higher disambiguation accuracy than path-based measures because they weight the path based on where it exists in the taxonomy coupled with the probability of the concepts occurring in a corpus of text. PMID:22195148

  18. A service-oriented distributed semantic mediator: integrating multiscale biomedical information.

    PubMed

    Mora, Oscar; Engelbrecht, Gerhard; Bisbal, Jesus

    2012-11-01

    Biomedical research continuously generates large amounts of heterogeneous and multimodal data spread over multiple data sources. These data, if appropriately shared and exploited, could dramatically improve the research practice itself, and ultimately the quality of health care delivered. This paper presents DISMED (DIstributed Semantic MEDiator), an open source semantic mediator that provides a unified view of a federated environment of multiscale biomedical data sources. DISMED is a Web-based software application to query and retrieve information distributed over a set of registered data sources, using semantic technologies. It also offers a userfriendly interface specifically designed to simplify the usage of these technologies by non-expert users. Although the architecture of the software mediator is generic and domain independent, in the context of this paper, DISMED has been evaluated for managing biomedical environments and facilitating research with respect to the handling of scientific data distributed in multiple heterogeneous data sources. As part of this contribution, a quantitative evaluation framework has been developed. It consist of a benchmarking scenario and the definition of five realistic use-cases. This framework, created entirely with public datasets, has been used to compare the performance of DISMED against other available mediators. It is also available to the scientific community in order to evaluate progress in the domain of semantic mediation, in a systematic and comparable manner. The results show an average improvement in the execution time by DISMED of 55% compared to the second best alternative in four out of the five use-cases of the experimental evaluation. PMID:22929464

  19. Categorization of services for seeking information in biomedical literature: a typology for improvement of practice.

    PubMed

    Kim, Jung-Jae; Rebholz-Schuhmann, Dietrich

    2008-11-01

    Biomedical researchers have to efficiently explore the scientific literature, keeping the focus on their research. This goal can only be achieved if the available means for accessing the literature meet the researchers' retrieval needs and if they understand how the tools filter the perpetually increasing number of documents. We have examined existing web-based services for information retrieval in order to give users guidance to improve their everyday practice of literature analysis. We propose two dimensions along which the services may be categorized: categories of input and output formats; and categories of behavioural usage. The categorization would be helpful for biologists to understand the differences in the input and output formats and the tasks they fulfil in information-retrieval activities. Also, they may inspire future bioinformaticians to further innovative development in this field. PMID:18660511

  20. Evaluating Biomedical Enhancement Research: Assessing Risk & Benefit and Obtaining Informed Consent

    PubMed Central

    Mehlman, Maxwell J.; Berg, Jessica W.

    2013-01-01

    There are two primary human subject protections: assessing and comparing the risks and potential benefits of proposed research, and obtaining potential subjects’ informed consent. While there has been extensive discussion in the literature on these two aspects, no attention has been paid to whether the processes should be different when the objective of an experimental biomedical intervention is to improve individual performance or capacity (“enhancement research”) rather than to prevent, cure, or mitigate disease (“health-oriented research”). This essay examines how both assessment of risks and benefits, and obtaining informed consent in an enhancement experiment might differ from the approaches used in health-oriented investigations, and considers appropriate protections for subjects in enhancement research. PMID:18840248

  1. Architecture for biomedical multimedia information delivery on the World Wide Web

    NASA Astrophysics Data System (ADS)

    Long, L. Rodney; Goh, Gin-Hua; Neve, Leif; Thoma, George R.

    1997-10-01

    Research engineers at the National Library of Medicine are building a prototype system for the delivery of multimedia biomedical information on the World Wide Web. This paper discuses the architecture and design considerations for the system, which will be used initially to make images and text from the third National Health and Nutrition Examination Survey (NHANES) publicly available. We categorized our analysis as follows: (1) fundamental software tools: we analyzed trade-offs among use of conventional HTML/CGI, X Window Broadway, and Java; (2) image delivery: we examined the use of unconventional TCP transmission methods; (3) database manager and database design: we discuss the capabilities and planned use of the Informix object-relational database manager and the planned schema for the HNANES database; (4) storage requirements for our Sun server; (5) user interface considerations; (6) the compatibility of the system with other standard research and analysis tools; (7) image display: we discuss considerations for consistent image display for end users. Finally, we discuss the scalability of the system in terms of incorporating larger or more databases of similar data, and the extendibility of the system for supporting content-based retrieval of biomedical images. The system prototype is called the Web-based Medical Information Retrieval System. An early version was built as a Java applet and tested on Unix, PC, and Macintosh platforms. This prototype used the MiniSQL database manager to do text queries on a small database of records of participants in the second NHANES survey. The full records and associated x-ray images were retrievable and displayable on a standard Web browser. A second version has now been built, also a Java applet, using the MySQL database manager.

  2. Laser-assisted development of titanium alloys: the search for new biomedical materials

    NASA Astrophysics Data System (ADS)

    Almeida, Amelia; Gupta, Dheeraj; Vilar, Rui

    2011-02-01

    Ti-alloys used in prosthetic applications are mostly alloys initially developed for aeronautical applications, so their behavior was not optimized for medical use. A need remains to design new alloys for biomedical applications, where requirements such as biocompatibility, in-body durability, specific manufacturing ability, and cost effectiveness are considered. Materials for this application must present excellent biocompatibility, ductility, toughness and wear and corrosion resistance, a large laser processing window and low sensitivity to changes in the processing parameters. Laser deposition has been investigated in order to access its applicability to laser based manufactured implants. In this study, variable powder feed rate laser cladding has been used as a method for the combinatorial investigation of new alloy systems that offers a unique possibility for the rapid and exhaustive preparation of a whole range of alloys with compositions variable along a single clad track. This method was used as to produce composition gradient Ti-Mo alloys. Mo has been used since it is among the few elements biocompatible, non-toxic β-Ti phase stabilizers. Alloy tracks with compositions in the range 0-19 wt.%Mo were produced and characterized in detail as a function of composition using microscale testing procedures for screening of compositions with promising properties. Microstructural analysis showed that alloys with Mo content above 8% are fully formed of β phase grains. However, these β grains present a cellular substructure that is associated to a Ti and Mo segregation pattern that occurs during solidification. Ultramicroindentation tests carried out to evaluate the alloys' hardness and Young's modulus showed that Ti-13%Mo alloys presented the lowest hardness and Young's modulus (70 GPa) closer to that of bone than common Ti alloys, thus showing great potential for implant applications.

  3. Laser-assisted development of titanium alloys: the search for new biomedical materials

    NASA Astrophysics Data System (ADS)

    Almeida, Amelia; Gupta, Dheeraj; Vilar, Rui

    2010-09-01

    Ti-alloys used in prosthetic applications are mostly alloys initially developed for aeronautical applications, so their behavior was not optimized for medical use. A need remains to design new alloys for biomedical applications, where requirements such as biocompatibility, in-body durability, specific manufacturing ability, and cost effectiveness are considered. Materials for this application must present excellent biocompatibility, ductility, toughness and wear and corrosion resistance, a large laser processing window and low sensitivity to changes in the processing parameters. Laser deposition has been investigated in order to access its applicability to laser based manufactured implants. In this study, variable powder feed rate laser cladding has been used as a method for the combinatorial investigation of new alloy systems that offers a unique possibility for the rapid and exhaustive preparation of a whole range of alloys with compositions variable along a single clad track. This method was used as to produce composition gradient Ti-Mo alloys. Mo has been used since it is among the few elements biocompatible, non-toxic β-Ti phase stabilizers. Alloy tracks with compositions in the range 0-19 wt.%Mo were produced and characterized in detail as a function of composition using microscale testing procedures for screening of compositions with promising properties. Microstructural analysis showed that alloys with Mo content above 8% are fully formed of β phase grains. However, these β grains present a cellular substructure that is associated to a Ti and Mo segregation pattern that occurs during solidification. Ultramicroindentation tests carried out to evaluate the alloys' hardness and Young's modulus showed that Ti-13%Mo alloys presented the lowest hardness and Young's modulus (70 GPa) closer to that of bone than common Ti alloys, thus showing great potential for implant applications.

  4. Searching for information on the Internet using the UMLS and Medical World Search.

    PubMed Central

    Suarez, H. H.; Hao, X.; Chang, I. F.

    1997-01-01

    Medical World Search is a search engine for medical information on the Internet that distinguishes itself from other search engines by its built-in knowledge of medical terminology through its use of the National Library of Medicine's UMLS and its carefully selected but large database of medical sites. After discussing some of the previous uses of the UMLS for medical information retrieval, we describe the Medical World Search system. In October 1996, Medical World Search became operational on the World Wide Web at http:@www.mwsearch.poly.edu. It has been operating uninterrupted since then. We review our experiences with creating a search engine for medical information on the Internet and using the UMLS in this application. The UMLS has some clear advantages in this application. Some aspects of the UMLS also decrease its usefulness in information retrieval. Medical World Search's usage by medical information seekers is summarized. future directions for research are outlined. PMID:9357740

  5. Generic Information Can Retrieve Known Biological Associations: Implications for Biomedical Knowledge Discovery

    PubMed Central

    van Haagen, Herman H. H. B. M.; 't Hoen, Peter A. C.; Mons, Barend; Schultes, Erik A.

    2013-01-01

    Motivation Weighted semantic networks built from text-mined literature can be used to retrieve known protein-protein or gene-disease associations, and have been shown to anticipate associations years before they are explicitly stated in the literature. Our text-mining system recognizes over 640,000 biomedical concepts: some are specific (i.e., names of genes or proteins) others generic (e.g., ‘Homo sapiens’). Generic concepts may play important roles in automated information retrieval, extraction, and inference but may also result in concept overload and confound retrieval and reasoning with low-relevance or even spurious links. Here, we attempted to optimize the retrieval performance for protein-protein interactions (PPI) by filtering generic concepts (node filtering) or links to generic concepts (edge filtering) from a weighted semantic network. First, we defined metrics based on network properties that quantify the specificity of concepts. Then using these metrics, we systematically filtered generic information from the network while monitoring retrieval performance of known protein-protein interactions. We also systematically filtered specific information from the network (inverse filtering), and assessed the retrieval performance of networks composed of generic information alone. Results Filtering generic or specific information induced a two-phase response in retrieval performance: initially the effects of filtering were minimal but beyond a critical threshold network performance suddenly drops. Contrary to expectations, networks composed exclusively of generic information demonstrated retrieval performance comparable to unfiltered networks that also contain specific concepts. Furthermore, an analysis using individual generic concepts demonstrated that they can effectively support the retrieval of known protein-protein interactions. For instance the concept “binding” is indicative for PPI retrieval and the concept “mutation abnormality” is

  6. PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool

    PubMed Central

    Mandloi, Sapan; Chakrabarti, Saikat

    2015-01-01

    Manual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity (e.g., gene/protein, drug, disease, biological processes, cellular component, etc.) information from the extracted text and subsequently mines various databases to provide their comprehensive inter-relation (e.g., interaction, expression, etc.). PALM-IST constructs protein interaction network and pathway information data relevant to the text search using multiple data mining tools and assembles them to create a meta-interaction network. It also analyzes scientific collaboration by extraction and creation of “co-authorship network,” for a given search context. Hence, this useful combination of literature and data mining provided in PALM-IST can be used to extract novel protein-protein interaction (PPI), to generate meta-pathways and further to identify key crosstalk and bottleneck proteins. PALM-IST is available at www.hpppi.iicb.res.in/ctm. PMID:25989388

  7. PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool.

    PubMed

    Mandloi, Sapan; Chakrabarti, Saikat

    2015-01-01

    Manual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity (e.g., gene/protein, drug, disease, biological processes, cellular component, etc.) information from the extracted text and subsequently mines various databases to provide their comprehensive inter-relation (e.g., interaction, expression, etc.). PALM-IST constructs protein interaction network and pathway information data relevant to the text search using multiple data mining tools and assembles them to create a meta-interaction network. It also analyzes scientific collaboration by extraction and creation of "co-authorship network," for a given search context. Hence, this useful combination of literature and data mining provided in PALM-IST can be used to extract novel protein-protein interaction (PPI), to generate meta-pathways and further to identify key crosstalk and bottleneck proteins. PALM-IST is available at www.hpppi.iicb.res.in/ctm. PMID:25989388

  8. Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop.

    PubMed

    Kettner, Carsten; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Aerts, Jan; Binns, Nigel; Blake, Andrew; Britten, Cedrik M; de Marco, Ario; Fostel, Jennifer; Gaudet, Pascale; González-Beltrán, Alejandra; Hardy, Nigel; Hellemans, Jan; Hermjakob, Henning; Juty, Nick; Leebens-Mack, Jim; Maguire, Eamonn; Neumann, Steffen; Orchard, Sandra; Parkinson, Helen; Piel, William; Ranganathan, Shoba; Rocca-Serra, Philippe; Santarsiero, Annapaola; Shotton, David; Sterk, Peter; Untergasser, Andreas; Whetzel, Patricia L

    2010-01-01

    This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://mibbi.org/. PMID:21304730

  9. Integrating Semantic Information into Multiple Kernels for Protein-Protein Interaction Extraction from Biomedical Literatures

    PubMed Central

    Li, Lishuang; Zhang, Panpan; Zheng, Tianfu; Zhang, Hongying; Jiang, Zhenchao; Huang, Degen

    2014-01-01

    Protein-Protein Interaction (PPI) extraction is an important task in the biomedical information extraction. Presently, many machine learning methods for PPI extraction have achieved promising results. However, the performance is still not satisfactory. One reason is that the semantic resources were basically ignored. In this paper, we propose a multiple-kernel learning-based approach to extract PPIs, combining the feature-based kernel, tree kernel and semantic kernel. Particularly, we extend the shortest path-enclosed tree kernel (SPT) by a dynamic extended strategy to retrieve the richer syntactic information. Our semantic kernel calculates the protein-protein pair similarity and the context similarity based on two semantic resources: WordNet and Medical Subject Heading (MeSH). We evaluate our method with Support Vector Machine (SVM) and achieve an F-score of 69.40% and an AUC of 92.00%, which show that our method outperforms most of the state-of-the-art systems by integrating semantic information. PMID:24622773

  10. Integrating semantic information into multiple kernels for protein-protein interaction extraction from biomedical literatures.

    PubMed

    Li, Lishuang; Zhang, Panpan; Zheng, Tianfu; Zhang, Hongying; Jiang, Zhenchao; Huang, Degen

    2014-01-01

    Protein-Protein Interaction (PPI) extraction is an important task in the biomedical information extraction. Presently, many machine learning methods for PPI extraction have achieved promising results. However, the performance is still not satisfactory. One reason is that the semantic resources were basically ignored. In this paper, we propose a multiple-kernel learning-based approach to extract PPIs, combining the feature-based kernel, tree kernel and semantic kernel. Particularly, we extend the shortest path-enclosed tree kernel (SPT) by a dynamic extended strategy to retrieve the richer syntactic information. Our semantic kernel calculates the protein-protein pair similarity and the context similarity based on two semantic resources: WordNet and Medical Subject Heading (MeSH). We evaluate our method with Support Vector Machine (SVM) and achieve an F-score of 69.40% and an AUC of 92.00%, which show that our method outperforms most of the state-of-the-art systems by integrating semantic information. PMID:24622773

  11. Cluster-Based Query Expansion Using Language Modeling for Biomedical Literature Retrieval

    ERIC Educational Resources Information Center

    Xu, Xuheng

    2011-01-01

    The tremendously huge volume of biomedical literature, scientists' specific information needs, long terms of multiples words, and fundamental problems of synonym and polysemy have been challenging issues facing the biomedical information retrieval community researchers. Search engines have significantly improved the efficiency and effectiveness of…

  12. Information searching protocol: a smart protocol for specific content search over the Internet

    NASA Astrophysics Data System (ADS)

    Bhattarakosol, Pattarasinee; Preechaveerakul, Ladda

    2006-10-01

    Currently, information is very important to Internet users. Unfortunately, searching for specific information from the Internet is not easy as wishes. The existing search engine mechanisms cannot be performed using a pathname of URL as a search key. Therefore, users who have a partial pathname of URL cannot use their knowledge to narrow down the search results. Thus, users have to spend a long time searching for the required web site from the result list. This paper proposes a search protocol named Information Searching Protocol (ISP) that supports the multiple search contents for users who know a partial pathname of URL and keywords. Moreover, the architecture of the Global Search Engine System (GSES) that cooperates with the ISP and is responsible for the search mechanism is also proposed. The GSES consists of two separated parts: an Internet Search Protocol agent at the client site, and GSES components at the server site. These components allow users to perform the search using a pathname of URL composing with keywords. The functions of GSES components indicate that the ISP enhances the search mechanism. So, users receive more specific URL and can, shortly, get access to the required site.

  13. Information retrieval in digital libraries: bringing search to the net.

    PubMed

    Schatz, B R

    1997-01-17

    A digital library enables users to interact effectively with information distributed across a network. These network information systems support search and display of items from organized collections. In the historical evolution of digital libraries, the mechanisms for retrieval of scientific literature have been particularly important. Grand visions in 1960 led first to the development of text search, from bibliographic databases to full-text retrieval. Next, research prototypes catalyzed the rise of document search, from multimedia browsing across local-area networks to distributed search on the Internet. By 2010, the visions will be realized, with concept search enabling semantic retrieval across large collections. PMID:8994022

  14. The Search for New Information Processing technologies

    NASA Astrophysics Data System (ADS)

    Cavin, Ralph K.

    2005-03-01

    Our society has benefited from the ‘Golden Age of Electronics’ for the last half century. The ubiquitous transistor, in its many manifestations, has enabled an explosion of capabilities in information processing, communications, and sensing that has spurred exponential growth in performance-benefit ratios. Much of the credit for this progress is due to the continued scaling of the silicon integrated circuit (IC) components and to the associated efficient fabrication processes that have made the IC affordable. There is a growing realization, from simple physics arguments, that as minimum features sizes approach the ten nanometer regime, scaling will very likely slow and eventually end. This doesn’t mean that the MOSFET will disappear, but more likely that it will need to be supplemented by other device and interconnect technologies if the exponential gains are to continue. In this talk we discuss the basis for the projected limitation of scaling of charge-based devices for logic and memory devices. We argue that a fundamental consideration for all devices, including those based on charge, relates to the capacity to manage heat generated by circuit operation. Our preference is for devices that operate at room temperature since the energy costs for cooling the devices must also be charged against the overall system energy consumption. (Cooling costs increase as a power of the difference between the ambient and the target temperature.) Therefore we seek new state variables to serve as an alternative to electrical charge for future information processing technologies. These technologies must provide the potential for sustaining exponential performance-cost benefits with time. The search must not only focus on device structures but on the underlying materials and process technologies that enable these structures. Indeed, to obtain extremely scaled CMOS, new materials and processes must also be developed. In this talk, we survey some of the candidates for

  15. 'Meatball searching' - The adversarial approach to online information retrieval

    NASA Technical Reports Server (NTRS)

    Jack, R. F.

    1985-01-01

    It is proposed that the different styles of online searching can be described as either formal (highly precise) or informal with the needs of the client dictating which is most applicable at a particular moment. The background and personality of the searcher also come into play. Particular attention is focused on meatball searching which is a form of online searching characterized by deliberate vagueness. It requires generally comprehensive searches, often on unusual topics and with tight deadlines. It is most likely to occur in search centers serving many different disciplines and levels of client information sophistication. Various information needs are outlined as well as the laws of meatball searching and the adversarial approach. Traits and characteristics important to sucessful searching include: (1) concept analysis, (2) flexibility of thinking, (3) ability to think in synonyms and (4) anticipation of variant word forms and spellings.

  16. [Advanced online search techniques and dedicated search engines for physicians].

    PubMed

    Nahum, Yoav

    2008-02-01

    In recent years search engines have become an essential tool in the work of physicians. This article will review advanced search techniques from the world of information specialists, as well as some advanced search engine operators that may help physicians improve their online search capabilities, and maximize the yield of their searches. This article also reviews popular dedicated scientific and biomedical literature search engines. PMID:18357673

  17. Simple tricks for improving pattern-based information extraction from the biomedical literature

    PubMed Central

    2010-01-01

    Background Pattern-based approaches to relation extraction have shown very good results in many areas of biomedical text mining. However, defining the right set of patterns is difficult; approaches are either manual, incurring high cost, or automatic, often resulting in large sets of noisy patterns. Results We propose several techniques for filtering sets of automatically generated patterns and analyze their effectiveness for different extraction tasks, as defined in the recent BioNLP 2009 shared task. We focus on simple methods that only take into account the complexity of the pattern and the complexity of the texts the patterns are applied to. We show that our techniques, despite their simplicity, yield large improvements in all tasks we analyzed. For instance, they raise the F-score for the task of extraction gene expression events from 24.8% to 51.9%. Conclusions Already very simple filtering techniques may improve the F-score of an information extraction method based on automatically generated patterns significantly. Furthermore, the application of such methods yields a considerable speed-up, as fewer matches need to be analysed. Due to their simplicity, the proposed filtering techniques also should be applicable to other methods using linguistic patterns for information extraction. PMID:20868467

  18. Biomedical Applications of the Information-efficient Spectral Imaging Sensor (ISIS)

    SciTech Connect

    Gentry, S.M.; Levenson, R.

    1999-01-21

    The Information-efficient Spectral Imaging Sensor (ISIS) approach to spectral imaging seeks to bridge the gap between tuned multispectral and fixed hyperspectral imaging sensors. By allowing the definition of completely general spectral filter functions, truly optimal measurements can be made for a given task. These optimal measurements significantly improve signal-to-noise ratio (SNR) and speed, minimize data volume and data rate, while preserving classification accuracy. The following paper investigates the application of the ISIS sensing approach in two sample biomedical applications: prostate and colon cancer screening. It is shown that in these applications, two to three optimal measurements are sufficient to capture the majority of classification information for critical sample constituents. In the prostate cancer example, the optimal measurements allow 8% relative improvement in classification accuracy of critical cell constituents over a red, green, blue (RGB) sensor. In the colon cancer example, use of optimal measurements boost the classification accuracy of critical cell constituents by 28% relative to the RGB sensor. In both cases, optimal measurements match the performance achieved by the entire hyperspectral data set. The paper concludes that an ISIS style spectral imager can acquire these optimal spectral images directly, allowing improved classification accuracy over an RGB sensor. Compared to a hyperspectral sensor, the ISIS approach can achieve similar classification accuracy using a significantly lower number of spectral samples, thus minimizing overall sample classification time and cost.

  19. Comparing Web search engine performance in searching consumer health information: evaluation and recommendations.

    PubMed Central

    Wu, G; Li, J

    1999-01-01

    Identifying and accessing reliable, relevant consumer health information rapidly on the Internet may challenge the health sciences librarian and layperson alike. In this study, seven search engines are compared using representative consumer health topics for their content relevancy, system features, and attributes. The paper discusses evaluation criteria; systematically compares relevant results; analyzes performance in terms of the strengths and weaknesses of the search engines; and illustrates effective search engine selection, search formulation, and strategies. PMID:10550031

  20. System architecture and information model for integrated access to distributed biomedical information

    NASA Astrophysics Data System (ADS)

    Kim, Dongkyu; Alaoui, Adil; Levine, Betty; Leondaridis, Leonidas; Shields, Peter; Byers, Steve; Cleary, Kevin

    2009-02-01

    The current trend towards systems medicine will rely heavily on computational and bioinformatics capabilities to collect, integrate, and analyze massive amounts of data from disparate sources. The objective is to use this information to make medical decisions that improve patient care. At Georgetown University Medical Center, we are developing an informatics capability to integrate several research and clinical databases. Our long term goal is to provide researchers at Georgetown's Lombardi Comprehensive Cancer Center better access to aggregated molecular and clinical information facilitating the investigation of new hypotheses that impact patient care. We also recognize the need for data mining tools and intelligent agents to help researchers in these efforts. This paper describes our initial work to create a flexible platform for researchers and physicians that provides access to information sources including clinical records, medical images, genomic, epigenomic, proteomic and metabolomic data. This paper describes the data sources selected for this pilot project and possible approaches to integrating these databases. We present the different database integration models that we considered. We conclude by outlining the proposed Information Model for the project.

  1. Personal health records: retrieving contextual information with Google Custom Search.

    PubMed

    Ahsan, Mahmud; Seldon, H Lee; Sayeed, Shohel

    2012-01-01

    Ubiquitous personal health records, which can accompany a person everywhere, are a necessary requirement for ubiquitous healthcare. Contextual information related to health events is important for the diagnosis and treatment of disease and for the maintenance of good health, yet it is seldom recorded in a health record. We describe a dual cellphone-and-Web-based personal health record system which can include 'external' contextual information. Much contextual information is available on the Internet and we can use ontologies to help identify relevant sites and information. But a search engine is required to retrieve information from the Web and developing a customized search engine is beyond our scope, so we can use Google Custom Search API Web service to get contextual data. In this paper we describe a framework which combines a health-and-environment 'knowledge base' or ontology with the Google Custom Search API to retrieve relevant contextual information related to entries in a ubiquitous personal health record. PMID:23138074

  2. The World Wide Web: a review of an emerging internet-based technology for the distribution of biomedical information.

    PubMed Central

    Lowe, H J; Lomax, E C; Polonkey, S E

    1996-01-01

    The Internet is rapidly evolving from a resource used primarily by the research community to a true global information network offering a wide range of databases and services. This evolution presents many opportunities for improved access to biomedical information, but Internet-based resources have often been difficult for the non-expert to develop and use. The World Wide Web (WWW) supports an inexpensive, easy-to-use, cross-platform, graphic interface to the Internet that may radically alter the way we retrieve and disseminate medical data. This paper summarizes the Internet and hypertext origins of the WWW, reviews WWW-specific technologies, and describes current and future applications of this technology in medicine and medical informatics. The paper also includes an appendix of useful biomedical WWW servers. PMID:8750386

  3. Growth Dynamics of Information Search Services

    ERIC Educational Resources Information Center

    Lindquist, Mats G.

    1978-01-01

    An analysis of computer-based search services (ISSs) from a system's viewpoint, using a continuous simulation model to reveal growth and stagnation of a typical system is presented, as well as an analysis of decision making for an ISS. (Author/MBR)

  4. The Development of Information Search Expertise of Research Students

    ERIC Educational Resources Information Center

    Kai-Wah Chu, Samuel; Law, Nancy

    2008-01-01

    This study identifies the development of information search expertise of 12 beginning research students (six in education and six in engineering) who were provided with a set of systematic search training sessions over a period of one year. The study adopts a longitudinal approach in investigating whether there were different stages in the…

  5. Exposome informatics: considerations for the design of future biomedical research information systems

    PubMed Central

    Martin Sanchez, Fernando; Gray, Kathleen; Bellazzi, Riccardo; Lopez-Campos, Guillermo

    2014-01-01

    The environment's contribution to health has been conceptualized as the exposome. Biomedical research interest in environmental exposures as a determinant of physiopathological processes is rising as such data increasingly become available. The panoply of miniaturized sensing devices now accessible and affordable for individuals to use to monitor a widening range of parameters opens up a new world of research data. Biomedical informatics (BMI) must provide a coherent framework for dealing with multi-scale population data including the phenome, the genome, the exposome, and their interconnections. The combination of these more continuous, comprehensive, and personalized data sources requires new research and development approaches to data management, analysis, and visualization. This article analyzes the implications of a new paradigm for the discipline of BMI, one that recognizes genome, phenome, and exposome data and their intricate interactions as the basis for biomedical research now and for clinical care in the near future. PMID:24186958

  6. A theory of information with special application to search problems.

    PubMed

    Wilbur, W J; Neuwald, A F

    2000-01-01

    Classical information theory concerns itself with communication through a noisy channel and how much one can infer about the channel input from a knowledge of the channel output. Because the channel is noisy the input and output are only related statistically and the rate of information transmission is a statistical concept with little meaning for the individual symbol used in transmission. Here we develop a more intuitive notion of information that is concerned with asking the right questions--that is, with finding those questions whose answer conveys the most information. We call this confirmatory information. In the first part of the paper we develop the general theory, show how it relates to classical information theory, and how in the special case of search problems it allows us to quantify the efficacy of information transmission regarding individual events. That is, confirmatory information measures how well a search for items having certain observable properties retrieves items having some unobserved property of interest. Thus confirmatory information facilitates a useful analysis of search problems and contrasts with classical information theory, which quantifies the efficiency of information transmission but is indifferent to the nature of the particular information being transmitted. The last part of the paper presents several examples where confirmatory information is used to quantify protein structural properties in a search setting. PMID:10642878

  7. Academic Users' Information Searching on Research Topics: Characteristics of Research Tasks and Search Strategies

    ERIC Educational Resources Information Center

    Du, Jia Tina; Evans, Nina

    2011-01-01

    This project investigated how academic users search for information on their real-life research tasks. This article presents the findings of the first of two studies. The study data were collected in the Queensland University of Technology (QUT) in Brisbane, Australia. Eleven PhD students' searching behaviors on personal research topics were…

  8. Turning Informal Thesauri Into Formal Ontologies: A Feasibility Study on Biomedical Knowledge re-Use

    PubMed Central

    2003-01-01

    This paper reports a large-scale knowledge conversion and curation experiment. Biomedical domain knowledge from a semantically weak and shallow terminological resource, the UMLS, is transformed into a rigorous description logics format. This way, the broad coverage of the UMLS is combined with inference mechanisms for consistency and cycle checking. They are the key to proper cleansing of the knowledge directly imported from the UMLS, as well as subsequent updating, maintenance and refinement of large knowledge repositories. The emerging biomedical knowledge base currently comprises more than 240 000 conceptual entities and hence constitutes one of the largest formal knowledge repositories ever built. PMID:18629112

  9. Searching to Translate and Translating to Search: When Information Retrieval Meets Machine Translation

    ERIC Educational Resources Information Center

    Ture, Ferhan

    2013-01-01

    With the adoption of web services in daily life, people have access to tremendous amounts of information, beyond any human's reading and comprehension capabilities. As a result, search technologies have become a fundamental tool for accessing information. Furthermore, the web contains information in multiple languages, introducing another barrier…

  10. [Application of the life sciences platform based on oracle to biomedical informations].

    PubMed

    Zhao, Zhi-Yun; Li, Tai-Huan; Yang, Hong-Qiao

    2008-03-01

    The life sciences platform based on Oracle database technology is introduced in this paper. By providing a powerful data access, integrating a variety of data types, and managing vast quantities of data, the software presents a flexible, safe and scalable management platform for biomedical data processing. PMID:18581881

  11. Information Searching Behaviour of Young Slovenian Researchers

    ERIC Educational Resources Information Center

    Vilar, Polona; Zumer, Maja

    2011-01-01

    Purpose: The purpose of this paper is to present the findings of an empirical study of information behaviour of young Slovenian researchers. Design/methodology/approach: Built on some well-known models of scholarly information behaviour the study complements a previously conducted study of the same population, which focused on the aspects of user…

  12. ISART: A Generic Framework for Searching Books with Social Information.

    PubMed

    Yin, Xu-Cheng; Zhang, Bo-Wen; Cui, Xiao-Ping; Qu, Jiao; Geng, Bin; Zhou, Fang; Song, Li; Hao, Hong-Wei

    2016-01-01

    Effective book search has been discussed for decades and is still future-proof in areas as diverse as computer science, informatics, e-commerce and even culture and arts. A variety of social information contents (e.g, ratings, tags and reviews) emerge with the huge number of books on the Web, but how they are utilized for searching and finding books is seldom investigated. Here we develop an Integrated Search And Recommendation Technology (IsArt), which breaks new ground by providing a generic framework for searching books with rich social information. IsArt comprises a search engine to rank books with book contents and professional metadata, a Generalized Content-based Filtering model to thereafter rerank books with user-generated social contents, and a learning-to-rank technique to finally combine a wide range of diverse reranking results. Experiments show that this technology permits embedding social information to promote book search effectiveness, and IsArt, by making use of it, has the best performance on CLEF/INEX Social Book Search Evaluation datasets of all 4 years (from 2011 to 2014), compared with some other state-of-the-art methods. PMID:26863545

  13. ISART: A Generic Framework for Searching Books with Social Information

    PubMed Central

    Cui, Xiao-Ping; Qu, Jiao; Geng, Bin; Zhou, Fang; Song, Li; Hao, Hong-Wei

    2016-01-01

    Effective book search has been discussed for decades and is still future-proof in areas as diverse as computer science, informatics, e-commerce and even culture and arts. A variety of social information contents (e.g, ratings, tags and reviews) emerge with the huge number of books on the Web, but how they are utilized for searching and finding books is seldom investigated. Here we develop an Integrated Search And Recommendation Technology (IsArt), which breaks new ground by providing a generic framework for searching books with rich social information. IsArt comprises a search engine to rank books with book contents and professional metadata, a Generalized Content-based Filtering model to thereafter rerank books with user-generated social contents, and a learning-to-rank technique to finally combine a wide range of diverse reranking results. Experiments show that this technology permits embedding social information to promote book search effectiveness, and IsArt, by making use of it, has the best performance on CLEF/INEX Social Book Search Evaluation datasets of all 4 years (from 2011 to 2014), compared with some other state-of-the-art methods. PMID:26863545

  14. Person perception informs understanding of cognition during visual search.

    PubMed

    Brennan, Allison A; Watson, Marcus R; Kingstone, Alan; Enns, James T

    2011-08-01

    Does person perception--the impressions we form from watching others--hold clues to the mental states of people engaged in cognitive tasks? We investigated this with a two-phase method: In Phase 1, participants searched on a computer screen (Experiment 1) or in an office (Experiment 2); in Phase 2, other participants rated the searchers' video-recorded behavior. The results showed that blind raters are sensitive to individual differences in search proficiency and search strategy, as well as to environmental factors affecting search difficulty. Also, different behaviors were linked to search success in each setting: Eye movement frequency predicted successful search on a computer screen; head movement frequency predicted search success in an office. In both settings, an active search strategy and positive emotional expressions were linked to search success. These data indicate that person perception informs cognition beyond the scope of performance measures, offering the potential for new measurements of cognition that are both rich and unobtrusive. PMID:21626239

  15. A model of clinical query management that supports integration of biomedical information over the World Wide Web.

    PubMed Central

    Detmer, W. M.; Shortliffe, E. H.

    1995-01-01

    A model of clinical query management is described that supports the integration of various types of biomedical information and the delivery of that information through a common interface. The model extends the architecture of the World Wide Web to include a Common Gateway Interface (CGI) mediator, which takes in user queries, performs syntactic and semantic processing to transform the input to a canonical form, selects the appropriate information sources to answer the query, translates the canonical query statement into a query of each information resource, queries the chosen information sources in parallel, and controls the analysis and display of results. We describe WebMedline, a CGI mediator that implements portions of this model, and discuss the benefits and limitations of this approach. PMID:8563422

  16. A Guide to Searching ONTAP ABI/INFORM.

    ERIC Educational Resources Information Center

    Data Courier, Inc., Louisville, KY.

    This manual is designed to assist searchers in developing cost-effective techniques for searching ABI/INFORM, a database which provides worldwide coverage of management trends, tactics, and techniques, citing articles from more than 550 business and management journals in English and other languages. ONTAP ABI/INFORM, a subset of the database, is…

  17. An automated aerial-photographic information-search system

    NASA Astrophysics Data System (ADS)

    Zhuchenko, A. G.; Morozova, L. A.; Petrov, V. Ia.

    1980-08-01

    The paper describes an automated system for the extraction of geological information from aerial photographs; the system used is an information-search language of descriptor type, represented in the form of classifiers. A block diagram of the system is presented.

  18. Flexible patient information search and retrieval framework: pilot implementation

    NASA Astrophysics Data System (ADS)

    Erdal, Selnur; Catalyurek, Umit V.; Saltz, Joel; Kamal, Jyoti; Gurcan, Metin N.

    2007-03-01

    Medical centers collect and store significant amount of valuable data pertaining to patients' visit in the form of medical free-text. In addition, standardized diagnosis codes (International Classification of Diseases, Ninth Revision, Clinical Modification: ICD9-CM) related to those dictated reports are usually available. In this work, we have created a framework where image searches could be initiated through a combination of free-text reports as well as ICD9 codes. This framework enables more comprehensive search on existing large sets of patient data in a systematic way. The free text search is enriched by computer-aided inclusion of additional search terms enhanced by a thesaurus. This combination of enriched search allows users to access to a larger set of relevant results from a patient-centric PACS in a simpler way. Therefore, such framework is of particular use in tasks such as gathering images for desired patient populations, building disease models, and so on. As the motivating application of our framework, we implemented a search engine. This search engine processed two years of patient data from the OSU Medical Center's Information Warehouse and identified lung nodule location information using a combination of UMLS Meta-Thesaurus enhanced text report searches along with ICD9 code searches on patients that have been discharged. Five different queries with various ICD9 codes involving lung cancer were carried out on 172552 cases. Each search was completed under a minute on average per ICD9 code and the inclusion of UMLS thesaurus increased the number of relevant cases by 45% on average.

  19. Issues in collecting, processing and storing human tissues and associated information to support biomedical research

    PubMed Central

    Grizzle, William E.; Bell, Walter C.; Sexton, Katherine C.

    2012-01-01

    The availability of human tissues to support biomedical research is critical to advance translational research focused on identifying and characterizing approaches to individualized (personalized) medical care. Providing such tissues relies on three acceptable models – a tissue banking model, a prospective collection model and a combination of these two models. An unacceptable model is the “catch as catch can” model in which tissues are collected, processed and stored without goals or a plan or without standard operating procedures, i.e., portions of tissues are collected as available and processed and stored when time permits. In the tissue banking model, aliquots of tissues are collected according to SOPs. Usually specific sizes and types of tissues are collected and processed (e.g., 0.1 gm of breast cancer frozen in OCT). Using the banking model, tissues may be collected that may not be used and/or do not meet specific needs of investigators; however, at the time of an investigator request, tissues are readily available as is clinical information including clinical outcomes. In the model of prospective collection, tissues are collected based upon investigator requests including specific requirements of investigators. For example, the investigator may request that two 0.15 gm matching aliquots of breast cancer be minced while fresh, put in RPMI media with and without fetal calf serum, cooled to 4°C and shipped to the investigator on wet ice. Thus, the tissues collected prospectively meet investigator needs, all collected specimens are utilized and storage of specimens is minimized; however, investigators must wait until specimens are collected, and if needed, for clinical outcome. The operation of any tissue repository requires well trained and dedicated personnel. A quality assurance program is required which provides quality control information on the diagnosis of a specimen that is matched specifically to the specimen provided to an investigator instead

  20. Discovering biomedical relations utilizing the World-wide Web.

    PubMed

    Mukherjea, Sougata; Sahay, Saurav

    2006-01-01

    To crate a Semantic Web for Life Sciences discovering relations between biomedical entities is essential. Journals and conference proceedings represent the dominant mechanisms of reporting newly discovered biomedical interactions. The unstructured nature of such publications makes it difficult to utilize data mining or knowledge discovery techniques to automatically incorporate knowledge from these publications into the ontologies. On the other hand, since biomedical information is growing explosively, it is difficult to have human curators manually extract all the information from literature. In this paper we present techniques to automatically discover biomedical relations from the World-wide Web. For this purpose we retrieve relevant information from Web Search engines using various lexico-syntactic patterns as queries. Experiments are presented to show the usefulness of our techniques. PMID:17094237

  1. Mapping individual logical processes in information searching

    NASA Technical Reports Server (NTRS)

    Smetana, F. O.

    1974-01-01

    An interactive dialog with a computerized information collection was recorded and plotted in the form of a flow chart. The process permits one to identify the logical processes employed in considerable detail and is therefore suggested as a tool for measuring individual thought processes in a variety of situations. A sample of an actual test case is given.

  2. The National Institutes of Health's Biomedical Translational Research Information System (BTRIS): Design, Contents, Functionality and Experience to Date

    PubMed Central

    Cimino, James J.; Ayres, Elaine J.; Remennik, Lyubov; Rath, Sachi; Freedman, Robert; Beri, Andrea; Chen, Yang; Huser, Vojtech

    2013-01-01

    The US National Institutes of Health (NIH) has developed the Biomedical Translational Research Information System (BTRIS) to support researchers’ access to translational and clinical data. BTRIS includes a data repository, a set of programs for loading data from NIH electronic health records and research data management systems, an ontology for coding the disparate data with a single terminology, and a set of user interface tools that provide access to identified data from individual research studies and data across all studies from which individually identifiable data have been removed. This paper reports on unique design elements of the system, progress to date and user experience after five years of development and operation. PMID:24262893

  3. Changing the face of reference: adapting biomedical and health information services for the classroom, clinic, and beyond.

    PubMed

    Tennant, Michele R; Auten, Beth; Botero, Cecilia E; Butson, Linda C; Edwards, Mary E; Garcia-Milian, Rolando; Lyon, Jennifer A; Norton, Hannah F

    2012-01-01

    This article describes how the reference department at a large academic health sciences library evolved to address the clinical and research information needs of the parent organization without losing its close connections to the classroom and curriculum. Closing the reference desk, moving to on-call and house call models, designing positions such as clinical research librarian and basic biomedical sciences librarian, finding alternative funding to grow the department, providing technology and training to facilitate librarians' work, and developing programming for and taking advice from library clients facilitated efforts to create a relevant presence and solidify the library's place in the university community. PMID:22853302

  4. Human gene mutation database-a biomedical information and research resource.

    PubMed

    Krawczak, M; Ball, E V; Fenton, I; Stenson, P D; Abeysinghe, S; Thomas, N; Cooper, D N

    2000-01-01

    Although 20 years have elapsed since the first single basepair substitution underlying an inherited disease in humans was characterised at the DNA level, the initiative has only recently been taken to establish central database resources for pathological genetic variants. Disease-associated gene lesions are currently collected and publicised by the Human Gene Mutation Database (HGMD) in Cardiff, locus-specific mutation databases, and to some extent also by the Genome Database (GDB) and Online Mendelian Inheritance in Man (OMIM). To date, HGMD represents the only comprehensive and publicly available database of gene lesions underlying human inherited disease. By July 1999, HGMD contained over 18,000 different mutations from some 900 human genes, the majority being single basepair substitutions. In addition to its potential as an information resource for clinicians and genetic counsellors, HGMD has allowed molecular geneticists to address a variety of biological questions through meta-analysis of the collated data. HGMD also promises to assist research workers in optimising mutation search strategies for a given gene. A questionnaire sent out to, and answered by, the editors of 20 key journals revealed that human genetics journals are increasingly reluctant to publish mutation reports. Electronic data submission and publication facilities are therefore urgently required. The World Wide Web (WWW) provides an excellent medium within which to combine the centralised management of basic mutation data, including rigorous quality control, with the possibility of publishing additional mutation-related information. In response to these needs, HGMD has both instituted a collaboration with Springer-Verlag GmbH, Heidelberg, to potentiate free online submission and electronic publication of human gene mutation data and developed links with the curators of locus-specific mutation databases. PMID:10612821

  5. 75 FR 76982 - Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ... AGENCY Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches for... literature searches for IRIS assessments; request for information. SUMMARY: The U.S. Environmental Protection Agency (EPA) is announcing the availability of literature searches for four IRIS...

  6. SEACOIN – An Investigative Tool for Biomedical Informatics Researchers

    PubMed Central

    Lee, Eva K.; Lee, Hee-Rin; Quarshie, Alexander

    2011-01-01

    Peer-reviewed scientific literature is a prime source for accessing knowledge in the biomedical field. Its rapid growth and diverse domain coverage require systematic efforts in developing interactive tools for efficiently searching and summarizing current advances for acquiring knowledge and referencing, and for furthering scientific discovery. Although information retrieval systems exist, the conventional tools and systems remain difficult for biomedical investigators to use. There remain gaps even in the state-of-the-art systems as little attention has been devoted to understanding the needs of biomedical researchers. Our work attempts to bridge the gap between the needs of biomedical users and systems design efforts. We first study the needs of users and then design a simple visual analytic application tool, SEACOIN. A key motivation stems from biomedical researchers’ request for a “simple interface” that is suitable for novice users in information technology. The system minimizes information overload, and allows users to search easily even in time-constrained situations. Users can manipulate the depth of information according to the purpose of usage. SEACOIN enables interactive exploration and filtering of search results via “metamorphose topological visualization” and “tag cloud,” visualization tools that are commonly used in social network sites. We illustrate SEACOIN’s usage through applications on PubMed publications on heart disease, cancer, Alzheimer’s disease, diabetes, and asthma. PMID:22195132

  7. SEACOIN--an investigative tool for biomedical informatics researchers.

    PubMed

    Lee, Eva K; Lee, Hee-Rin; Quarshie, Alexander

    2011-01-01

    Peer-reviewed scientific literature is a prime source for accessing knowledge in the biomedical field. Its rapid growth and diverse domain coverage require systematic efforts in developing interactive tools for efficiently searching and summarizing current advances for acquiring knowledge and referencing, and for furthering scientific discovery. Although information retrieval systems exist, the conventional tools and systems remain difficult for biomedical investigators to use. There remain gaps even in the state-of-the-art systems as little attention has been devoted to understanding the needs of biomedical researchers. Our work attempts to bridge the gap between the needs of biomedical users and systems design efforts. We first study the needs of users and then design a simple visual analytic application tool, SEACOIN. A key motivation stems from biomedical researchers' request for a "simple interface" that is suitable for novice users in information technology. The system minimizes information overload, and allows users to search easily even in time-constrained situations. Users can manipulate the depth of information according to the purpose of usage. SEACOIN enables interactive exploration and filtering of search results via "metamorphose topological visualization" and "tag cloud," visualization tools that are commonly used in social network sites. We illustrate SEACOIN's usage through applications on PubMed publications on heart disease, cancer, Alzheimer's disease, diabetes, and asthma. PMID:22195132

  8. Next-Generation Search Engines for Information Retrieval

    SciTech Connect

    Devarakonda, Ranjeet; Hook, Leslie A; Palanisamy, Giri; Green, James M

    2011-01-01

    centralized index. The harvested files are indexed against SOLR search API consistently, so that it can render search capabilities such as simple, fielded, spatial and temporal searches across a span of projects ranging from land, atmosphere, and ocean ecology. Mercury also provides data sharing capabilities using Open Archive Initiatives Protocol for Metadata Handling (OAI-PMH). In this paper we will discuss about the best practices for archiving data and metadata, new searching techniques, efficient ways of data retrieval and information display.

  9. Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information

    PubMed Central

    Fiszman, Marcelo; Hurdle, John F; Rindflesch, Thomas C

    2010-01-01

    Objective: This paper examines the development and evaluation of an automatic summarization system in the domain of molecular genetics. The system is a potential component of an advanced biomedical information management application called Semantic MEDLINE and could assist librarians in developing secondary databases of genetic information extracted from the primary literature. Methods: An existing summarization system was modified for identifying biomedical text relevant to the genetic etiology of disease. The summarization system was evaluated on the task of identifying data describing genes associated with bladder cancer in MEDLINE citations. A gold standard was produced using records from Genetics Home Reference and Online Mendelian Inheritance in Man. Genes in text found by the system were compared to the gold standard. Recall, precision, and F-measure were calculated. Results: The system achieved recall of 46%, and precision of 88% (F-measure = 0.61) by taking Gene References into Function (GeneRIFs) into account. Conclusion: The new summarization schema for genetic etiology has potential as a component in Semantic MEDLINE to support the work of data curators. PMID:20936065

  10. Biomedical information from a national collection of spine x-rays: film to content-based retrieval

    NASA Astrophysics Data System (ADS)

    Long, L. Rodney; Antani, Sameer; Lee, Dah-Jye; Krainak, Daniel M.; Thoma, George R.

    2003-05-01

    We summarize research and development for the extraction and distribution of biomedical information from a collection of 17,000 spine x-ray images collected by the second National Health and Nutrition Examination Survey (NHANES II). We present a history of the technical milestones of this work, including the data collection as film, digitization, quality control, archiving technology, database organization, medical expert content evaluation, and Web data distribution. We conclude by presenting our current work in content-based image retrieval (CBIR) to exploit the information content of these images directly by using image processing. We provide an overview and current research results from this CBIR work, which includes: extensive segmentation research, focusing on Active Shape Modeling and Active Contour methods; alternative techniques for shape representation, including invariant moments, simple polygon approximation, and Fourier descriptors; neural network classification of shapes into biomedical categories, such as "anterior osteophytes present/not present" and the implementation of a prototype CBIR system for the vertebrae that supports hybrid text/image queries using MATLAB and the MySQL relational database system.

  11. Neutrino Redshifts -- A Search for Information.

    NASA Astrophysics Data System (ADS)

    Gallo, Charles

    2005-04-01

    Neutrinos will undergo Redshifts due to Doppler and/or Space Expansion effects similar to Electromagnetic Radiation (Photons). However, in some situations (ex., Quasars, etc), Photon Redshifts may be due to cumulative energy-loss mechanisms with the intervening medium. In this situation, the corresponding Neutrino Redshifts will be much smaller since the interaction cross-section for neutrino-medium interactions will be much smaller than any photon-medium cross-section. Thus, observation and comparison of photon redshifts vs corresponding neutrinos redshifts will be very informative. If the photon and neutrino redshifts are similar, then a Doppler and/or Space Expansion interpretation is justified. If the neutrino redshift is much smaller than any corresponding photon redshift, then an interpretation via a cumulative energy-loss mechanism is justified. This is a very definitive experimental test of redshift interpretations. The latest neutrino data will be examined, particularly relevant to quasars and supernova. Reference: ``Redshifts of Cosmological Neutrinos as Definitive Experimental Test of Doppler versus Non-Doppler Redshifts'' by C. F. Gallo in IEEE Trans. Plasma Science, vol. 31, No. 6, pgs. 1230-1231, Dec. 2003.

  12. Information Commitments: Evaluative Standards and Information Searching Strategies in Web-Based Learning Environments

    ERIC Educational Resources Information Center

    Wu, Ying-Tien; Tsai, Chin-Chung

    2005-01-01

    "Information commitments" include both a set of evaluative standards that Web users utilize to assess the accuracy and usefulness of information in Web-based learning environments (implicit component), and the information searching strategies that Web users use on the Internet (explicit component). An "Information Commitment Survey" (ICS),…

  13. An Information Search Model of Evaluative Concerns in Intergroup Interaction

    ERIC Educational Resources Information Center

    Vorauer, Jacquie D.

    2006-01-01

    In an information search model, evaluative concerns during intergroup interaction are conceptualized as a joint function of uncertainty regarding and importance attached to out-group members' views of oneself. High uncertainty generally fosters evaluative concerns during intergroup exchanges. Importance depends on whether out-group members'…

  14. Subject Searching of the New York Times Information Bank

    ERIC Educational Resources Information Center

    Dolan, Donna R.

    1978-01-01

    The problems most frequently encountered in subject searching of the NY Times Information Bank are currency, multiconcept terms, generic descriptors, and verbosity. Vocabulary modifications are proposed and suggestions offered to help searchers overcome these problems and reduce their online connect time. These suggestions decreased the New York…

  15. Learning with New Technologies: Help Seeking and Information Searching Revisited

    ERIC Educational Resources Information Center

    Puustinen, Minna; Rouet, Jean-Francois

    2009-01-01

    Education researchers have amply documented the beneficial effects of help seeking on learning and understanding. Requesting help from teachers (or other human sources) when faced with a difficult task is now considered a self-regulated learning strategy. In a related domain, information search refers to learner-initiated efforts to obtain further…

  16. Searching the Visual Arts: An Analysis of Online Information Access.

    ERIC Educational Resources Information Center

    Brady, Darlene; Serban, William

    1981-01-01

    A search for stained glass bibliographic information using DIALINDEX identified 57 DIALOG files from a variety of subject categories and 646 citations as relevant. Files include applied science, biological sciences, chemistry, engineering, environment/pollution, people, business research, and public affairs. Eleven figures illustrate the search…

  17. Information Resource Selection of Undergraduate Students in Academic Search Tasks

    ERIC Educational Resources Information Center

    Lee, Jee Yeon; Paik, Woojin; Joo, Soohyung

    2012-01-01

    Introduction: This study aims to investigate the selection of information sources and to identify factors associated with the resource selection of undergraduate students for academic search tasks. Also, user perceptions of some factors, such as credibility, usefulness, accessibility and familiarity, were examined to classify resources by their…

  18. Finding Business Information on the "Invisible Web": Search Utilities vs. Conventional Search Engines.

    ERIC Educational Resources Information Center

    Darrah, Brenda

    Researchers for small businesses, which may have no access to expensive databases or market research reports, must often rely on information found on the Internet, which can be difficult to find. Although current conventional Internet search engines are now able to index over on billion documents, there are many more documents existing in…

  19. Quantifying spectral changes experienced by plasmonic nanoparticles in a cellular environment to inform biomedical nanoparticle design

    PubMed Central

    2014-01-01

    Metal nanoparticles (NPs) scatter and absorb light in precise, designable ways, making them agile candidates for a variety of biomedical applications. When NPs are introduced to a physiological environment and interact with cells, their physicochemical properties can change as proteins adsorb on their surface and they agglomerate within intracellular endosomal vesicles. Since the plasmonic properties of metal NPs are dependent on their geometry and local environment, these physicochemical changes may alter the NPs' plasmonic properties, on which applications such as plasmonic photothermal therapy and photonic gene circuits are based. Here we systematically study and quantify how metal NPs' optical spectra change upon introduction to a cellular environment in which NPs agglomerate within endosomal vesicles. Using darkfield hyperspectral imaging, we measure changes in the peak wavelength, broadening, and distribution of 100-nm spherical gold NPs' optical spectra following introduction to human breast adenocarcinoma Sk-Br-3 cells as a function of NP exposure dose and time. On a cellular level, spectra shift up to 78.6 ± 23.5 nm after 24 h of NP exposure. Importantly, spectra broaden with time, achieving a spectral width of 105.9 ± 11.7 nm at 95% of the spectrum's maximum intensity after 24 h. On an individual intracellular NP cluster (NPC) level, spectra also show significant shifting, broadening, and heterogeneity after 24 h. Cellular transmission electron microscopy (TEM) and electromagnetic simulations of NPCs support the trends in spectral changes we measured. These quantitative data can help guide the design of metal NPs introduced to cellular environments in plasmonic NP-mediated biomedical technologies. PMID:25258596

  20. Analysis of Online Information Searching for Cardiovascular Diseases on a Consumer Health Information Portal

    PubMed Central

    Jadhav, Ashutosh; Sheth, Amit; Pathak, Jyotishman

    2014-01-01

    Since the early 2000’s, Internet usage for health information searching has increased significantly. Studying search queries can help us to understand users “information need” and how do they formulate search queries (“expression of information need”). Although cardiovascular diseases (CVD) affect a large percentage of the population, few studies have investigated how and what users search for CVD. We address this knowledge gap in the community by analyzing a large corpus of 10 million CVD related search queries from MayoClinic.com. Using UMLS MetaMap and UMLS semantic types/concepts, we developed a rule-based approach to categorize the queries into 14 health categories. We analyzed structural properties, types (keyword-based/Wh-questions/Yes-No questions) and linguistic structure of the queries. Our results show that the most searched health categories are ‘Diseases/Conditions’, ‘Vital-Sings’, ‘Symptoms’ and ‘Living-with’. CVD queries are longer and are predominantly keyword-based. This study extends our knowledge about online health information searching and provides useful insights for Web search engines and health websites. PMID:25954380

  1. Analysis of online information searching for cardiovascular diseases on a consumer health information portal.

    PubMed

    Jadhav, Ashutosh; Sheth, Amit; Pathak, Jyotishman

    2014-01-01

    Since the early 2000's, Internet usage for health information searching has increased significantly. Studying search queries can help us to understand users "information need" and how do they formulate search queries ("expression of information need"). Although cardiovascular diseases (CVD) affect a large percentage of the population, few studies have investigated how and what users search for CVD. We address this knowledge gap in the community by analyzing a large corpus of 10 million CVD related search queries from MayoClinic.com. Using UMLS MetaMap and UMLS semantic types/concepts, we developed a rule-based approach to categorize the queries into 14 health categories. We analyzed structural properties, types (keyword-based/Wh-questions/Yes-No questions) and linguistic structure of the queries. Our results show that the most searched health categories are 'Diseases/Conditions', 'Vital-Sings', 'Symptoms' and 'Living-with'. CVD queries are longer and are predominantly keyword-based. This study extends our knowledge about online health information searching and provides useful insights for Web search engines and health websites. PMID:25954380

  2. Drug Information to Biomedical Informatics: A Three-Tier Approach to Building a University System for the Twenty-First Century.

    ERIC Educational Resources Information Center

    Ferrill, Mary J.; Norton, Linda L.

    1997-01-01

    Describes a University of the Pacific (California) biomedical informatics center that promotes student use of informatics for doctoral courses, facilitates course-related hands-on information seeking, encourages graduate and faculty use of information technology, and is self-supporting. Discusses organization, benefits, and problems encountered,…

  3. Test OSIRIS (On Line Search Information Retrieval Information Storage).

    ERIC Educational Resources Information Center

    Showalther, A. Kenneth

    The OSIRIS system is a prototype information retrieval system having the following components: an automated microfiche file having a capacity of 5000 punch card sized microfiche with a remote control 21 inch TV console for retrieving, magnifying (0-250X), and displaying any of the images on the microfiche; and a remote computer terminal for the…

  4. Selective Dissemination of Biomedical Information: A Series of Studies and a Model System

    ERIC Educational Resources Information Center

    Swanson, Don R.

    1974-01-01

    Describes a hypothetical model dissemination system in three stages: 1) multiple source subject search to find a field's most useful journals; 2) scanning these journals for each recipient; 3) use of citation and bibliographic coupling techniques to improve stage 2. (Author/LS)

  5. Understanding Search Failures in Consumer Health Information Systems

    PubMed Central

    McCray, Alexa T.; Tse, Tony

    2003-01-01

    We examined queries that led to search failures on two National Library of Medicine Web-based consumer health sites, ClincialTrials.gov and MEDLINEplus. The purpose of the study was to analyze and categorize queries resulting that led to no results with the ultimate goal of developing interventions to assist users in recovering from those failures. We first analyzed over 2,700 queries, iteratively developing a coding scheme. We subsequently applied the codes to an additional set of 2,000 queries. We found that most of the queries were in scope, relevant to the system being searched, and did not exhibit so-called consumer language. As the final step, we developed a taxonomy based on whether the search failures were due primarily to content issues, to problems in query formulation, or to limitations of the search system. The results reported here have informed the further development of our own systems, and they may be helpful to others as they seek to improve consumer access to health information. PMID:14728209

  6. Towards Evidence-based Precision Medicine: Extracting Population Information from Biomedical Text using Binary Classifiers and Syntactic Patterns

    PubMed Central

    Raja, Kalpana; Dasot, Naman; Goyal, Pawan; Jonnalagadda, Siddhartha R

    2016-01-01

    Precision Medicine is an emerging approach for prevention and treatment of disease that considers individual variability in genes, environment, and lifestyle for each person. The dissemination of individualized evidence by automatically identifying population information in literature is a key for evidence-based precision medicine at the point-of-care. We propose a hybrid approach using natural language processing techniques to automatically extract the population information from biomedical literature. Our approach first implements a binary classifier to classify sentences with or without population information. A rule-based system based on syntactic-tree regular expressions is then applied to sentences containing population information to extract the population named entities. The proposed two-stage approach achieved an F-score of 0.81 using a MaxEnt classifier and the rule- based system, and an F-score of 0.87 using a Nai've-Bayes classifier and the rule-based system, and performed relatively well compared to many existing systems. The system and evaluation dataset is being released as open source. PMID:27570671

  7. Towards Evidence-based Precision Medicine: Extracting Population Information from Biomedical Text using Binary Classifiers and Syntactic Patterns.

    PubMed

    Raja, Kalpana; Dasot, Naman; Goyal, Pawan; Jonnalagadda, Siddhartha R

    2016-01-01

    Precision Medicine is an emerging approach for prevention and treatment of disease that considers individual variability in genes, environment, and lifestyle for each person. The dissemination of individualized evidence by automatically identifying population information in literature is a key for evidence-based precision medicine at the point-of-care. We propose a hybrid approach using natural language processing techniques to automatically extract the population information from biomedical literature. Our approach first implements a binary classifier to classify sentences with or without population information. A rule-based system based on syntactic-tree regular expressions is then applied to sentences containing population information to extract the population named entities. The proposed two-stage approach achieved an F-score of 0.81 using a MaxEnt classifier and the rule- based system, and an F-score of 0.87 using a Nai've-Bayes classifier and the rule-based system, and performed relatively well compared to many existing systems. The system and evaluation dataset is being released as open source. PMID:27570671

  8. EIIS: An Educational Information Intelligent Search Engine Supported by Semantic Services

    ERIC Educational Resources Information Center

    Huang, Chang-Qin; Duan, Ru-Lin; Tang, Yong; Zhu, Zhi-Ting; Yan, Yong-Jian; Guo, Yu-Qing

    2011-01-01

    The semantic web brings a new opportunity for efficient information organization and search. To meet the special requirements of the educational field, this paper proposes an intelligent search engine enabled by educational semantic support service, where three kinds of searches are integrated into Educational Information Intelligent Search (EIIS)…

  9. From Shakespeare to Star Trek and beyond: a Medline search for literary and other allusions in biomedical titles

    PubMed Central

    Goodman, Neville W

    2005-01-01

    Objectives To document biomedical paper titles containing literary and other allusions. Design Retrospective survey. Setting Medline (1951 to mid-2005) through Dialog Datastar. Main outcome measure Allusions to Shakespeare, Hans Christian Andersen, proverbs, the Bible, Lewis Carroll, and movie titles, corrected and scaled for five year periods 1950-4 to 2000-4. Results More than 1400 Shakespearean allusions exist, a third of them to “What's in a name” and another third to Hamlet—mostly to “To be or not to be.” The trend of increasing use of allusive titles, identified from Shakespeare and Andersen, is paralleled by allusions to Carroll and proverbs; the trend of biblical allusions is also upward but is more erratic. Trends for newer allusions are also upwards, including the previously surveyed “paradigm shift.” Allusive titles are likely to be to editorial or comment rather than to original research. Conclusions The similar trends are presumably a mark of a particular learnt author behaviour. Newer allusions may be becoming more popular than older ones. Allusive titles can be unhelpful to reviewers and researchers, and many are now clichés. Whether they attract readers or citations is unknown, but better ways of gaining attention exist. PMID:16373745

  10. Approaching the Affective Factors of Information Seeking: The Viewpoint of the Information Search Process Model

    ERIC Educational Resources Information Center

    Savolainen, Reijo

    2015-01-01

    Introduction: The article contributes to the conceptual studies of affective factors in information seeking by examining Kuhlthau's information search process model. Method: This random-digit dial telephone survey of 253 people (75% female) living in a rural, medically under-serviced area of Ontario, Canada, follows-up a previous interview study…

  11. Information Spread of Emergency Events: Path Searching on Social Networks

    PubMed Central

    Hu, Hongzhi; Wu, Tunan

    2014-01-01

    Emergency has attracted global attentions of government and the public, and it will easily trigger a series of serious social problems if it is not supervised effectively in the dissemination process. In the Internet world, people communicate with each other and form various virtual communities based on social networks, which lead to a complex and fast information spread pattern of emergency events. This paper collects Internet data based on data acquisition and topic detection technology, analyzes the process of information spread on social networks, describes the diffusions and impacts of that information from the perspective of random graph, and finally seeks the key paths through an improved IBF algorithm. Application cases have shown that this algorithm can search the shortest spread paths efficiently, which may help us to guide and control the information dissemination of emergency events on early warning. PMID:24600323

  12. An Effective Approach to Biomedical Information Extraction with Limited Training Data

    ERIC Educational Resources Information Center

    Jonnalagadda, Siddhartha

    2011-01-01

    In the current millennium, extensive use of computers and the internet caused an exponential increase in information. Few research areas are as important as information extraction, which primarily involves extracting concepts and the relations between them from free text. Limitations in the size of training data, lack of lexicons and lack of…

  13. Extracting meaningful information from video sequences for intelligent searches.

    SciTech Connect

    Muguira, Maritza Rosa; Russ, Trina Denise

    2005-02-01

    Video and image data are knowledge-rich sources of information, but their utility for current and future systems is limited without autonomous methods for understanding and characterizing their content. Semantic-based video understanding may benefit systems dedicated to the detection of insiders, alarm patterns, unauthorized activities in material monitoring applications, etc. A direct benefit of this technology is not only intelligent alarm analysis, but the ability to browse and perform query-based searches for useful and interesting information after video data has been acquired and stored. These searches can provide a tremendous benefit for use in intelligence agency, government, military, and DOE site investigations. This report provides an initial investigation into the algorithms and methods needed to characterize and understand video content. Such algorithms include background modeling, detecting dynamic image regions, grouping dynamic pixels into coherent objects, and robust tracking strategies. With solid approaches for addressing these problems, analysis can be performed seeking to recognize distinctive objects and their motions leading to semantic-based video searches.

  14. Searching for Cancer Information on the Internet: Analyzing Natural Language Search Queries

    PubMed Central

    Theofanos, Mary Frances

    2003-01-01

    Background Searching for health information is one of the most-common tasks performed by Internet users. Many users begin searching on popular search engines rather than on prominent health information sites. We know that many visitors to our (National Cancer Institute) Web site, cancer.gov, arrive via links in search engine result. Objective To learn more about the specific needs of our general-public users, we wanted to understand what lay users really wanted to know about cancer, how they phrased their questions, and how much detail they used. Methods The National Cancer Institute partnered with AskJeeves, Inc to develop a methodology to capture, sample, and analyze 3 months of cancer-related queries on the Ask.com Web site, a prominent United States consumer search engine, which receives over 35 million queries per week. Using a benchmark set of 500 terms and word roots supplied by the National Cancer Institute, AskJeeves identified a test sample of cancer queries for 1 week in August 2001. From these 500 terms only 37 appeared ≥ 5 times/day over the trial test week in 17208 queries. Using these 37 terms, 204165 instances of cancer queries were found in the Ask.com query logs for the actual test period of June-August 2001. Of these, 7500 individual user questions were randomly selected for detailed analysis and assigned to appropriate categories. The exact language of sample queries is presented. Results Considering multiples of the same questions, the sample of 7500 individual user queries represented 76077 queries (37% of the total 3-month pool). Overall 78.37% of sampled Cancer queries asked about 14 specific cancer types. Within each cancer type, queries were sorted into appropriate subcategories including at least the following: General Information, Symptoms, Diagnosis and Testing, Treatment, Statistics, Definition, and Cause/Risk/Link. The most-common specific cancer types mentioned in queries were Digestive/Gastrointestinal/Bowel (15.0%), Breast (11

  15. Excerpta Medica Automated Storage and Retrieval Program of Biomedical Information. Excerpta Mark I System.

    ERIC Educational Resources Information Center

    Excerpta Medica Foundation, Amsterdam (Netherlands).

    This is a report of the international operations of the Excerpta Medica Foundation whose aim is to further the progress of medical knowledge by making information available to the medical and related professions on all significant basic research and clinical findings reported in any language, anywhere in the world. To accomplish this task,…

  16. The University of Washington Health Sciences Library BioCommons: an evolving Northwest biomedical research information support infrastructure

    PubMed Central

    Minie, Mark; Bowers, Stuart; Tarczy-Hornoch, Peter; Roberts, Edward; James, Rose A.; Rambo, Neil; Fuller, Sherrilynne

    2006-01-01

    Setting: The University of Washington Health Sciences Libraries and Information Center BioCommons serves the bioinformatics needs of researchers at the university and in the vibrant for-profit and not-for-profit biomedical research sector in the Washington area and region. Program Components: The BioCommons comprises services addressing internal University of Washington, not-for-profit, for-profit, and regional and global clientele. The BioCommons is maintained and administered by the BioResearcher Liaison Team. The BioCommons architecture provides a highly flexible structure for adapting to rapidly changing resources and needs. Evaluation Mechanisms: BioCommons uses Web-based pre- and post-course evaluations and periodic user surveys to assess service effectiveness. Recent surveys indicate substantial usage of BioCommons services and a high level of effectiveness and user satisfaction. Next Steps/Future Directions: BioCommons is developing novel collaborative Web resources to distribute bioinformatics tools and is experimenting with Web-based competency training in bioinformation resource use. PMID:16888667

  17. Information content and analysis methods for Multi-Modal High-Throughput Biomedical Data

    PubMed Central

    Ray, Bisakha; Henaff, Mikael; Ma, Sisi; Efstathiadis, Efstratios; Peskin, Eric R.; Picone, Marco; Poli, Tito; Aliferis, Constantin F.; Statnikov, Alexander

    2014-01-01

    The spectrum of modern molecular high-throughput assaying includes diverse technologies such as microarray gene expression, miRNA expression, proteomics, DNA methylation, among many others. Now that these technologies have matured and become increasingly accessible, the next frontier is to collect “multi-modal” data for the same set of subjects and conduct integrative, multi-level analyses. While multi-modal data does contain distinct biological information that can be useful for answering complex biology questions, its value for predicting clinical phenotypes and contributions of each type of input remain unknown. We obtained 47 datasets/predictive tasks that in total span over 9 data modalities and executed analytic experiments for predicting various clinical phenotypes and outcomes. First, we analyzed each modality separately using uni-modal approaches based on several state-of-the-art supervised classification and feature selection methods. Then, we applied integrative multi-modal classification techniques. We have found that gene expression is the most predictively informative modality. Other modalities such as protein expression, miRNA expression, and DNA methylation also provide highly predictive results, which are often statistically comparable but not superior to gene expression data. Integrative multi-modal analyses generally do not increase predictive signal compared to gene expression data. PMID:24651673

  18. Information content and analysis methods for Multi-Modal High-Throughput Biomedical Data

    NASA Astrophysics Data System (ADS)

    Ray, Bisakha; Henaff, Mikael; Ma, Sisi; Efstathiadis, Efstratios; Peskin, Eric R.; Picone, Marco; Poli, Tito; Aliferis, Constantin F.; Statnikov, Alexander

    2014-03-01

    The spectrum of modern molecular high-throughput assaying includes diverse technologies such as microarray gene expression, miRNA expression, proteomics, DNA methylation, among many others. Now that these technologies have matured and become increasingly accessible, the next frontier is to collect ``multi-modal'' data for the same set of subjects and conduct integrative, multi-level analyses. While multi-modal data does contain distinct biological information that can be useful for answering complex biology questions, its value for predicting clinical phenotypes and contributions of each type of input remain unknown. We obtained 47 datasets/predictive tasks that in total span over 9 data modalities and executed analytic experiments for predicting various clinical phenotypes and outcomes. First, we analyzed each modality separately using uni-modal approaches based on several state-of-the-art supervised classification and feature selection methods. Then, we applied integrative multi-modal classification techniques. We have found that gene expression is the most predictively informative modality. Other modalities such as protein expression, miRNA expression, and DNA methylation also provide highly predictive results, which are often statistically comparable but not superior to gene expression data. Integrative multi-modal analyses generally do not increase predictive signal compared to gene expression data.

  19. Sports Information Online: Searching the SPORT Database and Tips for Finding Sports Medicine Information Online.

    ERIC Educational Resources Information Center

    Janke, Richard V.; And Others

    1988-01-01

    The first article describes SPORT, a database providing international coverage of athletics and physical education, and compares it to other online services in terms of coverage, thesauri, possible search strategies, and actual usage. The second article reviews available online information on sports medicine. (CLB)

  20. What is biomedical informatics?

    PubMed Central

    Bernstam, Elmer V.; Smith, Jack W.; Johnson, Todd R.

    2009-01-01

    Biomedical informatics lacks a clear and theoretically grounded definition. Many proposed definitions focus on data, information, and knowledge, but do not provide an adequate definition of these terms. Leveraging insights from the philosophy of information, we define informatics as the science of information, where information is data plus meaning. Biomedical informatics is the science of information as applied to or studied in the context of biomedicine. Defining the object of study of informatics as data plus meaning clearly distinguishes the field from related fields, such as computer science, statistics and biomedicine, which have different objects of study. The emphasis on data plus meaning also suggests that biomedical informatics problems tend to be difficult when they deal with concepts that are hard to capture using formal, computational definitions. In other words, problems where meaning must be considered are more difficult than problems where manipulating data without regard for meaning is sufficient. Furthermore, the definition implies that informatics research, teaching, and service should focus on biomedical information as data plus meaning rather than only computer applications in biomedicine. PMID:19683067

  1. 78 FR 13624 - Proposed Information Collection; Comment Request; Age Search Service

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-28

    .... Census Bureau Proposed Information Collection; Comment Request; Age Search Service AGENCY: U.S. Census... . SUPPLEMENTARY INFORMATION I. Abstract Age Search is a service provided by the U.S. Census Bureau for persons who... provide evidence of family relationship for rights of inheritance. The Age Search forms are used by...

  2. 75 FR 67705 - Office of Postsecondary Education; Overview Information; Talent Search (TS) Program; Notice...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-03

    ... Office of Postsecondary Education; Overview Information; Talent Search (TS) Program; Notice Inviting... services to students enrolled in schools that are not currently being served by a Talent Search project... information on the implementation of their Talent Search projects and their participants'...

  3. 77 FR 41784 - Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-16

    ... AGENCY Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches for... literature search for benzo(a)pyrene; request for information. SUMMARY: The U.S. Environmental Protection Agency (EPA) is announcing the availability of a literature search for benzo(a)pyrene (CASRN 50-...

  4. 75 FR 25239 - Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-07

    ... AGENCY Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches for... of literature searches for IRIS assessments; request for information. SUMMARY: The U.S. Environmental Protection Agency (EPA) is announcing the availability of literature searches for four IRIS assessments...

  5. A Biomedical Information System for Retrieval and Manipulation of NHANES Data

    PubMed Central

    Mukherjee, Sukrit; Martins, David; Norris, Keith C.; Jenders, Robert A.

    2016-01-01

    The retrieval and manipulation of data from large public databases like the U.S. National Health and Nutrition Examination Survey (NHANES) may require sophisticated statistical software and significant expertise that may be unavailable in the university setting. In response, we have developed the Data Retrieval And Manipulation System (DReAMS), an automated information system to handle all processes of data extraction and cleaning and then joining different subsets to produce analysis-ready output. The system is a browser-based data warehouse application in which the input data from flat files or operational systems are aggregated in a structured way so that the desired data can be read, re-coded, queried and extracted efficiently. The current pilot implementation of the system provides access to a limited amount of NHANES database. We plan to increase the amount of data available through the system in the near future and to extend the techniques to other large databases from CDU archive with a current holding of about 53 databases. PMID:23920922

  6. Biomedical research

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Biomedical problems encountered by man in space which have been identified as a result of previous experience in simulated or actual spaceflight include cardiovascular deconditioning, motion sickness, bone loss, muscle atrophy, red cell alterations, fluid and electrolyte loss, radiation effects, radiation protection, behavior, and performance. The investigations and the findings in each of these areas were reviewed. A description of how biomedical research is organized within NASA, how it is funded, and how it is being reoriented to meet the needs of future manned space missions is also provided.

  7. Extracting semantically enriched events from biomedical literature

    PubMed Central

    2012-01-01

    Background Research into event-based text mining from the biomedical literature has been growing in popularity to facilitate the development of advanced biomedical text mining systems. Such technology permits advanced search, which goes beyond document or sentence-based retrieval. However, existing event-based systems typically ignore additional information within the textual context of events that can determine, amongst other things, whether an event represents a fact, hypothesis, experimental result or analysis of results, whether it describes new or previously reported knowledge, and whether it is speculated or negated. We refer to such contextual information as meta-knowledge. The automatic recognition of such information can permit the training of systems allowing finer-grained searching of events according to the meta-knowledge that is associated with them. Results Based on a corpus of 1,000 MEDLINE abstracts, fully manually annotated with both events and associated meta-knowledge, we have constructed a machine learning-based system that automatically assigns meta-knowledge information to events. This system has been integrated into EventMine, a state-of-the-art event extraction system, in order to create a more advanced system (EventMine-MK) that not only extracts events from text automatically, but also assigns five different types of meta-knowledge to these events. The meta-knowledge assignment module of EventMine-MK performs with macro-averaged F-scores in the range of 57-87% on the BioNLP’09 Shared Task corpus. EventMine-MK has been evaluated on the BioNLP’09 Shared Task subtask of detecting negated and speculated events. Our results show that EventMine-MK can outperform other state-of-the-art systems that participated in this task. Conclusions We have constructed the first practical system that extracts both events and associated, detailed meta-knowledge information from biomedical literature. The automatically assigned meta-knowledge information

  8. Electrophysiological measurement of information flow during visual search

    PubMed Central

    Cosman, Joshua D.; Arita, Jason T.; Ianni, Julianna D.; Woodman, Geoffrey F.

    2016-01-01

    The temporal relationship between different stages of cognitive processing is long-debated. This debate is ongoing, primarily because it is often difficult to measure the time course of multiple cognitive processes simultaneously. We employed a manipulation that allowed us to isolate ERP components related to perceptual processing, working memory, and response preparation, and then examined the temporal relationship between these components while observers performed a visual search task. We found that when response speed and accuracy were equally stressed, our index of perceptual processing ended before both the transfer of information into working memory and response preparation began. However, when we stressed speed over accuracy response preparation began before the completion of perceptual processing or transfer of information into working memory on trials with the fastest reaction times. These findings show that individuals can control the flow of information transmission between stages, either waiting for perceptual processing to be completed before preparing a response or configuring these stages to overlap in time. PMID:26669285

  9. Supporting undergraduate biomedical entrepreneurship.

    PubMed

    Patterson, P E

    2004-01-01

    As biomedical innovations become more sophisticated and expensive to bring to market, an approach is needed to ensure the survival of the best ideas. The tactic used by Iowa State University to provide entrepreneurship opportunities for undergraduate students in biomedical areas is a model that has proven to be both distinctive and effective. Iowa State supports and fosters undergraduate student entrepreneurship efforts through the Pappajohn Center for Entrepreneurship. This unique partnership encourages ISU faculty, researchers, and students to become involved in the world of entrepreneurship, while allowing Iowa's business communities to gain access to a wide array of available resources, skills, and information from Iowa State University. PMID:15134007

  10. Taming the Information Jungle with WWW Search Engines.

    ERIC Educational Resources Information Center

    Repman, Judi; And Others

    1997-01-01

    Because searching the Web with different engines often produces different results, the best strategy is to learn how each engine works. Discusses comparing search engines; qualities to consider (ease of use, relevance of hits, and speed); and six of the most popular search tools (Yahoo, Magellan. InfoSeek, Alta Vista, Lycos, and Excite). Lists…

  11. A Study of the Information Search Behaviour of the Millennial Generation

    ERIC Educational Resources Information Center

    Taylor, Arthur

    2012-01-01

    Introduction: Members of the millennial generation (born after 1982) have come of age in a society infused with technology and information. It is unclear how they determine the validity of information gathered, or whether or not validity is even a concern. Previous information search models based on mediated searches with different age groups may…

  12. How College Students Search the Internet for Weight Control and Weight Management Information: An Observational Study

    ERIC Educational Resources Information Center

    Senkowski, Valerie; Branscum, Paul

    2015-01-01

    Background: Few studies have attempted to examine how young adults search for health information on the Internet, especially information related to weight control and weight management. Purpose: The purpose of this study was to determine search strategies that college students used for finding information related to weight control and weight…

  13. Biomedical Applications of NASA Science and Technology

    NASA Technical Reports Server (NTRS)

    Brown, James N., Jr.

    1968-01-01

    During the period 15 September 1968 to 14 December 1968, the NASA supported Biomedical Application Team at the Research Triangle Institute has identified 6 new problems, performed significant activities on 15 of the active problems identified previously, performed 5 computer searches of the NASA aerospace literature, and maintained one current awareness search. As a partial result of these activities, one technology transfer was accomplished. As a part of continuing problem review, 13 problems were classified inactive. Activities during the quarter involved all phases of team activity with respect to biomedical problems. As has been observed in preceding years, it has been exceedingly difficult to arrange meetings with medical investigators during the fourth quarter of the calendar year. This is a result of a combination of factors. Teaching requirements, submission of grant applications and holidays are the most significant factors involved. As a result, the numbers of new problems identified and of transfers and potential transfers are relatively low during this quarter. Most of our activities have thus been directed toward obtaining information related to problems already identified. Consequently, during the next quarter we will follow up on these activities with the expectation that transfers will be accomplished on a number of them. In addition, the normal availability of researchers to the team is expected to be restored during this quarter, permitting an increase in new problem identification activities as well as follow-up with other researchers on old problems. Another activity scheduled for the next quarter is consultation with several interested biomedical equipment manufacturers to explore means of effective interaction between the Biomedical Application Team and these companies.

  14. Database search for safety information on cosmetic ingredients.

    PubMed

    Pauwels, Marleen; Rogiers, Vera

    2007-12-01

    Ethical considerations with respect to experimental animal use and regulatory testing are worldwide under heavy discussion and are, in certain cases, taken up in legislative measures. The most explicit example is the European cosmetic legislation, establishing a testing ban on finished cosmetic products since 11 September 2004 and enforcing that the safety of a cosmetic product is assessed by taking into consideration "the general toxicological profile of the ingredients, their chemical structure and their level of exposure" (OJ L151, 32-37, 23 June 1993; OJ L066, 26-35, 11 March 2003). Therefore the availability of referenced and reliable information on cosmetic ingredients becomes a dire necessity. Given the high-speed progress of the World Wide Web services and the concurrent drastic increase in free access to information, identification of relevant data sources and evaluation of the scientific value and quality of the retrieved data, are crucial. Based upon own practical experience, a survey is put together of freely and commercially available data sources with their individual description, field of application, benefits and drawbacks. It should be mentioned that the search strategies described are equally useful as a starting point for any quest for safety data on chemicals or chemical-related substances in general. PMID:17919791

  15. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

    PubMed

    Worley, K C; Wiese, B A; Smith, R F

    1995-09-01

    BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search

  16. The Pricing of Information--A Search-Based Approach to Pricing an Online Search Service.

    ERIC Educational Resources Information Center

    Boyle, Harry F.

    1982-01-01

    Describes innovative pricing structure consisting of low connect time fee, print fees, and search fees, offered by Chemical Abstracts Service (CAS) ONLINE--an online searching system used to locate chemical substances. Pricing options considered by CAS, the search-based pricing approach, and users' reactions to pricing structures are noted. (EJS)

  17. A Systematic Understanding of Successful Web Searches in Information-Based Tasks

    ERIC Educational Resources Information Center

    Zhou, Mingming

    2013-01-01

    The purpose of this study is to research how Chinese university students solve information-based problems. With the Search Performance Index as the measure of search success, participants were divided into high, medium and low-performing groups. Based on their web search logs, these three groups were compared along five dimensions of the search…

  18. 78 FR 42797 - Notice of Proposed Information Collection: Comment Request Focus Groups About the Housing Search...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-17

    ... Housing Search Process for Lesbian, Gay, Bisexual and Transgender (LGBT) People AGENCY: Office of Policy... information: Title of Proposal: Focus Groups about the Housing Search Process for Lesbian, Gay, Bisexual and..., the Department would like to learn more about the process that people use to search for...

  19. Library Instruction and College Student Self-Efficacy in Electronic Information Searching.

    ERIC Educational Resources Information Center

    Ren, Wen-Hua

    2000-01-01

    Explores whether library instruction can enhance college students' self-efficacy in electronic information searching. Assesses self-efficacy before and after library instruction; examines how self-esteem is related to students' attitudes toward acquiring electronic search skills, their emotions, and search performance; and discusses implications…

  20. Markov Models of Search State Patterns in a Hypertext Information Retrieval System.

    ERIC Educational Resources Information Center

    Qiu, Liwen

    1993-01-01

    Describes research that was conducted to determine the search state patterns through which users retrieve information in hypertext systems. Use of the Markov model to describe users' search behavior is discussed, and search patterns of different user groups were studied by comparing transition probability matrices. (Contains 25 references.) (LRW)

  1. 15 CFR 50.5 - Fee structure for age search and citizenship information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 15 Commerce and Foreign Trade 1 2014-01-01 2014-01-01 false Fee structure for age search and... THE CENSUS § 50.5 Fee structure for age search and citizenship information. Type of service Fee Searches of one census for one person and one transcript $65.00 Each additional copy of census transcript...

  2. 15 CFR 50.5 - Fee structure for age search and citizenship information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 1 2011-01-01 2011-01-01 false Fee structure for age search and... THE CENSUS § 50.5 Fee structure for age search and citizenship information. Type of service Fee Searches of one census for one person and one transcript $65.00 Each additional copy of census transcript...

  3. 15 CFR 50.5 - Fee structure for age search and citizenship information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 15 Commerce and Foreign Trade 1 2012-01-01 2012-01-01 false Fee structure for age search and... THE CENSUS § 50.5 Fee structure for age search and citizenship information. Type of service Fee Searches of one census for one person and one transcript $65.00 Each additional copy of census transcript...

  4. 15 CFR 50.5 - Fee structure for age search and citizenship information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 15 Commerce and Foreign Trade 1 2013-01-01 2013-01-01 false Fee structure for age search and... THE CENSUS § 50.5 Fee structure for age search and citizenship information. Type of service Fee Searches of one census for one person and one transcript $65.00 Each additional copy of census transcript...

  5. Biomedical Conferences

    NASA Technical Reports Server (NTRS)

    1976-01-01

    As a result of Biomedical Conferences, Vivo Metric Systems Co. has produced cardiac electrodes based on NASA technology. Frequently in science, one highly specialized discipline is unaware of relevant advances made in other areas. In an attempt to familiarize researchers in a variety of disciplines with medical problems and needs, NASA has sponsored conferences that bring together university scientists, practicing physicians and manufacturers of medical instruments.

  6. Effects of Individual Health Topic Familiarity on Activity Patterns During Health Information Searches

    PubMed Central

    Moriyama, Koichi; Fukui, Ken–ichi; Numao, Masayuki

    2015-01-01

    Background Non-medical professionals (consumers) are increasingly using the Internet to support their health information needs. However, the cognitive effort required to perform health information searches is affected by the consumer’s familiarity with health topics. Consumers may have different levels of familiarity with individual health topics. This variation in familiarity may cause misunderstandings because the information presented by search engines may not be understood correctly by the consumers. Objective As a first step toward the improvement of the health information search process, we aimed to examine the effects of health topic familiarity on health information search behaviors by identifying the common search activity patterns exhibited by groups of consumers with different levels of familiarity. Methods Each participant completed a health terminology familiarity questionnaire and health information search tasks. The responses to the familiarity questionnaire were used to grade the familiarity of participants with predefined health topics. The search task data were transcribed into a sequence of search activities using a coding scheme. A computational model was constructed from the sequence data using a Markov chain model to identify the common search patterns in each familiarity group. Results Forty participants were classified into L1 (not familiar), L2 (somewhat familiar), and L3 (familiar) groups based on their questionnaire responses. They had different levels of familiarity with four health topics. The video data obtained from all of the participants were transcribed into 4595 search activities (mean 28.7, SD 23.27 per session). The most frequent search activities and transitions in all the familiarity groups were related to evaluations of the relevancy of selected web pages in the retrieval results. However, the next most frequent transitions differed in each group and a chi-squared test confirmed this finding (P<.001). Next, according to the

  7. Biomedical informatics and translational medicine

    PubMed Central

    2010-01-01

    Biomedical informatics involves a core set of methodologies that can provide a foundation for crossing the "translational barriers" associated with translational medicine. To this end, the fundamental aspects of biomedical informatics (e.g., bioinformatics, imaging informatics, clinical informatics, and public health informatics) may be essential in helping improve the ability to bring basic research findings to the bedside, evaluate the efficacy of interventions across communities, and enable the assessment of the eventual impact of translational medicine innovations on health policies. Here, a brief description is provided for a selection of key biomedical informatics topics (Decision Support, Natural Language Processing, Standards, Information Retrieval, and Electronic Health Records) and their relevance to translational medicine. Based on contributions and advancements in each of these topic areas, the article proposes that biomedical informatics practitioners ("biomedical informaticians") can be essential members of translational medicine teams. PMID:20187952

  8. Knowledge-driven multidimensional indexing structure for biomedical media database retrieval.

    PubMed

    Scott, Grant; Shyu, Chi-Ren

    2007-05-01

    Today, biomedical media data are being generated at rates unimaginable only years ago. Content-based retrieval of biomedical media from large databases is becoming increasingly important to clinical, research, and educational communities. In this paper, we present the recently developed entropy balanced statistical (EBS) k-d tree and its applications to biomedical media, including a high-resolution computed tomography (HRCT) lung image database and the first real-time protein tertiary structure search engine. Our index utilizes statistical properties inherent in large-scale biomedical media databases for efficient and accurate searches. By applying concepts from pattern recognition and information theory, the EBS k-d tree is built through top-down decision tree induction. Experimentation shows similarity searches against a protein structure database of 53 363 structures consistently execute in less than 8.14 ms for the top 100 most similar structures. Additionally, we have shown improved retrieval precision over adaptive and statistical k-d trees. Retrieval precision of the EBS k-d tree is 81.6% for content-based retrieval of HRCT lung images and 94.9% at 10% recall for protein structure similarity search. The EBS k-d tree has enormous potential for use in biomedical applications embedded with ground-truth knowledge and multidimensional signatures. PMID:17521082

  9. End User Information Searching on the Internet: How Do Users Search and What Do They Search For? (SIG USE)

    ERIC Educational Resources Information Center

    Saracevic, Tefko

    2000-01-01

    Summarizes a presentation that discussed findings and implications of research projects using an Internet search service and Internet-accessible vendor databases, representing the two sides of public database searching: query formulation and resource utilization. Presenters included: Tefko Saracevic, Amanda Spink, Dietmar Wolfram and Hong Xie.…

  10. Folksonomical P2P File Sharing Networks Using Vectorized KANSEI Information as Search Tags

    NASA Astrophysics Data System (ADS)

    Ohnishi, Kei; Yoshida, Kaori; Oie, Yuji

    We present the concept of folksonomical peer-to-peer (P2P) file sharing networks that allow participants (peers) to freely assign structured search tags to files. These networks are similar to folksonomies in the present Web from the point of view that users assign search tags to information distributed over a network. As a concrete example, we consider an unstructured P2P network using vectorized Kansei (human sensitivity) information as structured search tags for file search. Vectorized Kansei information as search tags indicates what participants feel about their files and is assigned by the participant to each of their files. A search query also has the same form of search tags and indicates what participants want to feel about files that they will eventually obtain. A method that enables file search using vectorized Kansei information is the Kansei query-forwarding method, which probabilistically propagates a search query to peers that are likely to hold more files having search tags that are similar to the query. The similarity between the search query and the search tags is measured in terms of their dot product. The simulation experiments examine if the Kansei query-forwarding method can provide equal search performance for all peers in a network in which only the Kansei information and the tendency with respect to file collection are different among all of the peers. The simulation results show that the Kansei query forwarding method and a random-walk-based query forwarding method, for comparison, work effectively in different situations and are complementary. Furthermore, the Kansei query forwarding method is shown, through simulations, to be superior to or equal to the random-walk based one in terms of search speed.

  11. Automatically generating gene summaries from biomedical literature.

    PubMed

    Ling, Xu; Jiang, Jing; He, Xin; Mei, Qiaozhu; Zhai, Chengxiang; Schatz, Bruce

    2006-01-01

    Biologists often need to find information about genes whose function is not described in the genome databases. Currently they must try to search disparate biomedical literature to locate relevant articles, and spend considerable efforts reading the retrieved articles in order to locate the most relevant knowledge about the gene. We describe our software, the first that automatically generates gene summaries from biomedical literature. We present a two-stage summarization method, which involves first retrieving relevant articles and then extracting the most informative sentences from the retrieved articles to generate a structured gene summary. The generated summary explicitly covers multiple aspects of a gene, such as the sequence information, mutant phenotypes, and molecular interaction with other genes. We propose several heuristic approaches to improve the accuracy in both stages. The proposed methods are evaluated using 10 randomly chosen genes from FlyBase and a subset of Medline abstracts about Drosophila. The results show that the precision of the top selected sentences in the 6 aspects is typically about 50-70%, and the generated summaries are quite informative, indicating that our approaches are effective in automatically summarizing literature information about genes. The generated summaries not only are directly useful to biologists but also serve as useful entry points to enable them to quickly digest the retrieved literature articles. PMID:17094226

  12. 75 FR 12174 - Proposed Information Collection; Comment Request; AGE Search Service

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-15

    ... Census Bureau Proposed Information Collection; Comment Request; AGE Search Service AGENCY: U.S. Census....harkins@census.gov ). SUPPLEMENTARY INFORMATION: I. Abstract Age Search is a service provided by the U.S... obtain passports or to provide evidence of family relationship for rights of inheritance. The Age...

  13. Online Information Searching Strategy Inventory (OISSI): A Quick Version and a Complete Version

    ERIC Educational Resources Information Center

    Tsai, Meng-Jung

    2009-01-01

    This study developed an instrument to evaluate student online information searching strategies based on a framework comprising three domains and seven aspects. Two versions of the Online Information Searching Strategies Inventory (OISSI), including both quick and complete versions, were finally established and exhibited good validities and…

  14. Relationships among Information Search Activities When Shopping for a Credit Card.

    ERIC Educational Resources Information Center

    Lee, Jinkook; Hogarth, Jeanne M.

    2000-01-01

    Researchers examined consumer behavior regarding types and numbers of information sources consulted about credit cards and comparison of terms. Results showed that consumers have diverse patterns of information searching that cannot be captured by a global measure or a few single measures of search and strong interdependencies among some search…

  15. Moving beyond the Desktop: Searching for Information with Limited Display Size

    ERIC Educational Resources Information Center

    Marcial, Laura Haak

    2012-01-01

    Increasingly, users are performing more sophisticated types of tasks, like information search, across computing platforms including desktops/laptops, tablets, and smartphones. While much research has been done to improve efficiency for each of these devices in the area of information search, few investigations have taken a pragmatic approach to…

  16. Talk as a Metacognitive Strategy during the Information Search Process of Adolescents

    ERIC Educational Resources Information Center

    Bowler, Leanne

    2010-01-01

    Introduction: This paper describes a metacognitive strategy related to the social dimension of the information search process of adolescents. Method: A case study that used naturalistic methods to explore the metacognitive thinking nd associated emotions of ten adolescents. The study was framed by Kuhlthau's Information Search Process model and…

  17. A Longitudinal Study of World Wide Web Users' Information-Searching Behavior.

    ERIC Educational Resources Information Center

    Cothey, Vivian

    2002-01-01

    This study of the Web information searching behavior of 206 United Kingdom college students over a 10-month period showed that, contrary to expectations, the users adopted a more passive or browsing approach to Web information searching and became more eclectic in their selection of Web hosts as they gained experience. (Contains 61 references.)…

  18. Impact of Prior Knowledge of Informational Content and Organization on Learning Search Principles in a Database.

    ERIC Educational Resources Information Center

    Linde, Lena; Bergstrom, Monica

    1988-01-01

    The importance of prior knowledge of informational content and organization for search performance on a database was evaluated for 17 undergraduates. Pretraining related to content, and information did facilitate learning logical search principles in a relational database; contest pretraining was more efficient. (SLD)

  19. Identifying the Impact of Domain Knowledge and Cognitive Style on Web-Based Information Search Behavior

    ERIC Educational Resources Information Center

    Park, Young; Black, John B.

    2007-01-01

    Although information searching in hypermedia environments has become a new important problem solving capability, there is not much known about what types of individual characteristics constitute a successful information search behavior. This study mainly investigated which of the 2 factors, 1) natural characteristics (cognitive style), and 2)…

  20. 15 CFR 50.5 - Fee structure for age search and citizenship information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... THE CENSUS § 50.5 Fee structure for age search and citizenship information. Type of service Fee... 15 Commerce and Foreign Trade 1 2010-01-01 2010-01-01 false Fee structure for age search and citizenship information. 50.5 Section 50.5 Commerce and Foreign Trade Regulations Relating to Commerce...

  1. Evaluating the Process of Online Health Information Searching: A Qualitative Approach to Exploring Consumer Perspectives

    PubMed Central

    Fiksdal, Alexander S; Kumbamu, Ashok; Jadhav, Ashutosh S; Cocos, Cristian; Nelsen, Laurie A; Pathak, Jyotishman

    2014-01-01

    Background The Internet is a common resource that patients and consumers use to access health-related information. Multiple practical, cultural, and socioeconomic factors influence why, when, and how people utilize this tool. Improving the delivery of health-related information necessitates a thorough understanding of users’ searching-related needs, preferences, and experiences. Although a wide body of quantitative research examining search behavior exists, qualitative approaches have been under-utilized and provide unique perspectives that may prove useful in improving the delivery of health information over the Internet. Objective We conducted this study to gain a deeper understanding of online health-searching behavior in order to inform future developments of personalizing information searching and content delivery. Methods We completed three focus groups with adult residents of Olmsted County, Minnesota, which explored perceptions of online health information searching. Participants were recruited through flyers and classifieds advertisements posted throughout the community. We audio-recorded and transcribed all focus groups, and analyzed data using standard qualitative methods. Results Almost all participants reported using the Internet to gather health information. They described a common experience of searching, filtering, and comparing results in order to obtain information relevant to their intended search target. Information saturation and fatigue were cited as main reasons for terminating searching. This information was often used as a resource to enhance their interactions with health care providers. Conclusions Many participants viewed the Internet as a valuable tool for finding health information in order to support their existing health care resources. Although the Internet is a preferred source of health information, challenges persist in streamlining the search process. Content providers should continue to develop new strategies and technologies

  2. Holography In Biomedical Sciences

    NASA Astrophysics Data System (ADS)

    von Bally, G.

    1988-01-01

    Today not only physicists and engineers but also biological and medical scientists are exploring the potentials of holographic methods in their special field of work. Most of the underlying physical principles such as coherence, interference, diffraction and polarization as well as general features of holography e.g. storage and retrieval of amplitude and phase of a wavefront, 3-d-imaging, large field of depth, redundant storage of information, spatial filtering, high-resolving, non-contactive, 3-d form and motion analysis are explained in detail in other contributions to this book. Therefore, this article is confined to the applications of holography in biomedical sciences. Because of the great number of contributions and the variety of applications [1,2,3,4,5,6,7,8] in this review the investigations can only be mentioned briefly and the survey has to be confined to some examples. As in all fields of optics and laser metrology, a review of biomedical applications of holography would be incomplete if military developments and their utilization are not mentioned. As will be demonstrated by selected examples the increasing interlacing of science with the military does not stop at domains that traditionally are regarded as exclusively oriented to human welfare like biomedical research [9]. This fact is actually characterized and stressed by the expression "Star Wars Medicine", which becomes increasingly common as popular description for laser applications (including holography) in medicine [10]. Thus, the consequence - even in such highly specialized fields like biomedical applications of holography - have to be discussed.

  3. Development of Health Information Search Engine Based on Metadata and Ontology

    PubMed Central

    Song, Tae-Min; Jin, Dal-Lae

    2014-01-01

    Objectives The aim of the study was to develop a metadata and ontology-based health information search engine ensuring semantic interoperability to collect and provide health information using different application programs. Methods Health information metadata ontology was developed using a distributed semantic Web content publishing model based on vocabularies used to index the contents generated by the information producers as well as those used to search the contents by the users. Vocabulary for health information ontology was mapped to the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), and a list of about 1,500 terms was proposed. The metadata schema used in this study was developed by adding an element describing the target audience to the Dublin Core Metadata Element Set. Results A metadata schema and an ontology ensuring interoperability of health information available on the internet were developed. The metadata and ontology-based health information search engine developed in this study produced a better search result compared to existing search engines. Conclusions Health information search engine based on metadata and ontology will provide reliable health information to both information producer and information consumers. PMID:24872907

  4. [The search for medical information on the World Wide Web].

    PubMed

    Cappeliez, O; Ranschaert, E; Peetrons, P; Struyven, J

    1999-12-01

    The internet has experienced tremendous growth over the past few years and has currently many resources in the field of medicine. However, many physicians remain unaware of how to gain access to this powerful tool. This article briefly describes the World Wide Web and its potential applications for physicians. The basics of web search engines and medical directories, as well as the use of advanced search with boolean operators are explained. PMID:10672776

  5. Biomedical technology in Franconia.

    PubMed

    Efferth, T

    2000-01-01

    Medical instrumentation and biotechnology business is developing rapidly in Franconia. The universities of Bayreuth, Erlangen-Nürnberg, and Würzburg hold upper ranks in biomedical extramural funding research. They have a high competence in biomedical research, medical instrumentation, and biotechnology. The association "BioMedTec Franken e.V" has been founded at the beginning of 1999 both to foster the information exchange between universities, industry and politics and to facilitate the establishment of biomedical companies by means of science parks. In the IGZ (Innovation and Foundation Center Nürnberg-Fürth-Erlangen) 4,500 square meters of space are currently shared by 19 novel companies. Since 1985 60 companies in the IGZ had a total turnover of about 74 Mio Euro. The TGZ (Technologie- und Gründerzentrum) in Würzburg provides space for 11 companies. For the specific needs of biomedical technology companies further science parks will be set up in the near future. A science park for medical instrumentation will be founded in Erlangen (IZMP, Innovations- und Gründerzentrum für Medizintechnik und Pharma in der Region Nürnberg, Fürch, Erlangen). Furthermore, a Biomedical Technology Center and a Research Center for Bicompatible Materials are to be founded in Würzburg and Bayreuth, respectively. Several communication platforms (Bayern Innovativ, FORWISS, FTT, KIM, N-TEC-VISIT, TBU, WETTI etc.) allow the transfer of local academic research activities to industrial utilization and open new co-operation possibilities. International pharmaceutical companies (Novartis, Nürnberg; Pharmacia Upjohn, Erlangen) are located in Franconia. Central Franconia represents a national focus for medical instrumentation. The Erlangen settlement of the Medical Engineering Section of Siemens employs 4,500 people including approximately 1,000 employees in the Siemens research center. PMID:10683721

  6. The application of foraging theory to the information searching behaviour of general practitioners

    PubMed Central

    2011-01-01

    Background General Practitioners (GPs) employ strategies to identify and retrieve medical evidence for clinical decision making which take workload and time constraints into account. Optimal Foraging Theory (OFT) initially developed to study animal foraging for food is used to explore the information searching behaviour of General Practitioners. This study is the first to apply foraging theory within this context. Study objectives were: 1. To identify the sequence and steps deployed in identifiying and retrieving evidence for clinical decision making. 2. To utilise Optimal Foraging Theory to assess the effectiveness and efficiency of General Practitioner information searching. Methods GPs from the Wellington region of New Zealand were asked to document in a pre-formatted logbook the steps and outcomes of an information search linked to their clinical decision making, and fill in a questionnaire about their personal, practice and information-searching backgrounds. Results A total of 115/155 eligible GPs returned a background questionnaire, and 71 completed their information search logbook. GPs spent an average of 17.7 minutes addressing their search for clinical information. Their preferred information sources were discussions with colleagues (38% of sources) and books (22%). These were the two most profitable information foraging sources (15.9 min and 9.5 min search time per answer, compared to 34.3 minutes in databases). GPs nearly always accessed another source when unsuccessful (95% after 1st source), and frequently when successful (43% after 2nd source). Use of multiple sources accounted for 41% of searches, and increased search success from 70% to 89%. Conclusions By consulting in foraging terms the most 'profitable' sources of information (colleagues, books), rapidly switching sources when unsuccessful, and frequently double checking, GPs achieve an efficient trade-off between maximizing search success and information reliability, and minimizing searching

  7. Empowering Students to Make Sense of an Information-Saturated World: The Evolution of "Information Searching and Analysis"

    ERIC Educational Resources Information Center

    Wittebols, James H.

    2016-01-01

    How well students conduct research online is an increasing concern for educators at all levels, especially higher education. This paper describes the evolution of a course that examines confirmation bias, information searching, and the political economy of information as keys to becoming more information and media literate. After a key assignment…

  8. Precision with Ease: Refining Thesaurus Support for Quality Health Information Searching on Health"Insite"

    ERIC Educational Resources Information Center

    Smith, Jill Buckley; Deacon, Prue

    2009-01-01

    Health"Insite" is the Australian Government's Internet gateway to reliable health information online, providing access to over 15,000 information items on the websites of more than 80 approved information partners. The gateway provides a variety of searching and browsing options to assist users to find information on a wide range of health topics.…

  9. The Effects of Presentation Method and Information Density on Visual Search Ability and Working Memory Load

    ERIC Educational Resources Information Center

    Chang, Ting-Wen; Kinshuk; Chen, Nian-Shing; Yu, Pao-Ta

    2012-01-01

    This study investigates the effects of successive and simultaneous information presentation methods on learner's visual search ability and working memory load for different information densities. Since the processing of information in the brain depends on the capacity of visual short-term memory (VSTM), the limited information processing capacity…

  10. BioEve Search: A Novel Framework to Facilitate Interactive Literature Search

    PubMed Central

    Ahmed, Syed Toufeeq; Davulcu, Hasan; Tikves, Sukru; Nair, Radhika; Zhao, Zhongming

    2012-01-01

    Background. Recent advances in computational and biological methods in last two decades have remarkably changed the scale of biomedical research and with it began the unprecedented growth in both the production of biomedical data and amount of published literature discussing it. An automated extraction system coupled with a cognitive search and navigation service over these document collections would not only save time and effort, but also pave the way to discover hitherto unknown information implicitly conveyed in the texts. Results. We developed a novel framework (named “BioEve”) that seamlessly integrates Faceted Search (Information Retrieval) with Information Extraction module to provide an interactive search experience for the researchers in life sciences. It enables guided step-by-step search query refinement, by suggesting concepts and entities (like genes, drugs, and diseases) to quickly filter and modify search direction, and thereby facilitating an enriched paradigm where user can discover related concepts and keywords to search while information seeking. Conclusions. The BioEve Search framework makes it easier to enable scalable interactive search over large collection of textual articles and to discover knowledge hidden in thousands of biomedical literature articles with ease. PMID:22693501

  11. Adolescents Searching for Health Information on the Internet: An Observational Study

    PubMed Central

    Derry, Holly A; Resnick, Paul J; Richardson, Caroline R

    2003-01-01

    Background Adolescents' access to health information on the Internet is partly a function of their ability to search for and find answers to their health-related questions. Adolescents may have unique health and computer literacy needs. Although many surveys, interviews, and focus groups have been utilized to understand the information-seeking and information-retrieval behavior of adolescents looking for health information online, we were unable to locate observations of individual adolescents that have been conducted in this context. Objective This study was designed to understand how adolescents search for health information using the Internet and what implications this may have on access to health information. Methods A convenience sample of 12 students (age 12-17 years) from 1 middle school and 2 high schools in southeast Michigan were provided with 6 health-related questions and asked to look for answers using the Internet. Researchers recorded 68 specific searches using software that captured screen images as well as synchronized audio recordings. Recordings were reviewed later and specific search techniques and strategies were coded. A qualitative review of the verbal communication was also performed. Results Out of 68 observed searches, 47 (69%) were successful in that the adolescent found a correct and useful answer to the health question. The majority of sites that students attempted to access were retrieved directly from search engine results (77%) or a search engine's recommended links (10%); only a small percentage were directly accessed (5%) or linked from another site (7%). The majority (83%) of followed links from search engine results came from the first 9 results. Incorrect spelling (30 of 132 search terms), number of pages visited within a site (ranging from 1-15), and overall search strategy (eg, using a search engine versus directly accessing a site), were each important determinants of success. Qualitative analysis revealed that participants

  12. Using Internet Search Engines to Obtain Medical Information: A Comparative Study

    PubMed Central

    Wang, Liupu; Wang, Juexin; Wang, Michael; Li, Yong; Liang, Yanchun

    2012-01-01

    Background The Internet has become one of the most important means to obtain health and medical information. It is often the first step in checking for basic information about a disease and its treatment. The search results are often useful to general users. Various search engines such as Google, Yahoo!, Bing, and Ask.com can play an important role in obtaining medical information for both medical professionals and lay people. However, the usability and effectiveness of various search engines for medical information have not been comprehensively compared and evaluated. Objective To compare major Internet search engines in their usability of obtaining medical and health information. Methods We applied usability testing as a software engineering technique and a standard industry practice to compare the four major search engines (Google, Yahoo!, Bing, and Ask.com) in obtaining health and medical information. For this purpose, we searched the keyword breast cancer in Google, Yahoo!, Bing, and Ask.com and saved the results of the top 200 links from each search engine. We combined nonredundant links from the four search engines and gave them to volunteer users in an alphabetical order. The volunteer users evaluated the websites and scored each website from 0 to 10 (lowest to highest) based on the usefulness of the content relevant to breast cancer. A medical expert identified six well-known websites related to breast cancer in advance as standards. We also used five keywords associated with breast cancer defined in the latest release of Systematized Nomenclature of Medicine-Clinical Terms (SNOMED CT) and analyzed their occurrence in the websites. Results Each search engine provided rich information related to breast cancer in the search results. All six standard websites were among the top 30 in search results of all four search engines. Google had the best search validity (in terms of whether a website could be opened), followed by Bing, Ask.com, and Yahoo!. The search

  13. The role of information search in seeking alternative treatment for back pain: a qualitative analysis

    PubMed Central

    2014-01-01

    Background Health consumers have moved away from a reliance on medical practitioner advice to more independent decision processes and so their information search processes have subsequently widened. This study examined how persons with back pain searched for alternative treatment types and service providers. That is, what information do they seek and how; what sources do they use and why; and by what means do they search for it? Methods 12 persons with back pain were interviewed. The method used was convergent interviewing. This involved a series of semi-structured questions to obtain open-ended answers. The interviewer analysed the responses and refined the questions after each interview, to converge on the dominant factors influencing decisions about treatment patterns. Results Persons with back pain mainly search their memories and use word of mouth (their doctor and friends) for information about potential treatments and service providers. Their search is generally limited due to personal, provider-related and information-supply reasons. However, they did want in-depth information about the alternative treatments and providers in an attempt to establish apriori their efficacy in treating their specific back problems. They searched different sources depending on the type of information they required. Conclusions The findings differ from previous studies about the types of information health consumers require when searching for information about alternative or mainstream healthcare services. The results have identified for the first time that limited information availability was only one of three categories of reasons identified about why persons with back pain do not search for more information particularly from external non-personal sources. PMID:24725300

  14. Randomization of Symbol Repetition of Punch Cards with Superimposed Coding in Information-Search Systems.

    ERIC Educational Resources Information Center

    Pirovich, L. Ya

    The article shows the effect of the irregularity of using separate symbols on search noise on punch cards with superimposed symbol coding in information-search system (IPS). A binomial law of random value distribution of repetition of each symbol is established and analyzed. A method of determining the maximum value of symbol repetition is…

  15. 76 FR 13402 - Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-11

    ... Agency (EPA) is announcing the availability of literature searches for cobalt (CASRN 7440-48-4) and inorganic cobalt compounds, vanadium pentoxide (CASRN 1314-62-1), vinyl acetate (CASRN 108-05-4), and Libby... information to EPA. Literature searches are now available for cobalt (CAS No. 7440-48-4) and inorganic...

  16. Information Searching Strategies in Web-Based Science Learning: The Role of Internet Self-Efficacy.

    ERIC Educational Resources Information Center

    Tsai, Meng-Jung; Tsai, Chin-Chung

    2003-01-01

    Describes a study that explored Taiwanese college freshmen students' information searching strategies in Web-based science learning activities and examined the influences of students' self-efficacy on these strategies. Discusses the use of in-depth case studies and comparisons to analyze students' Web-based searching and learning achievement,…

  17. A Personalised Information Support System for Searching Portals and E-Resources

    ERIC Educational Resources Information Center

    Sirisha, B. S.; Jeevan, V. K. J.; Raja Kumar, R. V.; Goswami, A.

    2009-01-01

    Purpose: The purpose of this paper is to describe the development of a personalised information support system to help faculty members to search various portals and e-resources without typing the search terms in different interfaces and to obtain results re-ordered without human intervention. Design/methodology/approach: After a careful survey of…

  18. Searching for Information On-Line and Off-Line: Gender Differences among Middle School Students

    ERIC Educational Resources Information Center

    Roy, Marguerite; Taylor, Roger; Chi, Michelene T. H.

    2003-01-01

    There has been a national call for increased use of computers and technology in schools. Currently, however, little is known about how students use and learn from these new technologies. This study examines how students search for, browse, and learn specific information when performing an on-line (Web) versus an off-line (Library) search.…

  19. Finding Information on the World Wide Web: The Retrieval Effectiveness of Search Engines.

    ERIC Educational Resources Information Center

    Pathak, Praveen; Gordon, Michael

    1999-01-01

    Describes a study that examined the effectiveness of eight search engines for the World Wide Web. Calculated traditional information-retrieval measures of recall and precision at varying numbers of retrieved documents to use as the bases for statistical comparisons of retrieval effectiveness. Also examined the overlap between search engines.…

  20. What do Web-Use Skill Differences Imply for Online Health Information Searches?

    PubMed Central

    2012-01-01

    Background Online health information is of variable and often low scientific quality. In particular, elderly less-educated populations are said to struggle in accessing quality online information (digital divide). Little is known about (1) how their online behavior differs from that of younger, more-educated, and more-frequent Web users, and (2) how the older population may be supported in accessing good-quality online health information. Objective To specify the digital divide between skilled and less-skilled Web users, we assessed qualitative differences in technical skills, cognitive strategies, and attitudes toward online health information. Based on these findings, we identified educational and technological interventions to help Web users find and access good-quality online health information. Methods We asked 22 native German-speaking adults to search for health information online. The skilled cohort consisted of 10 participants who were younger than 30 years of age, had a higher level of education, and were more experienced using the Web than 12 participants in the less-skilled cohort, who were at least 50 years of age. We observed online health information searches to specify differences in technical skills and analyzed concurrent verbal protocols to identify health information seekers’ cognitive strategies and attitudes. Results Our main findings relate to (1) attitudes: health information seekers in both cohorts doubted the quality of information retrieved online; among poorly skilled seekers, this was mainly because they doubted their skills to navigate vast amounts of information; once a website was accessed, quality concerns disappeared in both cohorts, (2) technical skills: skilled Web users effectively filtered information according to search intentions and data sources; less-skilled users were easily distracted by unrelated information, and (3) cognitive strategies: skilled Web users searched to inform themselves; less-skilled users searched to

  1. Confirmation Bias in Web-Based Search: A Randomized Online Study on the Effects of Expert Information and Social Tags on Information Search and Evaluation

    PubMed Central

    Oeberst, Aileen; Cress, Ulrike

    2014-01-01

    Background The public typically believes psychotherapy to be more effective than pharmacotherapy for depression treatments. This is not consistent with current scientific evidence, which shows that both types of treatment are about equally effective. Objective The study investigates whether this bias towards psychotherapy guides online information search and whether the bias can be reduced by explicitly providing expert information (in a blog entry) and by providing tag clouds that implicitly reveal experts’ evaluations. Methods A total of 174 participants completed a fully automated Web-based study after we invited them via mailing lists. First, participants read two blog posts by experts that either challenged or supported the bias towards psychotherapy. Subsequently, participants searched for information about depression treatment in an online environment that provided more experts’ blog posts about the effectiveness of treatments based on alleged research findings. These blogs were organized in a tag cloud; both psychotherapy tags and pharmacotherapy tags were popular. We measured tag and blog post selection, efficacy ratings of the presented treatments, and participants’ treatment recommendation after information search. Results Participants demonstrated a clear bias towards psychotherapy (mean 4.53, SD 1.99) compared to pharmacotherapy (mean 2.73, SD 2.41; t 173=7.67, P<.001, d=0.81) when rating treatment efficacy prior to the experiment. Accordingly, participants exhibited biased information search and evaluation. This bias was significantly reduced, however, when participants were exposed to tag clouds with challenging popular tags. Participants facing popular tags challenging their bias (n=61) showed significantly less biased tag selection (F 2,168=10.61, P<.001, partial eta squared=0.112), blog post selection (F 2,168=6.55, P=.002, partial eta squared=0.072), and treatment efficacy ratings (F 2,168=8.48, P<.001, partial eta squared=0.092), compared

  2. Biomedical ultrasonoscope

    NASA Technical Reports Server (NTRS)

    Lee, R. D. (Inventor)

    1979-01-01

    The combination of a "C" mode scan electronics in a portable, battery powered biomedical ultrasonoscope having "A" and "M" mode scan electronics, the latter including a clock generator for generating clock pulses, a cathode ray tube having X, Y and Z axis inputs, a sweep generator connected between the clock generator and the X axis input of the cathode ray tube for generating a cathode ray sweep signal synchronized by the clock pulses, and a receiver adapted to be connected to the Z axis input of the cathode ray tube. The "C" mode scan electronics comprises a plurality of transducer elements arranged in a row and adapted to be positioned on the skin of the patient's body for converting a pulsed electrical signal to a pulsed ultrasonic signal, radiating the ultrasonic signal into the patient's body, picking up the echoes reflected from interfaces in the patient's body and converting the echoes to electrical signals; a plurality of transmitters, each transmitter being coupled to a respective transducer for transmitting a pulsed electrical signal thereto and for transmitting the converted electrical echo signals directly to the receiver, a sequencer connected between the clock generator and the plurality of transmitters and responsive to the clock pulses for firing the transmitters in cyclic order; and a staircase voltage generator connected between the clock generator and the Y axis input of the cathode ray tube for generating a staircase voltage having steps synchronized by the clock pulses.

  3. A New Model of Information Behaviour Based on the Search Situation Transition Schema

    ERIC Educational Resources Information Center

    Pharo, Nils

    2004-01-01

    This paper presents a conceptual model of information behaviour. The model is part of the Search Situation Transition method schema. The method schema is developed to discover and analyse interplay between phenomena traditionally analysed as factors influencing either information retrieval or information seeking. In this paper the focus is on the…

  4. Visual Working Memory Supports the Inhibition of Previously Processed Information: Evidence from Preview Search

    ERIC Educational Resources Information Center

    Al-Aidroos, Naseem; Emrich, Stephen M.; Ferber, Susanne; Pratt, Jay

    2012-01-01

    In four experiments we assessed whether visual working memory (VWM) maintains a record of previously processed visual information, allowing old information to be inhibited, and new information to be prioritized. Specifically, we evaluated whether VWM contributes to the inhibition (i.e., visual marking) of previewed distractors in a preview search.…

  5. Constructing Uniform Resource Locators (URLs) for Searching the Marine Realms Information Bank

    USGS Publications Warehouse

    Linck, Guthrie A.; Allwardt, Alan O.; Lightsom, Frances L.

    2009-01-01

    The Marine Realms Information Bank (MRIB) is a digital library that provides access to free online scientific information about the oceans and coastal regions. To search its collection, MRIB uses a Common Gateway Interface (CGI) program, which allows automated search requests using Uniform Resource Locators (URLs). This document provides an overview of how to construct URLs to execute MRIB queries. The parameters listed allow detailed control of which records are retrieved, how they are returned, and how their display is formatted.

  6. [Construction and operation of Internet Search Engine specialized in information on asthma. A Search Engine-based investigation to identify asthma-related information needed by Internet users].

    PubMed

    Saito, Naruo

    2003-12-01

    To support asthmatic patients in collecting information through the Internet, we have constructed and operated a search engine specialized in asthma-related information making use of the search engine software available free of charge and other programs. A questionnaire was attached to the bottom of the Web page presenting the search results, asking the users to respond to several questions. During the three-year period since its start of operation on June 1, 2000, there was 66689 visits to this site and 786 responses to the questionnaire were collected. Of all respondents, 19.3% were medical professionals, 63.7% were patients or their family members, and 11.3% belonged to the other categories (5.3% did not specify their position). In each of these three user groups, only about half of the users were able to find a route to the information they needed. This seems to reflect the absence of adequate asthma-related information sources on the Internet in Japanese language. However, more than 70% of all users in each group answered that this search engine site was useful. PMID:14739773

  7. Biomedical term mapping databases.

    PubMed

    Wren, Jonathan D; Chang, Jeffrey T; Pustejovsky, James; Adar, Eytan; Garner, Harold R; Altman, Russ B

    2005-01-01

    Longer words and phrases are frequently mapped onto a shorter form such as abbreviations or acronyms for efficiency of communication. These abbreviations are pervasive in all aspects of biology and medicine and as the amount of biomedical literature grows, so does the number of abbreviations and the average number of definitions per abbreviation. Even more confusing, different authors will often abbreviate the same word/phrase differently. This ambiguity impedes our ability to retrieve information, integrate databases and mine textual databases for content. Efforts to standardize nomenclature, especially those doing so retrospectively, need to be aware of different abbreviatory mappings and spelling variations. To address this problem, there have been several efforts to develop computer algorithms to identify the mapping of terms between short and long form within a large body of literature. To date, four such algorithms have been applied to create online databases that comprehensively map biomedical terms and abbreviations within MEDLINE: ARGH (http://lethargy.swmed.edu/ARGH/argh.asp), the Stanford Biomedical Abbreviation Server (http://bionlp.stanford.edu/abbreviation/), AcroMed (http://medstract.med.tufts.edu/acro1.1/index.htm) and SaRAD (http://www.hpl.hp.com/research/idl/projects/abbrev.html). In addition to serving as useful computational tools, these databases serve as valuable references that help biologists keep up with an ever-expanding vocabulary of terms. PMID:15608198

  8. Disease Related Knowledge Summarization Based on Deep Graph Search

    PubMed Central

    Wu, Xiaofang; Yang, Zhihao; Li, ZhiHeng; Lin, Hongfei; Wang, Jian

    2015-01-01

    The volume of published biomedical literature on disease related knowledge is expanding rapidly. Traditional information retrieval (IR) techniques, when applied to large databases such as PubMed, often return large, unmanageable lists of citations that do not fulfill the searcher's information needs. In this paper, we present an approach to automatically construct disease related knowledge summarization from biomedical literature. In this approach, firstly Kullback-Leibler Divergence combined with mutual information metric is used to extract disease salient information. Then deep search based on depth first search (DFS) is applied to find hidden (indirect) relations between biomedical entities. Finally random walk algorithm is exploited to filter out the weak relations. The experimental results show that our approach achieves a precision of 60% and a recall of 61% on salient information extraction for Carcinoma of bladder and outperforms the method of Combo. PMID:26413521

  9. Global polar geospatial information service retrieval based on search engine and ontology reasoning

    USGS Publications Warehouse

    Chen, Nengcheng; E, Dongcheng; Di, Liping; Gong, Jianya; Chen, Zeqiang

    2007-01-01

    In order to improve the access precision of polar geospatial information service on web, a new methodology for retrieving global spatial information services based on geospatial service search and ontology reasoning is proposed, the geospatial service search is implemented to find the coarse service from web, the ontology reasoning is designed to find the refined service from the coarse service. The proposed framework includes standardized distributed geospatial web services, a geospatial service search engine, an extended UDDI registry, and a multi-protocol geospatial information service client. Some key technologies addressed include service discovery based on search engine and service ontology modeling and reasoning in the Antarctic geospatial context. Finally, an Antarctica multi protocol OWS portal prototype based on the proposed methodology is introduced.

  10. PhysiomeSpace: digital library service for biomedical data.

    PubMed

    Testi, Debora; Quadrani, Paolo; Viceconti, Marco

    2010-06-28

    Every research laboratory has a wealth of biomedical data locked up, which, if shared with other experts, could dramatically improve biomedical and healthcare research. With the PhysiomeSpace service, it is now possible with a few clicks to share with selected users biomedical data in an easy, controlled and safe way. The digital library service is managed using a client-server approach. The client application is used to import, fuse and enrich the data information according to the PhysiomeSpace resource ontology and upload/download the data to the library. The server services are hosted on the Biomed Town community portal, where through a web interface, the user can complete the metadata curation and share and/or publish the data resources. A search service capitalizes on the domain ontology and on the enrichment of metadata for each resource, providing a powerful discovery environment. Once the users have found the data resources they are interested in, they can add them to their basket, following a metaphor popular in e-commerce web sites. When all the necessary resources have been selected, the user can download the basket contents into the client application. The digital library service is now in beta and open to the biomedical research community. PMID:20478910