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Sample records for biomedical information searching

  1. Complementary use of the SciSearch database for improved biomedical information searching.

    PubMed Central

    Brown, C M

    1998-01-01

    The use of at least two complementary online biomedical databases is generally considered critical for biomedical scientists seeking to keep fully abreast of recent research developments as well as to retrieve the highest number of relevant citations possible. Although the National Library of Medicine's MEDLINE is usually the database of choice, this paper illustrates the benefits of using another database, the Institute for Scientific Information's SciSearch, when conducting a biomedical information search. When a simple query about red wine consumption and coronary artery disease was posed simultaneously in both MEDLINE and SciSearch, a greater number of relevant citations were retrieved through SciSearch. This paper also provides suggestions for carrying out a comprehensive biomedical literature search in a rapid and efficient manner by using SciSearch in conjunction with MEDLINE. PMID:9549014

  2. 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.

  3. [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.

  4. Developing a search engine for pharmacotherapeutic information that is not published in biomedical journals.

    PubMed

    Do Pazo-Oubiña, F; Calvo Pita, C; Puigventós Latorre, F; Periañez-Párraga, L; Ventayol Bosch, P

    2011-01-01

    To identify publishers of pharmacotherapeutic information not found in biomedical journals that focuses on evaluating and providing advice on medicines and to develop a search engine to access this information. Compiling web sites that publish information on the rational use of medicines and have no commercial interests. Free-access web sites in Spanish, Galician, Catalan or English. Designing a search engine using the Google "custom search" application. Overall 159 internet addresses were compiled and were classified into 9 labels. We were able to recover the information from the selected sources using a search engine, which is called "AlquimiA" and available from http://www.elcomprimido.com/FARHSD/AlquimiA.htm. The main sources of pharmacotherapeutic information not published in biomedical journals were identified. The search engine is a useful tool for searching and accessing "grey literature" on the internet. Copyright © 2010 SEFH. Published by Elsevier Espana. All rights reserved.

  5. BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines.

    PubMed

    Jácome, Alberto G; Fdez-Riverola, Florentino; Lourenço, Anália

    2016-07-01

    meaningful to that particular scope of research. Conversely, indirect concept associations, i.e. concepts related by other intermediary concepts, can be useful to integrate information from different studies and look into non-trivial relations. The BIOMedical Search Engine Framework supports the development of domain-specific search engines. The key strengths of the framework are modularity and extensibilityin terms of software design, the use of open-source consolidated Web technologies, and the ability to integrate any number of biomedical text mining tools and information resources. Currently, the Smart Drug Search keeps over 1,186,000 documents, containing more than 11,854,000 annotations for 77,200 different concepts. The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Information extraction from biomedical text.

    PubMed

    Hobbs, Jerry R

    2002-08-01

    Information extraction is the process of scanning text for information relevant to some interest, including extracting entities, relations, and events. It requires deeper analysis than key word searches, but its aims fall short of the very hard and long-term problem of full text understanding. Information extraction represents a midpoint on this spectrum, where the aim is to capture structured information without sacrificing feasibility. One of the key ideas in this technology is to separate processing into several stages, in cascaded finite-state transducers. The earlier stages recognize smaller linguistic objects and work in a largely domain-independent fashion. The later stages take these linguistic objects as input and find domain-dependent patterns among them. There are now initial efforts to apply this technology to biomedical text. In other domains, the technology plateaued at about 60% recall and precision. Even if applications to biomedical text do no better than this, they could still prove to be of immense help to curatorial activities.

  7. 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.

  8. 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

  9. 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

    Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Siążnik, Artur

    2013-03-01

    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. 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. search GenBank extends standard capabilities of the

  10. A Commentary on the Biomedical Information System

    ERIC Educational Resources Information Center

    Stokes, Joseph, III; Hayes, Robert M.

    1970-01-01

    The Biomedical Information System is described as one which includes closed intermediate and open data, mobilizing all biomedical information for physicians, teachers, students and administrators. (Editor/IE)

  11. TPX: Biomedical literature search made easy

    PubMed Central

    Joseph, Thomas; Saipradeep, Vangala G; Raghavan, Ganesh Sekar Venkat; Srinivasan, Rajgopal; Rao, Aditya; Kotte, Sujatha; Sivadasan, Naveen

    2012-01-01

    TPX is a web-based PubMed search enhancement tool that enables faster article searching using analysis and exploration features. These features include identification of relevant biomedical concepts from search results with linkouts to source databases, concept based article categorization, concept assisted search and filtering, query refinement. A distinguishing feature here is the ability to add user-defined concept names and/or concept types for named entity recognition. The tool allows contextual exploration of knowledge sources by providing concept association maps derived from the MEDLINE repository. It also has a full-text search mode that can be configured on request to access local text repositories, incorporating entity co-occurrence search at sentence/paragraph levels. Local text files can also be analyzed on-the-fly. Availability http://tpx.atc.tcs.com/ PMID:22829734

  12. TPX: Biomedical literature search made easy.

    PubMed

    Joseph, Thomas; Saipradeep, Vangala G; Raghavan, Ganesh Sekar Venkat; Srinivasan, Rajgopal; Rao, Aditya; Kotte, Sujatha; Sivadasan, Naveen

    2012-01-01

    TPX is a web-based PubMed search enhancement tool that enables faster article searching using analysis and exploration features. These features include identification of relevant biomedical concepts from search results with linkouts to source databases, concept based article categorization, concept assisted search and filtering, query refinement. A distinguishing feature here is the ability to add user-defined concept names and/or concept types for named entity recognition. The tool allows contextual exploration of knowledge sources by providing concept association maps derived from the MEDLINE repository. It also has a full-text search mode that can be configured on request to access local text repositories, incorporating entity co-occurrence search at sentence/paragraph levels. Local text files can also be analyzed on-the-fly. http://tpx.atc.tcs.com

  13. BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature

    PubMed Central

    Lee, Kyubum; Choi, Jaehoon; Kim, Seongsoon; Jeon, Minji; Lim, Sangrak; Choi, Donghee; Kim, Sunkyu; Tan, Aik-Choon

    2016-01-01

    As the volume of publications rapidly increases, searching for relevant information from the literature becomes more challenging. To complement standard search engines such as PubMed, it is desirable to have an advanced search tool that directly returns relevant biomedical entities such as targets, drugs, and mutations rather than a long list of articles. Some existing tools submit a query to PubMed and process retrieved abstracts to extract information at query time, resulting in a slow response time and limited coverage of only a fraction of the PubMed corpus. Other tools preprocess the PubMed corpus to speed up the response time; however, they are not constantly updated, and thus produce outdated results. Further, most existing tools cannot process sophisticated queries such as searches for mutations that co-occur with query terms in the literature. To address these problems, we introduce BEST, a biomedical entity search tool. BEST returns, as a result, a list of 10 different types of biomedical entities including genes, diseases, drugs, targets, transcription factors, miRNAs, and mutations that are relevant to a user’s query. To the best of our knowledge, BEST is the only system that processes free text queries and returns up-to-date results in real time including mutation information in the results. BEST is freely accessible at http://best.korea.ac.kr. PMID:27760149

  14. BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature.

    PubMed

    Lee, Sunwon; Kim, Donghyeon; Lee, Kyubum; Choi, Jaehoon; Kim, Seongsoon; Jeon, Minji; Lim, Sangrak; Choi, Donghee; Kim, Sunkyu; Tan, Aik-Choon; Kang, Jaewoo

    2016-01-01

    As the volume of publications rapidly increases, searching for relevant information from the literature becomes more challenging. To complement standard search engines such as PubMed, it is desirable to have an advanced search tool that directly returns relevant biomedical entities such as targets, drugs, and mutations rather than a long list of articles. Some existing tools submit a query to PubMed and process retrieved abstracts to extract information at query time, resulting in a slow response time and limited coverage of only a fraction of the PubMed corpus. Other tools preprocess the PubMed corpus to speed up the response time; however, they are not constantly updated, and thus produce outdated results. Further, most existing tools cannot process sophisticated queries such as searches for mutations that co-occur with query terms in the literature. To address these problems, we introduce BEST, a biomedical entity search tool. BEST returns, as a result, a list of 10 different types of biomedical entities including genes, diseases, drugs, targets, transcription factors, miRNAs, and mutations that are relevant to a user's query. To the best of our knowledge, BEST is the only system that processes free text queries and returns up-to-date results in real time including mutation information in the results. BEST is freely accessible at http://best.korea.ac.kr.

  15. 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.

  16. BOSS: context-enhanced search for biomedical objects

    PubMed Central

    2012-01-01

    Background There exist many academic search solutions and most of them can be put on either ends of spectrum: general-purpose search and domain-specific "deep" search systems. The general-purpose search systems, such as PubMed, offer flexible query interface, but churn out a list of matching documents that users have to go through the results in order to find the answers to their queries. On the other hand, the "deep" search systems, such as PPI Finder and iHOP, return the precompiled results in a structured way. Their results, however, are often found only within some predefined contexts. In order to alleviate these problems, we introduce a new search engine, BOSS, Biomedical Object Search System. Methods Unlike the conventional search systems, BOSS indexes segments, rather than documents. A segment refers to a Maximal Coherent Semantic Unit (MCSU) such as phrase, clause or sentence that is semantically coherent in the given context (e.g., biomedical objects or their relations). For a user query, BOSS finds all matching segments, identifies the objects appearing in those segments, and aggregates the segments for each object. Finally, it returns the ranked list of the objects along with their matching segments. Results The working prototype of BOSS is available at http://boss.korea.ac.kr. The current version of BOSS has indexed abstracts of more than 20 million articles published during last 16 years from 1996 to 2011 across all science disciplines. Conclusion BOSS fills the gap between either ends of the spectrum by allowing users to pose context-free queries and by returning a structured set of results. Furthermore, BOSS exhibits the characteristic of good scalability, just as with conventional document search engines, because it is designed to use a standard document-indexing model with minimal modifications. Considering the features, BOSS notches up the technological level of traditional solutions for search on biomedical information. PMID:22595092

  17. BOSS: context-enhanced search for biomedical objects.

    PubMed

    Choi, Jaehoon; Kim, Donghyeon; Kim, Seongsoon; Lee, Sunwon; Lee, Kyubum; Kang, Jaewoo

    2012-04-30

    There exist many academic search solutions and most of them can be put on either ends of spectrum: general-purpose search and domain-specific "deep" search systems. The general-purpose search systems, such as PubMed, offer flexible query interface, but churn out a list of matching documents that users have to go through the results in order to find the answers to their queries. On the other hand, the "deep" search systems, such as PPI Finder and iHOP, return the precompiled results in a structured way. Their results, however, are often found only within some predefined contexts. In order to alleviate these problems, we introduce a new search engine, BOSS, Biomedical Object Search System. Unlike the conventional search systems, BOSS indexes segments, rather than documents. A segment refers to a Maximal Coherent Semantic Unit (MCSU) such as phrase, clause or sentence that is semantically coherent in the given context (e.g., biomedical objects or their relations). For a user query, BOSS finds all matching segments, identifies the objects appearing in those segments, and aggregates the segments for each object. Finally, it returns the ranked list of the objects along with their matching segments. The working prototype of BOSS is available at http://boss.korea.ac.kr. The current version of BOSS has indexed abstracts of more than 20 million articles published during last 16 years from 1996 to 2011 across all science disciplines. BOSS fills the gap between either ends of the spectrum by allowing users to pose context-free queries and by returning a structured set of results. Furthermore, BOSS exhibits the characteristic of good scalability, just as with conventional document search engines, because it is designed to use a standard document-indexing model with minimal modifications. Considering the features, BOSS notches up the technological level of traditional solutions for search on biomedical information.

  18. 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

  19. On-line biomedical databases-the best source for quick search of the scientific information in the biomedicine.

    PubMed

    Masic, Izet; Milinovic, Katarina

    2012-06-01

    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.

  20. 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

  1. Electronic biomedical literature search for budding researcher.

    PubMed

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

    2013-09-01

    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.

  2. The Information Search

    ERIC Educational Resources Information Center

    Doraiswamy, Uma

    2011-01-01

    This paper in the form of story discusses a college student's information search process. In this story we see Kuhlthau's information search process: initiation, selection, exploration, formulation, collection, and presentation. Katie is a student who goes in search of information for her class research paper. Katie's class readings, her interest…

  3. 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

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

    PubMed

    Masseroli, Marco; Picozzi, Matteo; Ghisalberti, Giorgio; Ceri, Stefano

    2014-01-01

    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. 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. 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 fundamental for Life Science data

  5. 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…

  6. Improve Biomedical Information Retrieval using Modified Learning to Rank Methods.

    PubMed

    Xu, Bo; Lin, Hongfei; Lin, Yuan; Ma, Yunlong; Yang, Liang; Wang, Jian; Yang, Zhihao

    2016-06-14

    In these years, the number of biomedical articles has increased exponentially, which becomes a problem for biologists to capture all the needed information manually. Information retrieval technologies, as the core of search engines, can deal with the problem automatically, providing users with the needed information. However, it is a great challenge to apply these technologies directly for biomedical retrieval, because of the abundance of domain specific terminologies. To enhance biomedical retrieval, we propose a novel framework based on learning to rank. Learning to rank is a series of state-of-the-art information retrieval techniques, and has been proved effective in many information retrieval tasks. In the proposed framework, we attempt to tackle the problem of the abundance of terminologies by constructing ranking models, which focus on not only retrieving the most relevant documents, but also diversifying the searching results to increase the completeness of the resulting list for a given query. In the model training, we propose two novel document labeling strategies, and combine several traditional retrieval models as learning features. Besides, we also investigate the usefulness of different learning to rank approaches in our framework. Experimental results on TREC Genomics datasets demonstrate the effectiveness of our framework for biomedical information retrieval.

  7. The Development of Specialized Biomedical Information.

    ERIC Educational Resources Information Center

    Ginn, David S.

    1993-01-01

    Discussion of specialized biomedical information and its management and dissemination focuses on the development of information concerning AIDS (Acquired Immune Deficiency Syndrome). Topics addressed include services to specialized user groups; selection, collection, and information evaluation in libraries; AIDS terminology; recent developments in…

  8. Mining biomarker information in biomedical literature

    PubMed Central

    2012-01-01

    Background For selection and evaluation of potential biomarkers, inclusion of already published information is of utmost importance. In spite of significant advancements in text- and data-mining techniques, the vast knowledge space of biomarkers in biomedical text has remained unexplored. Existing named entity recognition approaches are not sufficiently selective for the retrieval of biomarker information from the literature. The purpose of this study was to identify textual features that enhance the effectiveness of biomarker information retrieval for different indication areas and diverse end user perspectives. Methods A biomarker terminology was created and further organized into six concept classes. Performance of this terminology was optimized towards balanced selectivity and specificity. The information retrieval performance using the biomarker terminology was evaluated based on various combinations of the terminology's six classes. Further validation of these results was performed on two independent corpora representing two different neurodegenerative diseases. Results The current state of the biomarker terminology contains 119 entity classes supported by 1890 different synonyms. The result of information retrieval shows improved retrieval rate of informative abstracts, which is achieved by including clinical management terms and evidence of gene/protein alterations (e.g. gene/protein expression status or certain polymorphisms) in combination with disease and gene name recognition. When additional filtering through other classes (e.g. diagnostic or prognostic methods) is applied, the typical high number of unspecific search results is significantly reduced. The evaluation results suggest that this approach enables the automated identification of biomarker information in the literature. A demo version of the search engine SCAIView, including the biomarker retrieval, is made available to the public through http

  9. Kuhlthau's Information Search Process.

    ERIC Educational Resources Information Center

    Shannon, Donna

    2002-01-01

    Explains Kuhlthau's Information Search Process (ISP) model which is based on a constructivist view of learning and provides a framework for school library media specialists for the design of information services and instruction. Highlights include a shift from library skills to information skills; attitudes; process approach; and an interview with…

  10. Semantic Predications for Complex Information Needs in Biomedical Literature

    PubMed Central

    Cameron, Delroy; Kavuluru, Ramakanth; Bodenreider, Olivier; Mendes, Pablo N.; Sheth, Amit P.; Thirunarayan, Krishnaprasad

    2015-01-01

    Many complex information needs that arise in biomedical disciplines require exploring multiple documents in order to obtain information. While traditional information retrieval techniques that return a single ranked list of documents are quite common for such tasks, they may not always be adequate. The main issue is that ranked lists typically impose a significant burden on users to filter out irrelevant documents. Additionally, users must intuitively reformulate their search query when relevant documents have not been not highly ranked. Furthermore, even after interesting documents have been selected, very few mechanisms exist that enable document-to-document transitions. In this paper, we demonstrate the utility of assertions extracted from biomedical text (called semantic predications) to facilitate retrieving relevant documents for complex information needs. Our approach offers an alternative to query reformulation by establishing a framework for transitioning from one document to another. We evaluate this novel knowledge-driven approach using precision and recall metrics on the 2006 TREC Genomics Track. PMID:25699291

  11. 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;…

  12. Semantic similarity measure in biomedical domain leverage web search engine.

    PubMed

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

    2010-01-01

    Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

  13. [The need for information in biomedical research].

    PubMed

    Kumate, J

    1981-01-01

    This paper focuses on the need of every researcher to be informed on advances in his field. It reviews the means available for keeping abreast of developments in a specific area of scientific inquiry. In the author's view, articles in reference journals on a specific specialty are the best source of information. However, the interval between the writing and publication of a scientific paper is sometimes long, which poses a considerable impediment to the use of the traditional media as a means of keeping up. He also examines the limitations of information in biomedical research and reviews the characteristics of this research in Latin America. Finally, he makes a number of recommendations for improving scientific communications and making the most of the services of national and international information dissemination systems.

  14. 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.

  15. 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

  16. Undergraduate Students' Information Search Practices

    ERIC Educational Resources Information Center

    Nikolopoulou, Kleopatra; Gialamas, Vasilis

    2011-01-01

    This paper investigates undergraduate students' information search practices. The subjects were 250 undergraduate students from two university departments in Greece, and a questionnaire was used to document their search practices. The results showed that the Web was the primary information system searched in order to find information for…

  17. 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.

  18. 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.

  19. 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.

  20. Should we search Chinese biomedical databases when performing systematic reviews?

    PubMed

    Cohen, Jérémie F; Korevaar, Daniël A; Wang, Junfeng; Spijker, René; Bossuyt, Patrick M

    2015-03-06

    Chinese biomedical databases contain a large number of publications available to systematic reviewers, but it is unclear whether they are used for synthesizing the available evidence. We report a case of two systematic reviews on the accuracy of anti-cyclic citrullinated peptide for diagnosing rheumatoid arthritis. In one of these, the authors did not search Chinese databases; in the other, they did. We additionally assessed the extent to which Cochrane reviewers have searched Chinese databases in a systematic overview of the Cochrane Library (inception to 2014). The two diagnostic reviews included a total of 269 unique studies, but only 4 studies were included in both reviews. The first review included five studies published in the Chinese language (out of 151) while the second included 114 (out of 118). The summary accuracy estimates from the two reviews were comparable. Only 243 of the published 8,680 Cochrane reviews (less than 3%) searched one or more of the five major Chinese databases. These Chinese databases index about 2,500 journals, of which less than 6% are also indexed in MEDLINE. All 243 Cochrane reviews evaluated an intervention, 179 (74%) had at least one author with a Chinese affiliation; 118 (49%) addressed a topic in complementary or alternative medicine. Although searching Chinese databases may lead to the identification of a large amount of additional clinical evidence, Cochrane reviewers have rarely included them in their search strategy. We encourage future initiatives to evaluate more systematically the relevance of searching Chinese databases, as well as collaborative efforts to allow better incorporation of Chinese resources in systematic reviews.

  1. PubMed and beyond: a survey of web tools for searching biomedical literature

    PubMed Central

    Lu, Zhiyong

    2011-01-01

    The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search PMID:21245076

  2. Supporting inter-topic entity search for biomedical Linked Data based on heterogeneous relationships.

    PubMed

    Zong, Nansu; Lee, Sungin; Ahn, Jinhyun; Kim, Hong-Gee

    2017-08-01

    The keyword-based entity search restricts search space based on the preference of search. When given keywords and preferences are not related to the same biomedical topic, existing biomedical Linked Data search engines fail to deliver satisfactory results. This research aims to tackle this issue by supporting an inter-topic search-improving search with inputs, keywords and preferences, under different topics. This study developed an effective algorithm in which the relations between biomedical entities were used in tandem with a keyword-based entity search, Siren. The algorithm, PERank, which is an adaptation of Personalized PageRank (PPR), uses a pair of input: (1) search preferences, and (2) entities from a keyword-based entity search with a keyword query, to formalize the search results on-the-fly based on the index of the precomputed Individual Personalized PageRank Vectors (IPPVs). Our experiments were performed over ten linked life datasets for two query sets, one with keyword-preference topic correspondence (intra-topic search), and the other without (inter-topic search). The experiments showed that the proposed method achieved better search results, for example a 14% increase in precision for the inter-topic search than the baseline keyword-based search engine. The proposed method improved the keyword-based biomedical entity search by supporting the inter-topic search without affecting the intra-topic search based on the relations between different entities. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. An information technology emphasis in biomedical informatics education.

    PubMed

    Kane, Michael D; Brewer, Jeffrey L

    2007-02-01

    Unprecedented growth in the interdisciplinary domain of biomedical informatics reflects the recent advancements in genomic sequence availability, high-content biotechnology screening systems, as well as the expectations of computational biology to command a leading role in drug discovery and disease characterization. These forces have moved much of life sciences research almost completely into the computational domain. Importantly, educational training in biomedical informatics has been limited to students enrolled in the life sciences curricula, yet much of the skills needed to succeed in biomedical informatics involve or augment training in information technology curricula. This manuscript describes the methods and rationale for training students enrolled in information technology curricula in the field of biomedical informatics, which augments the existing information technology curriculum and provides training on specific subjects in Biomedical Informatics not emphasized in bioinformatics courses offered in life science programs, and does not require prerequisite courses in the life sciences.

  4. Information Searching Behavior of Physicians.

    ERIC Educational Resources Information Center

    Trueswell, R.W.; Rubenstein, A.H.

    The purpose of this study was to provide some preliminary data about the information-searching behavior of the physician in order to (1) facilitate the development of models describing the search behavior and (2) provide the behavioral data necessary for the development of effective information retrieval systems for use by the medical profession.…

  5. 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…

  6. 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…

  7. 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

  8. 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…

  9. 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

  10. 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. © The Author(s) 2016. Published by Oxford University Press.

  11. Sequential Result Refinement for Searching the Biomedical Literature ☆

    PubMed Central

    Herskovic, J. R.; Iyengar, M. S.

    2009-01-01

    Information overload is a problem for users of MEDLINE, the database of biomedical literature that indexes over 17 million articles. Various techniques have been developed to retrieve high quality or important articles. Some techniques rely on using the number of citations as a measurement of an article’s importance. Unfortunately, citation information is proprietary, expensive, and suffers from “citation lag.” MEDLINE users have a variety of information needs. Although some users require high recall, many users are looking for a “few good articles” on a topic. For these users, precision is more important than recall. We present and evaluate a method for identifying articles likely to be highly cited by using information available at the time of listing in MEDLINE. The method uses a score based on Medical Subject Headings (MeSH) terms, journal impact factor (JIF), and number of authors. This method can filter large MEDLINE result sets (>1,000 articles) returned by actual user queries to produce small, highly cited result sets. PMID:19272463

  12. [3D visualization and information interaction in biomedical applications].

    PubMed

    Pu, F; Fan, Y; Jiang, W; Zhang, M; Mak, A F; Chen, J

    2001-06-01

    3D visualization and virtual reality are important trend in the development of modern science and technology, and as well in the studies on biomedical engineering. This paper presents a computer procedure developed for 3D visualization in biomedical applications. The biomedical models are constructed in slice sequences based on polygon cells and information interaction is realized on the basis of OpenGL selection mode in particular consideration of the specialties in this field such as irregularity in geometry and complexity in material etc. The software developed has functions of 3D model construction and visualization, real-time modeling transformation, information interaction and so on. It could serve as useful platform for 3D visualization in biomedical engineering research.

  13. 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

  14. Using a search engine-based mutually reinforcing approach to assess the semantic relatedness of biomedical terms.

    PubMed

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

    2013-01-01

    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. 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. 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.

  15. Successive Searching: User Searches during Information Seeking (SIG USE).

    ERIC Educational Resources Information Center

    Spink, Amanda

    2000-01-01

    Presents a session abstract that included speakers discussing current studies in successive searching during the information seeking process. Highlights include mediated successive searching; end-user successive searching; designing information retrieval systems to support successive searching; and search histories for user support in legal…

  16. 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

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

    PubMed

    Campagne, Fabien

    2008-02-29

    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. 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. 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 protocols can fully substitute

  18. Crossing the chasm: information technology to biomedical informatics.

    PubMed

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

    2011-06-01

    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 Science 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 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 article 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.

  19. 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

  20. 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.

  1. Unsupervised discovery of information structure in biomedical documents.

    PubMed

    Kiela, Douwe; Guo, Yufan; Stenius, Ulla; Korhonen, Anna

    2015-04-01

    Information structure (IS) analysis is a text mining technique, which classifies text in biomedical articles into categories that capture different types of information, such as objectives, methods, results and conclusions of research. It is a highly useful technique that can support a range of Biomedical Text Mining tasks and can help readers of biomedical literature find information of interest faster, accelerating the highly time-consuming process of literature review. Several approaches to IS analysis have been presented in the past, with promising results in real-world biomedical tasks. However, all existing approaches, even weakly supervised ones, require several hundreds of hand-annotated training sentences specific to the domain in question. Because biomedicine is subject to considerable domain variation, such annotations are expensive to obtain. This makes the application of IS analysis across biomedical domains difficult. In this article, we investigate an unsupervised approach to IS analysis and evaluate the performance of several unsupervised methods on a large corpus of biomedical abstracts collected from PubMed. Our best unsupervised algorithm (multilevel-weighted graph clustering algorithm) performs very well on the task, obtaining over 0.70 F scores for most IS categories when applied to well-known IS schemes. This level of performance is close to that of lightly supervised IS methods and has proven sufficient to aid a range of practical tasks. Thus, using an unsupervised approach, IS could be applied to support a wide range of tasks across sub-domains of biomedicine. We also demonstrate that unsupervised learning brings novel insights into IS of biomedical literature and discovers information categories that are not present in any of the existing IS schemes. The annotated corpus and software are available at http://www.cl.cam.ac.uk/∼dk427/bio14info.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For

  2. NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources.

    PubMed

    Jonquet, Clement; Lependu, Paea; Falconer, Sean; Coulet, Adrien; Noy, Natalya F; Musen, Mark A; Shah, Nigam H

    2011-09-01

    The volume of publicly available data in biomedicine is constantly increasing. However, these data are stored in different formats and on different platforms. Integrating these data will enable us to facilitate the pace of medical discoveries by providing scientists with a unified view of this diverse information. Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index-a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources. The resources come from a variety of repositories maintained by organizations from around the world. We use a set of over 200 publicly available ontologies contributed by researchers in various domains to annotate the elements in these resources. We use the semantics that the ontologies encode, such as different properties of classes, the class hierarchies, and the mappings between ontologies, in order to improve the search experience for the Resource Index user. Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics "under the hood."

  3. NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources

    PubMed Central

    Jonquet, Clement; LePendu, Paea; Falconer, Sean; Coulet, Adrien; Noy, Natalya F.; Musen, Mark A.; Shah, Nigam H.

    2011-01-01

    The volume of publicly available data in biomedicine is constantly increasing. However, these data are stored in different formats and on different platforms. Integrating these data will enable us to facilitate the pace of medical discoveries by providing scientists with a unified view of this diverse information. Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index—a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources. The resources come from a variety of repositories maintained by organizations from around the world. We use a set of over 200 publicly available ontologies contributed by researchers in various domains to annotate the elements in these resources. We use the semantics that the ontologies encode, such as different properties of classes, the class hierarchies, and the mappings between ontologies, in order to improve the search experience for the Resource Index user. Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics “under the hood.” PMID:21918645

  4. 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

  5. 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.

  6. 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…

  7. Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search.

    PubMed

    Ji, Yanqing; Ying, Hao; Tran, John; Dews, Peter; Massanari, R Michael

    2016-07-19

    Finding highly relevant articles from biomedical databases is challenging not only because it is often difficult to accurately express a user's underlying intention through keywords but also because a keyword-based query normally returns a long list of hits with many citations being unwanted by the user. This paper proposes a novel biomedical literature search system, called BiomedSearch, which supports complex queries and relevance feedback. The system employed association mining techniques to build a k-profile representing a user's relevance feedback. More specifically, we developed a weighted interest measure and an association mining algorithm to find the strength of association between a query and each concept in the article(s) selected by the user as feedback. The top concepts were utilized to form a k-profile used for the next-round search. BiomedSearch relies on Unified Medical Language System (UMLS) knowledge sources to map text files to standard biomedical concepts. It was designed to support queries with any levels of complexity. A prototype of BiomedSearch software was made and it was preliminarily evaluated using the Genomics data from TREC (Text Retrieval Conference) 2006 Genomics Track. Initial experiment results indicated that BiomedSearch increased the mean average precision (MAP) for a set of queries. With UMLS and association mining techniques, BiomedSearch can effectively utilize users' relevance feedback to improve the performance of biomedical literature search.

  8. 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.

  9. 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. Copyright © 2013 Elsevier Inc. All rights reserved.

  10. Classifying and identifying servers for biomedical information retrieval.

    PubMed

    Patrick, T B; Springer, G K

    1994-01-01

    Useful retrieval of biomedical information from network information sources requires methods for organized access to those information sources. This access must be organized in terms of the information content of information sources and in terms of the discovery of the network location of those information sources. We have developed an approach to providing organized access to information sources based on a scheme of hierarchical classifiers and identifiers of the servers providing access to those information sources. This approach uses MeSH tree numbers as both classifiers and identifiers of servers. MeSH tree numbers are used to indicate the information content of servers, and also as OSF/DCE server identifiers. This allows the identity and location of a server providing access to a given information source to be determined from the information classification of that information source.

  11. Semantic reasoning with XML-based biomedical information models.

    PubMed

    O'Connor, Martin J; Das, Amar

    2010-01-01

    The Extensible Markup Language (XML) is increasingly being used for biomedical data exchange. The parallel growth in the use of ontologies in biomedicine presents opportunities for combining the two technologies to leverage the semantic reasoning services provided by ontology-based tools. There are currently no standardized approaches for taking XML-encoded biomedical information models and representing and reasoning with them using ontologies. To address this shortcoming, we have developed a workflow and a suite of tools for transforming XML-based information models into domain ontologies encoded using OWL. In this study, we applied semantics reasoning methods to these ontologies to automatically generate domain-level inferences. We successfully used these methods to develop semantic reasoning methods for information models in the HIV and radiological image domains.

  12. [The system of biomedical scientific information of Serbia].

    PubMed

    Dacić, M

    1995-09-01

    Building of the System of biomedical scientific information of Yugoslavia (SBMSI YU) began, by the end of 1980, and the system became operative officially in 1986. After the political disintegration of former Yugoslavia SBMSI of Serbia was formed. SBMSI is developed according to the policy of developing of the System of scientific technologic information of Serbia (SSTI S), and with technical support of SSTI S. Reconstruction of the System is done by using former SBMSI YU as a model. Unlike the former SBMSI YU, SBMSI S owns besides the database Biomedicina Serbica, three important databases: database of doctoral dissertations promoted at University Medical School in Belgrade in the period from 1955-1993, database of Master's theses promoted at the University School of Medicine in Belgrade from 1965-1993; A database of foreign biomedical periodicals in libraries of Serbia.

  13. 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…

  14. Supporting effective health and biomedical information retrieval and navigation: a novel facet view interface evaluation.

    PubMed

    Mu, Xiangming; Ryu, Hohyon; Lu, Kun

    2011-08-01

    There is a need to provide a more effective user interface to facilitate non-domain experts' health information seeking in authoritative online databases such as MEDLINE. We developed a new topic cluster based information navigation system called SimMed. Instead of offering a list of documents, SimMed presents users with a list of ranked clusters. Topically similar documents are grouped together to provide users with a better overview of the search results and to support exploration of similar literature within a cluster. We conducted an empirical user study to compare SimMed to a traditional document list based search interface. A total of 42 study participants were recruited to use both interfaces for health information exploration search tasks. The results showed that SimMed is more effective in terms of users' perceived topic knowledge changes and their engagement in user-system interactions. We also developed a new metric to assess users' efforts to find relevant citations. On average, users need significantly fewer clicks to find relevant information in SimMed than in the baseline system. Comments from study participants indicated that SimMed is more helpful in finding similar citations, providing related medical terms, and presenting better organized search results, particularly when the initial search is unsatisfactory. Findings from the study shed light on future health and biomedical information retrieval system and interface designs. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews

    PubMed Central

    2013-01-01

    Background The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. Methods The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. Results GS’ overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Conclusions Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to

  16. The comparative recall of Google Scholar versus PubMed in identical searches for biomedical systematic reviews: a review of searches used in systematic reviews.

    PubMed

    Bramer, Wichor M; Giustini, Dean; Kramer, Bianca Mr; Anderson, Pf

    2013-12-23

    The usefulness of Google Scholar (GS) as a bibliographic database for biomedical systematic review (SR) searching is a subject of current interest and debate in research circles. Recent research has suggested GS might even be used alone in SR searching. This assertion is challenged here by testing whether GS can locate all studies included in 21 previously published SRs. Second, it examines the recall of GS, taking into account the maximum number of items that can be viewed, and tests whether more complete searches created by an information specialist will improve recall compared to the searches used in the 21 published SRs. The authors identified 21 biomedical SRs that had used GS and PubMed as information sources and reported their use of identical, reproducible search strategies in both databases. These search strategies were rerun in GS and PubMed, and analyzed as to their coverage and recall. Efforts were made to improve searches that underperformed in each database. GS' overall coverage was higher than PubMed (98% versus 91%) and overall recall is higher in GS: 80% of the references included in the 21 SRs were returned by the original searches in GS versus 68% in PubMed. Only 72% of the included references could be used as they were listed among the first 1,000 hits (the maximum number shown). Practical precision (the number of included references retrieved in the first 1,000, divided by 1,000) was on average 1.9%, which is only slightly lower than in other published SRs. Improving searches with the lowest recall resulted in an increase in recall from 48% to 66% in GS and, in PubMed, from 60% to 85%. Although its coverage and precision are acceptable, GS, because of its incomplete recall, should not be used as a single source in SR searching. A specialized, curated medical database such as PubMed provides experienced searchers with tools and functionality that help improve recall, and numerous options in order to optimize precision. Searches for SRs should be

  17. Generalizability of hybrid search algorithms to map multiple biomedical vocabulary domains.

    PubMed

    Nachimuthu, Senthil K; Woolstenhulme, R Dean

    2006-01-01

    Hybrid text matching algorithms similar to those used for DNA sequencing were developed by 3M Health Information Systems to map a noisy legacy codeset to the 3M Healthcare Data Dictionary (3M HDD). Applying these techniques to map other biomedical vocabularies was briefly introduced in an earlier paper describing the algorithms. We now present results from successfully utilizing them to map different vocabularies across multiple biomedical domains, proving their generalizability.

  18. Generalizability of Hybrid Search Algorithms to Map Multiple Biomedical Vocabulary Domains

    PubMed Central

    Nachimuthu, Senthil K.; Woolstenhulme, R. Dean

    2006-01-01

    Hybrid text matching algorithms similar to those used for DNA sequencing were developed by 3M Health Information Systems to map a noisy legacy codeset to the 3M Healthcare Data Dictionary (3M HDD). Applying these techniques to map other biomedical vocabularies was briefly introduced in an earlier paper describing the algorithms [1]. We now present results from successfully utilizing them to map different vocabularies across multiple biomedical domains, proving their generalizability. PMID:17238661

  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. Improving biomedical information retrieval by linear combinations of different query expansion techniques.

    PubMed

    Abdulla, Ahmed AbdoAziz Ahmed; Lin, Hongfei; Xu, Bo; Banbhrani, Santosh Kumar

    2016-07-25

    Biomedical literature retrieval is becoming increasingly complex, and there is a fundamental need for advanced information retrieval systems. Information Retrieval (IR) programs scour unstructured materials such as text documents in large reserves of data that are usually stored on computers. IR is related to the representation, storage, and organization of information items, as well as to access. In IR one of the main problems is to determine which documents are relevant and which are not to the user's needs. Under the current regime, users cannot precisely construct queries in an accurate way to retrieve particular pieces of data from large reserves of data. Basic information retrieval systems are producing low-quality search results. In our proposed system for this paper we present a new technique to refine Information Retrieval searches to better represent the user's information need in order to enhance the performance of information retrieval by using different query expansion techniques and apply a linear combinations between them, where the combinations was linearly between two expansion results at one time. Query expansions expand the search query, for example, by finding synonyms and reweighting original terms. They provide significantly more focused, particularized search results than do basic search queries. The retrieval performance is measured by some variants of MAP (Mean Average Precision) and according to our experimental results, the combination of best results of query expansion is enhanced the retrieved documents and outperforms our baseline by 21.06 %, even it outperforms a previous study by 7.12 %. We propose several query expansion techniques and their combinations (linearly) to make user queries more cognizable to search engines and to produce higher-quality search results.

  1. 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.

  2. Psychological determinants of information searching activity.

    PubMed

    Gorunova, L

    2012-01-01

    The paper deals with the application of the activity theory in describing psychological determinants of the information searching activity. The notions of information behavior, information retrieval, information competence, information retrieval activity given in Russian and English scientific literature are compared. The research approach to the information retrieval activity based on the principles developed in the Russian theory of activity is described; and the fundamentals of G. Sukhodolsky's generalized conception of activity are presented for the first time. Analysis of empirical researches showed that specific features of information search depend on how the user evaluates information resources, information, conditions and results of search. Psychological determiners of information search may be detected as the system of evaluative alternatives, which is generated by the user during the process of his experience growth. We discovered that user's evaluation system is also related to his individual typological and personal regulative features and determines the choice of the search strategy.

  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. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. 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. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Optimal search filters for renal information in EMBASE.

    PubMed

    Iansavichus, Arthur V; Haynes, R Brian; Shariff, Salimah Z; Weir, Matthew; Wilczynski, Nancy L; McKibbon, Ann; Rehman, Faisal; Garg, Amit X

    2010-07-01

    EMBASE is a popular database used to retrieve biomedical information. Our objective was to develop and test search filters to help clinicians and researchers efficiently retrieve articles with renal information in EMBASE. We used a diagnostic test assessment framework because filters operate similarly to screening tests. We divided a sample of 5,302 articles from 39 journals into development and validation sets of articles. Information retrieval properties were assessed by treating each search filter as a "diagnostic test" or screening procedure for the detection of relevant articles. We tested the performance of 1,936,799 search filters made of unique renal terms and their combinations. REFERENCE STANDARD & OUTCOME: The reference standard was manual review of each article. We calculated the sensitivity and specificity of each filter to identify articles with renal information. The best renal filters consisted of multiple search terms, such as "renal replacement therapy," "renal," "kidney disease," and "proteinuria," and the truncated terms "kidney," "dialy," "neph," "glomerul," and "hemodial." These filters achieved peak sensitivities of 98.7% (95% CI, 97.9-99.6) and specificities of 98.5% (95% CI, 98.0-99.0). The retrieval performance of these filters remained excellent in the validation set of independent articles. The retrieval performance of any search will vary depending on the quality of all search concepts used, not just renal terms. We empirically developed and validated high-performance renal search filters for EMBASE. These filters can be programmed into the search engine or used on their own to improve the efficiency of searching.

  6. 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.

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

    PubMed

    Hu, Qinmin; Huang, Jimmy Xiangji; Hu, Xiaohua

    2012-06-11

    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. 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. 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 term associations. These latent

  8. Yale Image Finder (YIF): a new search engine for retrieving biomedical images.

    PubMed

    Xu, Songhua; McCusker, James; Krauthammer, Michael

    2008-09-01

    Yale Image Finder (YIF) is a publicly accessible search engine featuring a new way of retrieving biomedical images and associated papers based on the text carried inside the images. Image queries can also be issued against the image caption, as well as words in the associated paper abstract and title. A typical search scenario using YIF is as follows: a user provides few search keywords and the most relevant images are returned and presented in the form of thumbnails. Users can click on the image of interest to retrieve the high resolution image. In addition, the search engine will provide two types of related images: those that appear in the same paper, and those from other papers with similar image content. Retrieved images link back to their source papers, allowing users to find related papers starting with an image of interest. Currently, YIF has indexed over 140 000 images from over 34 000 open access biomedical journal papers. http://krauthammerlab.med.yale.edu/imagefinder/

  9. Searching biomedical databases on complementary medicine: the use of controlled vocabulary among authors, indexers and investigators.

    PubMed

    Murphy, Linda S; Reinsch, Sibylle; Najm, Wadie I; Dickerson, Vivian M; Seffinger, Michael A; Adams, Alan; Mishra, Shiraz I

    2003-07-07

    The optimal retrieval of a literature search in biomedicine depends on the appropriate use of Medical Subject Headings (MeSH), descriptors and keywords among authors and indexers. We hypothesized that authors, investigators and indexers in four biomedical databases are not consistent in their use of terminology in Complementary and Alternative Medicine (CAM). Based on a research question addressing the validity of spinal palpation for the diagnosis of neuromuscular dysfunction, we developed four search concepts with their respective controlled vocabulary and key terms. We calculated the frequency of MeSH, descriptors, and keywords used by authors in titles and abstracts in comparison to standard practices in semantic and analytic indexing in MEDLINE, MANTIS, CINAHL, and Web of Science. Multiple searches resulted in the final selection of 38 relevant studies that were indexed at least in one of the four selected databases. Of the four search concepts, validity showed the greatest inconsistency in terminology among authors, indexers and investigators. The use of spinal terms showed the greatest consistency. Of the 22 neuromuscular dysfunction terms provided by the investigators, 11 were not contained in the controlled vocabulary and six were never used by authors or indexers. Most authors did not seem familiar with the controlled vocabulary for validity in the area of neuromuscular dysfunction. Recently, standard glossaries have been developed to assist in the research development of manual medicine. Searching biomedical databases for CAM is challenging due to inconsistent use of controlled vocabulary and indexing procedures in different databases. A standard terminology should be used by investigators in conducting their search strategies and authors when writing titles, abstracts and submitting keywords for publications.

  10. Searching biomedical databases on complementary medicine: the use of controlled vocabulary among authors, indexers and investigators

    PubMed Central

    Murphy, Linda S; Reinsch, Sibylle; Najm, Wadie I; Dickerson, Vivian M; Seffinger, Michael A; Adams, Alan; Mishra, Shiraz I

    2003-01-01

    Background The optimal retrieval of a literature search in biomedicine depends on the appropriate use of Medical Subject Headings (MeSH), descriptors and keywords among authors and indexers. We hypothesized that authors, investigators and indexers in four biomedical databases are not consistent in their use of terminology in Complementary and Alternative Medicine (CAM). Methods Based on a research question addressing the validity of spinal palpation for the diagnosis of neuromuscular dysfunction, we developed four search concepts with their respective controlled vocabulary and key terms. We calculated the frequency of MeSH, descriptors, and keywords used by authors in titles and abstracts in comparison to standard practices in semantic and analytic indexing in MEDLINE, MANTIS, CINAHL, and Web of Science. Results Multiple searches resulted in the final selection of 38 relevant studies that were indexed at least in one of the four selected databases. Of the four search concepts, validity showed the greatest inconsistency in terminology among authors, indexers and investigators. The use of spinal terms showed the greatest consistency. Of the 22 neuromuscular dysfunction terms provided by the investigators, 11 were not contained in the controlled vocabulary and six were never used by authors or indexers. Most authors did not seem familiar with the controlled vocabulary for validity in the area of neuromuscular dysfunction. Recently, standard glossaries have been developed to assist in the research development of manual medicine. Conclusions Searching biomedical databases for CAM is challenging due to inconsistent use of controlled vocabulary and indexing procedures in different databases. A standard terminology should be used by investigators in conducting their search strategies and authors when writing titles, abstracts and submitting keywords for publications. PMID:12846931

  11. Information needs and information seeking in a biomedical research setting: a study of scientists and science administrators

    PubMed Central

    Grefsheim, Suzanne F.; Rankin, Jocelyn A.

    2007-01-01

    Objective: An information needs study of clinical specialists and biomedical researchers was conducted at the US National Institutes of Health (NIH) to inform library services and contribute to a broader understanding of information use in academic and research settings. Methods: A random stratified sample by job category of 500 NIH scientists was surveyed by telephone by an independent consultant using a standardized information industry instrument, augmented with locally developed questions. Results were analyzed for statistical significance using t- tests and chi square. Findings were compared with published studies and an aggregated dataset of information users in business, government, and health care from Outsell. Results: The study results highlighted similarities and differences with other studies and the industry standard, providing insights into user preferences, including new technologies. NIH scientists overwhelmingly used the NIH Library (424/500), began their searches at the library's Website rather than Google (P = < 0.001), were likely to seek information themselves (474/500), and valued desktop resources and services. Conclusion: While NIH staff work in a unique setting, they share some information characteristics with other researchers. The findings underscored the need to continue assessing specialized needs and seek innovative solutions. The study led to improvements or expansion of services such as developing a Website search engine, organizing gene sequence data, and assisting with manuscript preparation. PMID:17971890

  12. 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.

  13. Michigan Occupational Information System (MOIS) Structured Search.

    ERIC Educational Resources Information Center

    Michigan State Board of Education, Lansing.

    This guide leads users through a structured search of the Michigan Occupational Information System (MOIS). It is intended to help the user prepare a profile of interests and preferences that will be used in career exploration. The booklet asks the user to make choices in seven categories and to enter the responses on the MOIS Search Worksheet. The…

  14. 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…

  15. 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…

  16. 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…

  17. Personalized online information search and visualization

    PubMed Central

    Chen, Dongquan; Orthner, Helmuth F; Sell, Susan M

    2005-01-01

    Background The rapid growth of online publications such as the Medline and other sources raises the questions how to get the relevant information efficiently. It is important, for a bench scientist, e.g., to monitor related publications constantly. It is also important, for a clinician, e.g., to access the patient records anywhere and anytime. Although time-consuming, this kind of searching procedure is usually similar and simple. Likely, it involves a search engine and a visualization interface. Different words or combination reflects different research topics. The objective of this study is to automate this tedious procedure by recording those words/terms in a database and online sources, and use the information for an automated search and retrieval. The retrieved information will be available anytime and anywhere through a secure web server. Results We developed such a database that stored searching terms, journals and et al., and implement a piece of software for searching the medical subject heading-indexed sources such as the Medline and other online sources automatically. The returned information were stored locally, as is, on a server and visible through a Web-based interface. The search was performed daily or otherwise scheduled and the users logon to the website anytime without typing any words. The system has potentials to retrieve similarly from non-medical subject heading-indexed literature or a privileged information source such as a clinical information system. The issues such as security, presentation and visualization of the retrieved information were thus addressed. One of the presentation issues such as wireless access was also experimented. A user survey showed that the personalized online searches saved time and increased and relevancy. Handheld devices could also be used to access the stored information but less satisfactory. Conclusion The Web-searching software or similar system has potential to be an efficient tool for both bench scientists

  18. 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. Copyright © 2015 Central Police University.

  19. 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

  20. A passage retrieval method based on probabilistic information retrieval model and UMLS concepts in biomedical question answering.

    PubMed

    Sarrouti, Mourad; Ouatik El Alaoui, Said

    2017-04-01

    Passage retrieval, the identification of top-ranked passages that may contain the answer for a given biomedical question, is a crucial component for any biomedical question answering (QA) system. Passage retrieval in open-domain QA is a longstanding challenge widely studied over the last decades. However, it still requires further efforts in biomedical QA. In this paper, we present a new biomedical passage retrieval method based on Stanford CoreNLP sentence/passage length, probabilistic information retrieval (IR) model and UMLS concepts. In the proposed method, we first use our document retrieval system based on PubMed search engine and UMLS similarity to retrieve relevant documents to a given biomedical question. We then take the abstracts from the retrieved documents and use Stanford CoreNLP for sentence splitter to make a set of sentences, i.e., candidate passages. Using stemmed words and UMLS concepts as features for the BM25 model, we finally compute the similarity scores between the biomedical question and each of the candidate passages and keep the N top-ranked ones. Experimental evaluations performed on large standard datasets, provided by the BioASQ challenge, show that the proposed method achieves good performances compared with the current state-of-the-art methods. The proposed method significantly outperforms the current state-of-the-art methods by an average of 6.84% in terms of mean average precision (MAP). We have proposed an efficient passage retrieval method which can be used to retrieve relevant passages in biomedical QA systems with high mean average precision. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Improving the Search Environment: Informed Decision Making in the Search for Statistical Information.

    ERIC Educational Resources Information Center

    Haas, Stephanie W.

    2003-01-01

    Discusses information searching as a series of user decisions and considers the effects of the user's knowledge and the configuration of the information retrieval system. Investigates what the user needs to know to make informed search decisions at the United States Bureau of Labor Statistics Web site and describes user queries. (Author/LRW)

  2. Improving the Search Environment: Informed Decision Making in the Search for Statistical Information.

    ERIC Educational Resources Information Center

    Haas, Stephanie W.

    2003-01-01

    Discusses information searching as a series of user decisions and considers the effects of the user's knowledge and the configuration of the information retrieval system. Investigates what the user needs to know to make informed search decisions at the United States Bureau of Labor Statistics Web site and describes user queries. (Author/LRW)

  3. 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…

  4. A Part-Of-Speech term weighting scheme for biomedical information retrieval.

    PubMed

    Wang, Yanshan; Wu, Stephen; Li, Dingcheng; Mehrabi, Saeed; Liu, Hongfang

    2016-10-01

    In the era of digitalization, information retrieval (IR), which retrieves and ranks documents from large collections according to users' search queries, has been popularly applied in the biomedical domain. Building patient cohorts using electronic health records (EHRs) and searching literature for topics of interest are some IR use cases. Meanwhile, natural language processing (NLP), such as tokenization or Part-Of-Speech (POS) tagging, has been developed for processing clinical documents or biomedical literature. We hypothesize that NLP can be incorporated into IR to strengthen the conventional IR models. In this study, we propose two NLP-empowered IR models, POS-BoW and POS-MRF, which incorporate automatic POS-based term weighting schemes into bag-of-word (BoW) and Markov Random Field (MRF) IR models, respectively. In the proposed models, the POS-based term weights are iteratively calculated by utilizing a cyclic coordinate method where golden section line search algorithm is applied along each coordinate to optimize the objective function defined by mean average precision (MAP). In the empirical experiments, we used the data sets from the Medical Records track in Text REtrieval Conference (TREC) 2011 and 2012 and the Genomics track in TREC 2004. The evaluation on TREC 2011 and 2012 Medical Records tracks shows that, for the POS-BoW models, the mean improvement rates for IR evaluation metrics, MAP, bpref, and P@10, are 10.88%, 4.54%, and 3.82%, compared to the BoW models; and for the POS-MRF models, these rates are 13.59%, 8.20%, and 8.78%, compared to the MRF models. Additionally, we experimentally verify that the proposed weighting approach is superior to the simple heuristic and frequency based weighting approaches, and validate our POS category selection. Using the optimal weights calculated in this experiment, we tested the proposed models on the TREC 2004 Genomics track and obtained average of 8.63% and 10.04% improvement rates for POS-BoW and POS

  5. Natural experimental models: The global search for biomedical paradigms among traditional, modernizing, and modern populations

    PubMed Central

    Garruto, R. M.; Little, M. A.; James, G. D.; Brown, D. E.

    1999-01-01

    During the past four decades, biomedical scientists have slowly begun to recognize the unique opportunities for studying biomedical processes, disease etiology, and mechanisms of pathogenesis in populations with unusual genetic structures, physiological characteristics, focal endemic disease, or special circumstances. Such populations greatly extend our research capabilities and provide a natural laboratory for studying relationships among biobehavioral, genetic, and ecological processes that are involved in the development of disease. The models presented illustrate three different types of natural experiments: those occurring in traditionally living, modernizing, and modern populations. The examples are drawn from current research that involves population mechanisms of adaptation among East African Turkana pastoralists; a search for etiology and mechanisms of pathogenesis of an emerging disease among the Yakut people of Siberia; and psychosocial stress, hypertension, and cardiovascular disease in women working outside the home in New York City and among subpopulations in Hawaii. The models in general, and the examples in specific, represent natural laboratories in which relatively small intrapopulation differences and large interpopulation differences can be used to evaluate health and disease outcomes. PMID:10468644

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. A comparison of hypertext and Boolean access to biomedical information.

    PubMed Central

    Friedman, C. P.; Wildemuth, B. M.; Muriuki, M.; Gant, S. P.; Downs, S. M.; Twarog, R. G.; de Bliek, R.

    1996-01-01

    This study explored which of two modes of access to a biomedical database better supported problem solving in bacteriology. Boolean access, which allowed subjects to frame their queries as combinations of keywords, was compared to hypertext access, which allowed subjects to navigate from one database node to another. The accessible biomedical data were identical across systems. Data were collected from 42 first year medical students, each randomized to the Boolean or hypertext system, before and after their bacteriology course. Subjects worked eight clinical case problems, first using only their personal knowledge and, subsequently, with aid from the database. Database retrievals enabled students to answer questions they could not answer based on personal knowledge only. This effect was greater when personal knowledge of bacteriology was lower. The results also suggest that hypertext was superior to Boolean access in helping subjects identify possible infectious agents in these clinical case problems. PMID:8947616

  11. A comparison of hypertext and Boolean access to biomedical information.

    PubMed

    Friedman, C P; Wildemuth, B M; Muriuki, M; Gant, S P; Downs, S M; Twarog, R G; de Bliek, R

    1996-01-01

    This study explored which of two modes of access to a biomedical database better supported problem solving in bacteriology. Boolean access, which allowed subjects to frame their queries as combinations of keywords, was compared to hypertext access, which allowed subjects to navigate from one database node to another. The accessible biomedical data were identical across systems. Data were collected from 42 first year medical students, each randomized to the Boolean or hypertext system, before and after their bacteriology course. Subjects worked eight clinical case problems, first using only their personal knowledge and, subsequently, with aid from the database. Database retrievals enabled students to answer questions they could not answer based on personal knowledge only. This effect was greater when personal knowledge of bacteriology was lower. The results also suggest that hypertext was superior to Boolean access in helping subjects identify possible infectious agents in these clinical case problems.

  12. Utilization of ontology look-up services in information retrieval for biomedical literature.

    PubMed

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

    2013-01-01

    With the vast amount of biomedical data we face the necessity to improve information retrieval processes in biomedical domain. The use of biomedical ontologies facilitated the combination of various data sources (e.g. scientific literature, clinical data repository) by increasing the quality of information retrieval and reducing the maintenance efforts. In this context, we developed Ontology Look-up services (OLS), based on NEWT and MeSH vocabularies. Our services were involved in some information retrieval tasks such as gene/disease normalization. The implementation of OLS services significantly accelerated the extraction of particular biomedical facts by structuring and enriching the data context. The results of precision in normalization tasks were boosted on about 20%.

  13. 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.

  14. 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…

  15. 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…

  16. 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. Copyright © 2016. Published by Elsevier Ltd.

  17. 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…

  18. Information flow, job search, and migration.

    PubMed

    Vishwanath, T

    1991-10-01

    "In this paper, an individual model of rural-urban migration is studied, emphasizing the effects of information flow and urban wage dispersion. Migration is viewed in the context of a lifetime program of job search. It is shown that migration can occur even when the mean urban wage is no larger than the rural income flow.... Both the shape and spread of the urban wage dispersion are shown to affect migration behavior significantly." The geographical focus is on developing countries.

  19. A proposed key escrow system for secure patient information disclosure in biomedical research databases.

    PubMed

    Ferris, Todd A; Garrison, Gregory M; Lowe, Henry J

    2002-01-01

    Access to clinical data is of increasing importance to biomedical research. The pending HIPAA privacy regulations provide specific requirements for the release of protected health information. Under the regulations, biomedical researchers may utilize anonymized data, or adhere to HIPAA requirements regarding protected health information. In order to provide researchers with anonymized data from a clinical research database, we reviewed several published strategies for de-identification of protected health information. Critical analysis with respect to this project suggests that de-identification alone is problematic when applied to clinical research databases. We propose a hybrid system; utilizing secure key escrow, de-identification, and role-based access for IRB approved researchers.

  20. 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…

  1. 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…

  2. Biomedical information technology: medicine and health care in the digital future.

    PubMed

    Laxminarayan, S N; Coatrieux, J L; Roux, C; Finkelstein, S M; Sahakian, A V; Blanchard, S M

    1997-03-01

    Advancements in medicine and health care are being significantly influenced by the exploding information technology developments. The IEEE Transactions on Information Technology in Biomedicine will address the applications and the infrastructure innovations that would harness biomedical and health care programs in the 21st century.

  3. 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…

  4. 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…

  5. 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…

  6. 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…

  7. Cloud computing: a new business paradigm for biomedical information sharing.

    PubMed

    Rosenthal, Arnon; Mork, Peter; Li, Maya Hao; Stanford, Jean; Koester, David; Reynolds, Patti

    2010-04-01

    We examine how the biomedical informatics (BMI) community, especially consortia that share data and applications, can take advantage of a new resource called "cloud computing". Clouds generally offer resources on demand. In most clouds, charges are pay per use, based on large farms of inexpensive, dedicated servers, sometimes supporting parallel computing. Substantial economies of scale potentially yield costs much lower than dedicated laboratory systems or even institutional data centers. Overall, even with conservative assumptions, for applications that are not I/O intensive and do not demand a fully mature environment, the numbers suggested that clouds can sometimes provide major improvements, and should be seriously considered for BMI. Methodologically, it was very advantageous to formulate analyses in terms of component technologies; focusing on these specifics enabled us to bypass the cacophony of alternative definitions (e.g., exactly what does a cloud include) and to analyze alternatives that employ some of the component technologies (e.g., an institution's data center). Relative analyses were another great simplifier. Rather than listing the absolute strengths and weaknesses of cloud-based systems (e.g., for security or data preservation), we focus on the changes from a particular starting point, e.g., individual lab systems. We often find a rough parity (in principle), but one needs to examine individual acquisitions--is a loosely managed lab moving to a well managed cloud, or a tightly managed hospital data center moving to a poorly safeguarded cloud? 2009 Elsevier Inc. All rights reserved.

  8. 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…

  9. 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…

  10. The Biomedical Information Explosion: From the Index-Catalogue to MEDLARS

    PubMed Central

    Jablonski, Stanley

    1971-01-01

    This study demonstrates the growth of medical periodical literature by means of the increase of titles indexed in the Index-Catalogue and in Index Medicus, with reference to other biomedical-related titles not covered in these publications. Stress is laid on the fact that information outside the biomedical area is needed by the researcher. Problems of information retrieval, with the specific needs of the user in mind, are discussed, together with the particular problems of indexing which this specificity raises. PMID:5542923

  11. Negotiating health-related uncertainties: biomedical and religious sources of information and support.

    PubMed

    Cadge, Wendy; Bergey, Meredith

    2013-09-01

    This article explores how people experience health-related uncertainties and how they look to biomedical and religious sources of information in response. Data were gathered in a larger project focused on spirituality in everyday life. Respondents were not asked any direct questions about their health or health care, but almost all of the 95 participants brought up the topics in response to other questions. About one-third spoke of being uncertain about some aspect of their health or healthcare. We explore the health-related topics about which people were uncertain and how they looked to biomedical and religious sources of information, most often seeing the religious as a support for the biomedical. We outline the range of ways they experienced God in this process pointing to the multiple complex ways they make sense of health-related uncertainties.

  12. [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.

  13. 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

  14. Reengineering the biomedical-equipment procurement process through an integrated management information system.

    PubMed

    Larios, Y G; Matsopoulos, G K; Askounis, D T; Nikita, K S

    2000-01-01

    The design of each new hospital site is typically preceded by decisions on the most appropriate level of biomedical equipment which significantly influences the layout of the hospital departments which are under construction. The most appropriate biomedical equipment should ideally be decided upon considering a series of demographic and social parameters of the hospital and international regulations and standards. This information should ultimately be distilled to proper technical specifications. This paper proposes a streamlined management process related to the procurement of biomedical equipment for new hospital sites or for those under expansion. The new management process aims to increase the efficiency of the experts involved in the definition of the most appropriate level of equipment and its technical specifications. It also addresses all aspects of the biomedical equipment-selection cycle, including the evaluation of the bids submitted by the equipment suppliers. The proposed process is assisted by a management information system, which integrates all related data-handling operations. It provides extensive decision-support facilities to the expert and a platform for the support of knowledge re-use in the field of biomedical-equipment selection.

  15. Use of a systematic review to inform the infection risk for biomedical engineers and technicians servicing biomedical devices.

    PubMed

    Smith, Anne-Louise

    2011-12-01

    Many microorganisms responsible for hospital-acquired infections are able to stay viable on surfaces with no visible sign of contamination, in dry conditions and on non-porous surfaces. The infection risk to biomedical staff when servicing biomedical devices is not documented. An indirect approach has been used to examine the different aspects that will affect the risk of infection including a systematic review of microbial contamination and transmission relating to biomedical devices. A systematic review found 58% of biomedical devices have microbial contamination with 13% having at least one pathogenic organism. These microbes can persist for some months. Occupational-infections of biomedical service staff are low compared to other healthcare workers. A biomedical device with contaminated surface or dust was identified as the source of patient outbreaks in 13 papers. The cleaning agent most tested for removal of micro-organisms from devices was alcohol swabs, but sterile water swabs were also effective. However, manufacturers mainly recommend (74%) cleaning devices with water and detergent. Biomedical engineers and technicians have a small risk of being exposed to dangerous micro-organisms on most biomedical devices, but without skin breakage, this exposure is unlikely to cause ill-health. It is recommended that biomedical staff follow good infection control practices, wipe devices with detergent, sterile water or alcohol swabs as recommended by the manufacturer before working on them, and keep alcohol hand rubs accessible at all benches.

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

    PubMed Central

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

    2015-01-01

    Abstract. 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

  17. 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.

  18. Improving Biomedical Signal Search Results in Big Data Case-Based Reasoning Environments.

    PubMed

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

    2016-06-01

    Time series subsequence matching has importance in a variety of areas in healthcare informatics. These include case-based diagnosis and treatment as well as discovery of trends among patients. However, few medical systems employ subsequence matching due to high computational and memory complexities. This manuscript proposes a randomized Monte Carlo sampling method to broaden search criteria with minimal increases in computational and memory complexities over R-NN indexing. Information gain improves while producing result sets that approximate the theoretical result space, query results increase by several orders of magnitude, and recall is improved with no signi cant degradation to precision over R-NN matching.

  19. On the application of the auto mutual information rate of decrease to biomedical signals.

    PubMed

    Escudero, Javier; Hornero, Roberto; Abasolo, Daniel; Lopez, Miguel

    2008-01-01

    The auto mutual information function (AMIF) evaluates the signal predictability by assessing linear and non-linear dependencies between two measurements taken from a single time series. Furthermore, the AMIF rate of decrease (AMIFRD) is correlated with signal entropy. This metric has been used to analyze biomedical data, including cardiac and brain activity recordings. Hence, the AMIFRD can be a relevant parameter in the context of biomedical signal analysis. Thus, in this pilot study, we have analyzed a synthetic sequence (a Lorenz system) and real biosignals (electroencephalograms recorded with eyes open and closed) with the AMIFRD. We aimed at illustrating the application of this parameter to biomedical time series. Our results show that the AMIFRD can detect changes in the non-linear dynamics of a sequence and that it can distinguish different physiological conditions.

  20. Toward a fully de-identified biomedical information warehouse.

    PubMed

    Liu, Jianhua; Erdal, Selnur; Silvey, Scott A; Ding, Jing; Riedel, John D; Marsh, Clay B; Kamal, Jyoti

    2009-11-14

    The Information Warehouse at the Ohio State University Medical Center is a comprehensive repository of business, clinical, and research data from various source systems. Data collected here is a valuable resource that facilitates both translational research and personalized healthcare. The use of such data in research is governed by federal privacy regulations with oversight by the Institutional Review Board. In 2006, the Information Warehouse was recognized by the OSU IRB as an "Honest Broker" of clinical data, providing investigators with de-identified or limited datasets under stipulations contained in a signed data use agreement. In order to streamline this process even further, the Information Warehouse is developing a de-identified data warehouse that is suitable for direct user access through a controlled query tool that is aimed to support both research and education activities. In this paper we report our findings on performance evaluation of different de-identification schemes that may be used to ensure regulatory compliance while also facilitating practical database updating and querying. We also discuss how date-shifting in the de-identification process can impact other data elements such as diagnosis and procedure codes and consider a possible solution to those problems.

  1. Biomedical device interfacing to clinical information systems: a primer.

    PubMed

    Moorman, Bridget

    2008-01-01

    I am pleased that we get to take advantage of Bridget Moorman's background, experience, and perspective in this installment of IT World. One of the most nerve-racking tasks we run into these days is getting disparate medical devices to talk to each other over a network. This is especially so if the device you're trying to communicate with doesn't support network connectivity. Bridget shares her experience here not only with a great high-level view of network interfacing, but also with references to dig into all the grim details. She shows us a lot of facets to consider when assembling such a network. You've got to convert to hit the ramp then translate and aggregate before gaining access to the clinical information system cloud. If that doesn't make sense, read on! -Jeff Kabachinski, IT World columnist.

  2. 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

  3. 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.

  4. A proposed key escrow system for secure patient information disclosure in biomedical research databases.

    PubMed Central

    Ferris, Todd A.; Garrison, Gregory M.; Lowe, Henry J.

    2002-01-01

    Access to clinical data is of increasing importance to biomedical research. The pending HIPAA privacy regulations provide specific requirements for the release of protected health information. Under the regulations, biomedical researchers may utilize anonymized data, or adhere to HIPAA requirements regarding protected health information. In order to provide researchers with anonymized data from a clinical research database, we reviewed several published strategies for de-identification of protected health information. Critical analysis with respect to this project suggests that de-identification alone is problematic when applied to clinical research databases. We propose a hybrid system; utilizing secure key escrow, de-identification, and role-based access for IRB approved researchers. PMID:12463824

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

    PubMed Central

    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

    2015-01-01

    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 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

  6. 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

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

    PubMed

    Myneni, Sahiti; Patel, Vimla L

    2010-06-01

    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.

  8. 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

  9. Institute for Scientific Information-indexed biomedical journals of Saudi Arabia

    PubMed Central

    Rohra, Dileep K.; Rohra, Vikram K.; Cahusac, Peter

    2016-01-01

    Objectives: To compare the journal impact factor (JIF) and Eigenfactor score (ES) of Institute for Scientific Information (ISI)-indexed biomedical journals published from the Kingdom of Saudi Arabia (KSA) over the last 8 years. Methods: This is a retrospective study, conducted at Alfaisal University, Riyadh, KSA from January to March 2016. The Journal Citation Reports of ISI Web of Knowledge were accessed, and 6 Saudi biomedical journals were included for analysis. Results: All Saudi journals have improved their IF compared with their baseline. However, the performance of the Journal of Pharmaceutical Sciences and Neurosciences has been exceptionally good. The biggest improvement in percent growth in JIF was seen in the Saudi Pharmaceutical Journal (approximately 887%) followed by Neurosciences (approximately 462%). Interestingly, the ES of all biomedical journals, except Saudi Journal of Gastroenterology and Saudi Medical Journal, increased over the years. The greatest growth in ES (more than 5 fold) was noted for Neurosciences and Saudi Pharmaceutical Journal. Conclusion: This study shows that the overall quality of all Saudi biomedical journals has improved in the last 8 years. PMID:27761565

  10. Information Search and Satisfaction of Carpet Buyers.

    ERIC Educational Resources Information Center

    Grieve-Malpass, Jennifer; Crown, E. M.

    1989-01-01

    A study was conducted to determine the relationship between prepurchase search behavior and postpurchase satisfaction with carpeting. It was found that respondents who purchased carpets with greater store search were more satisfied than those who relied upon magazine and newspaper advertisements. (JOW)

  11. [Biomedical informatics].

    PubMed

    Capurro, Daniel; Soto, Mauricio; Vivent, Macarena; Lopetegui, Marcelo; Herskovic, Jorge R

    2011-12-01

    Biomedical Informatics is a new discipline that arose from the need to incorporate information technologies to the generation, storage, distribution and analysis of information in the domain of biomedical sciences. This discipline comprises basic biomedical informatics, and public health informatics. The development of the discipline in Chile has been modest and most projects have originated from the interest of individual people or institutions, without a systematic and coordinated national development. Considering the unique features of health care system of our country, research in the area of biomedical informatics is becoming an imperative.

  12. 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

  13. 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%.

  14. 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

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

    PubMed Central

    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

  16. Information Retrieval for Education: Making Search Engines Language Aware

    ERIC Educational Resources Information Center

    Ott, Niels; Meurers, Detmar

    2010-01-01

    Search engines have been a major factor in making the web the successful and widely used information source it is today. Generally speaking, they make it possible to retrieve web pages on a topic specified by the keywords entered by the user. Yet web searching currently does not take into account which of the search results are comprehensible for…

  17. 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.

  18. BioTCM-SE: A Semantic Search Engine for the Information Retrieval of Modern Biology and Traditional Chinese Medicine

    PubMed Central

    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

  19. 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

  20. Real time biomedical signal transmission of mixed ECG signal and patient information using visible light communication.

    PubMed

    Tan, Yee Yong; Jung, Sang-Joong; Chung, Wan-Young

    2013-01-01

    The utilization of radio-frequency (RF) communication technology in healthcare application, especially in the transmission of health-related data such as biomedical signal and patient information is often perturbed by electromagnetic interference (EMI). This will not only significantly reduce the accuracy and reliability of the data transmitted, but could also compromise the safety of the patients due to radio frequency (RF) radiation. In this paper, we propose a method which utilizes visible light communication technology as a platform for transmission and to provide real-time monitoring of heart rate and patient information. White LED beam is used as the illuminating source to simultaneously transmit biomedical signal as well as patient record. On-off Keying (OOK) modulation technique is used to modulate all the data onto the visible light beam. Both types of data will be transmitted using a single data packet. At the receiving end, a receiver circuit consisting of a high-speed PIN photodetector and a demodulation circuit is employed to demodulate the data from the visible light beam. The demodulated data is then serially transmitted to a personal computer where the biomedical signal, patient information and heart rate can be monitored in real-time.

  1. Improving validity of informed consent for biomedical research in Zambia using a laboratory exposure intervention.

    PubMed

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

    2014-01-01

    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. 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. 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. 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.

  2. 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

  3. '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.

  4. '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.

  5. The evolving state of online search for consumer health information.

    PubMed

    Hunscher, Dale A

    2008-11-06

    Online search for consumer health information is a public health concern. General-purpose search engines have historically returned health-related query results of dubious relevance and quality. Meanwhile, consumers have become increasingly reliant on and trusting of these engines. General-purpose search engines have attempted to make their interfaces more consumer-friendly with respect to consumer health queries and their results more relevant and trustworthy. We illustrate the characteristics of the evolving health search landscape using network visualization.

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

    PubMed

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

    2013-01-01

    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. 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. 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. 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.

  8. Biomedical radiography: radiation protection and safety. (latest citations from the NTIS data base). Published Search

    SciTech Connect

    Not Available

    1992-04-01

    The bibliography contains citations concerning the safety of biomedical radiography. Radiation protection methods and techniques are described for both patients and operators. Safety techniques for dental radiology, routine x-rays, radiotherapy, thoracic radiography and other radiology procedures are included. Radiation exposure limits for patients and healthcare workers are defined. (Contains a minimum of 247 citations and includes a subject term index and title list.)

  9. Patient-Centered Tools for Medication Information Search

    PubMed Central

    Wilcox, Lauren; Feiner, Steven; Elhadad, Noémie; Vawdrey, David; Tran, Tran H.

    2016-01-01

    Recent research focused on online health information seeking highlights a heavy reliance on general-purpose search engines. However, current general-purpose search interfaces do not necessarily provide adequate support for non-experts in identifying suitable sources of health information. Popular search engines have recently introduced search tools in their user interfaces for a range of topics. In this work, we explore how such tools can support non-expert, patient-centered health information search. Scoping the current work to medication-related search, we report on findings from a formative study focused on the design of patient-centered, medication-information search tools. Our study included qualitative interviews with patients, family members, and domain experts, as well as observations of their use of Remedy, a technology probe embodying a set of search tools. Post-operative cardiothoracic surgery patients and their visiting family members used the tools to find information about their hospital medications and were interviewed before and after their use. Domain experts conducted similar search tasks and provided qualitative feedback on their preferences and recommendations for designing these tools. Findings from our study suggest the importance of four valuation principles underlying our tools: credibility, readability, consumer perspective, and topical relevance. PMID:28163972

  10. Patient-Centered Tools for Medication Information Search.

    PubMed

    Wilcox, Lauren; Feiner, Steven; Elhadad, Noémie; Vawdrey, David; Tran, Tran H

    2014-05-20

    Recent research focused on online health information seeking highlights a heavy reliance on general-purpose search engines. However, current general-purpose search interfaces do not necessarily provide adequate support for non-experts in identifying suitable sources of health information. Popular search engines have recently introduced search tools in their user interfaces for a range of topics. In this work, we explore how such tools can support non-expert, patient-centered health information search. Scoping the current work to medication-related search, we report on findings from a formative study focused on the design of patient-centered, medication-information search tools. Our study included qualitative interviews with patients, family members, and domain experts, as well as observations of their use of Remedy, a technology probe embodying a set of search tools. Post-operative cardiothoracic surgery patients and their visiting family members used the tools to find information about their hospital medications and were interviewed before and after their use. Domain experts conducted similar search tasks and provided qualitative feedback on their preferences and recommendations for designing these tools. Findings from our study suggest the importance of four valuation principles underlying our tools: credibility, readability, consumer perspective, and topical relevance.

  11. 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)

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

    PubMed

    Mandloi, Sapan; Chakrabarti, Saikat

    2015-05-19

    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.

  13. 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

  14. Semantics-driven modelling of user preferences for information retrieval in the biomedical domain.

    PubMed

    Gladun, Anatoly; Rogushina, Julia; Valencia-García, Rafael; Béjar, Rodrigo Martínez

    2013-03-01

    A large amount of biomedical and genomic data are currently available on the Internet. However, data are distributed into heterogeneous biological information sources, with little or even no organization. Semantic technologies provide a consistent and reliable basis with which to confront the challenges involved in the organization, manipulation and visualization of data and knowledge. One of the knowledge representation techniques used in semantic processing is the ontology, which is commonly defined as a formal and explicit specification of a shared conceptualization of a domain of interest. The work presented here introduces a set of interoperable algorithms that can use domain and ontological information to improve information-retrieval processes. This work presents an ontology-based information-retrieval system for the biomedical domain. This system, with which some experiments have been carried out that are described in this paper, is based on the use of domain ontologies for the creation and normalization of lightweight ontologies that represent user preferences in a determined domain in order to improve information-retrieval processes.

  15. Online information search behaviour of physicians.

    PubMed

    Mikalef, Patrick; Kourouthanassis, Panos E; Pateli, Adamantia G

    2017-03-01

    Although doctors increasingly engage in online information seeking to complement their medical practice, little is known regarding what online information sources are used and how effective they are. Grounded on self-determination and needs theory, this study posits that doctors tend to use online information sources to fulfil their information requirements in three pre-defined areas: patient care, knowledge development and research activities. Fulfilling these information needs is argued to improve doctors' perceived medical practice competence. Performing PLS-SEM analysis on primary survey data from 303 medical doctors practicing in four major Greek hospitals, a conceptual model is empirically tested. Using authoritative online information sources was found to fulfil all types of information needs. Contrarily, using non-authoritative information sources had no significant effect. Satisfying information requirements relating to patient care and research activities enhanced doctors' perceptions about their medical practice competence. In contrast, meeting knowledge development information needs had the opposite result. Consistent with past studies, outcomes indicate that doctors tend to use non-authoritative online information sources; yet their use was found to have no significant value in fulfilling their information requirements. Authoritative online information sources are found to improve perceived medical practice competence by satisfying doctors' diverse information requirements. © 2017 Health Libraries Group.

  16. 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

  17. Information Literacy: Search Strategies, Tools & Resources.

    ERIC Educational Resources Information Center

    Ercegovac, Zorana

    This book was created to teach information literacy. It takes a user-centered perspective in using information technology as a tool to accomplish a variety of tasks and is divided into a series of nine interrelated yet independent chapters. Chapter 1 is an introduction to basic concepts, focusing on fundamental models of information sources and…

  18. The role of health anxiety in online health information search.

    PubMed

    Baumgartner, Susanne E; Hartmann, Tilo

    2011-10-01

    This article is one of the first to empirically explore the relationship between health anxiety and online health information search. Two studies investigate how health anxiety influences the use of the Internet for health information and how health anxious individuals respond to online health information. An exploratory survey study with 104 Dutch participants indicates that health anxiety is related to an increase in online health information search. Moreover, results suggest that health anxious individuals experience more negative consequences from online health information search. Findings from an experimental study (n=120) indicate that online health information results in greater worries among health anxious individuals compared to nonhealth anxious individuals only if the information stems from a trustworthy governmental Web site. Information from a less trustworthy online forum does not lead to greater worries among health anxious individuals. In sum, the Internet appears to play a pivotal role in the lives of health anxious individuals.

  19. Career Planning and Job Searching in the Information Age.

    ERIC Educational Resources Information Center

    Lorenzen, Elizabeth A., Ed.

    This book contains 11 papers examining career planning and job searching in the information age. The following papers are included: "The Librarian's Role in the Job Search of the Future: Issues and Ethics in the Electronic Environment" (Elizabeth A. Lorenzen); "The Internet as Career, Job, and Employment Resource: Transition, Assimilation,…

  20. [Radiological information searching on the Internet: data banks, search machines and intelligent agents].

    PubMed

    Achenbach, S; Alfke, H

    2000-04-01

    The Internet plays an important role in a growing number of medical applications. Finding relevant information is not always easy as the amount of available information on the Web is rising quickly. Even the best search engines can only collect links to a fraction of all existing Web pages. In addition, many of these indexed documents have been changed or deleted. The vast majority of information on the Web is not searchable with conventional methods. New search strategies, technologies and standards are combined in intelligent search agents (ISA) and robots, which can retrieve desired information in a specific approach. The article describes differences between ISAs and conventional search engines and how communication between agents improves their ability to find information. Examples of existing ISAs are given and the possible influences on the current and future work in radiology is discussed.

  1. 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…

  2. Searching Memory for Congruent or Incongruent Information.

    ERIC Educational Resources Information Center

    Foos, Paul W.

    1982-01-01

    Discusses the cognitive processes involved in constructing linear orderings from pairwise relationships of information items. Examines the effects that sentence types used in presenting information have on these processes, and tests two models designed to clarify the acquisition of spatial knowledge and the processing of locative and comparative…

  3. In Search of Ideal Information Pricing.

    ERIC Educational Resources Information Center

    Hawkins, Donald T.

    1989-01-01

    Reviews some of the models used for pricing online information services and discusses some of the implications of these pricing algorithms. Topics discussed include online versus print pricing; charges for the retrieval process; charges for the retrieved information; telecommunications charges; and the pricing policies of Chemical Abstracts…

  4. In Search of Ideal Information Pricing.

    ERIC Educational Resources Information Center

    Hawkins, Donald T.

    1989-01-01

    Reviews some of the models used for pricing online information services and discusses some of the implications of these pricing algorithms. Topics discussed include online versus print pricing; charges for the retrieval process; charges for the retrieved information; telecommunications charges; and the pricing policies of Chemical Abstracts…

  5. 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…

  6. 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…

  7. Expert Search Strategies: The Information Retrieval Practices of Healthcare Information Professionals.

    PubMed

    Russell-Rose, Tony; Chamberlain, Jon

    2017-10-02

    Healthcare information professionals play a key role in closing the knowledge gap between medical research and clinical practice. Their work involves meticulous searching of literature databases using complex search strategies that can consist of hundreds of keywords, operators, and ontology terms. This process is prone to error and can lead to inefficiency and bias if performed incorrectly. The aim of this study was to investigate the search behavior of healthcare information professionals, uncovering their needs, goals, and requirements for information retrieval systems. A survey was distributed to healthcare information professionals via professional association email discussion lists. It investigated the search tasks they undertake, their techniques for search strategy formulation, their approaches to evaluating search results, and their preferred functionality for searching library-style databases. The popular literature search system PubMed was then evaluated to determine the extent to which their needs were met. The 107 respondents indicated that their information retrieval process relied on the use of complex, repeatable, and transparent search strategies. On average it took 60 minutes to formulate a search strategy, with a search task taking 4 hours and consisting of 15 strategy lines. Respondents reviewed a median of 175 results per search task, far more than they would ideally like (100). The most desired features of a search system were merging search queries and combining search results. Healthcare information professionals routinely address some of the most challenging information retrieval problems of any profession. However, their needs are not fully supported by current literature search systems and there is demand for improved functionality, in particular regarding the development and management of search strategies.

  8. How to Search for Information about Pesticide Ingredients and Labels

    EPA Pesticide Factsheets

    How to use the databases Pesticide Chemical Search, Pesticide Product Label System (PPLS), and InertFinder to find information such as Chemical Abstract Service (CAS) numbers, active and inert ingredients, and regulatory actions.

  9. Figure mining for biomedical research.

    PubMed

    Rodriguez-Esteban, Raul; Iossifov, Ivan

    2009-08-15

    Figures from biomedical articles contain valuable information difficult to reach without specialized tools. Currently, there is no search engine that can retrieve specific figure types. This study describes a retrieval method that takes advantage of principles in image understanding, text mining and optical character recognition (OCR) to retrieve figure types defined conceptually. A search engine was developed to retrieve tables and figure types to aid computational and experimental research. http://iossifovlab.cshl.edu/figurome/.

  10. Sources of Developmental Change in the Efficiency of Information Search

    ERIC Educational Resources Information Center

    Ruggeri, Azzurra; Lombrozo, Tania; Griffiths, Thomas L.; Xu, Fei

    2016-01-01

    Children are active learners: they learn not only from the information people offer and the evidence they happen to observe, but by actively seeking information. However, children's information search strategies are typically less efficient than those of adults. In two studies, we isolate potential sources of developmental change in how children…

  11. Sources of Developmental Change in the Efficiency of Information Search

    ERIC Educational Resources Information Center

    Ruggeri, Azzurra; Lombrozo, Tania; Griffiths, Thomas L.; Xu, Fei

    2016-01-01

    Children are active learners: they learn not only from the information people offer and the evidence they happen to observe, but by actively seeking information. However, children's information search strategies are typically less efficient than those of adults. In two studies, we isolate potential sources of developmental change in how children…

  12. Self Esteem, Information Search and Problem Solving Efficiency.

    DTIC Science & Technology

    1979-05-01

    Weiss (1977, 1978) has shown that low self esteem workers are more likely to model the role behaviors and work values of superiors than are high self ...situation. He has also argued that high self esteem individuals search for less information on problem solving tasks and are therefore less likely to...seek and use models to help them define their roles. This study examined whether self esteem is, in fact, negatively related to information search

  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. Relemed: sentence-level search engine with relevance score for the MEDLINE database of biomedical articles

    PubMed Central

    Siadaty, Mir S; Shu, Jianfen; Knaus, William A

    2007-01-01

    Background Receiving extraneous articles in response to a query submitted to MEDLINE/PubMed is common. When submitting a multi-word query (which is the majority of queries submitted), the presence of all query words within each article may be a necessary condition for retrieving relevant articles, but not sufficient. Ideally a relationship between the query words in the article is also required. We propose that if two words occur within an article, the probability that a relation between them is explained is higher when the words occur within adjacent sentences versus remote sentences. Therefore, sentence-level concurrence can be used as a surrogate for existence of the relationship between the words. In order to avoid the irrelevant articles, one solution would be to increase the search specificity. Another solution is to estimate a relevance score to sort the retrieved articles. However among the >30 retrieval services available for MEDLINE, only a few estimate a relevance score, and none detects and incorporates the relation between the query words as part of the relevance score. Results We have developed "Relemed", a search engine for MEDLINE. Relemed increases specificity and precision of retrieval by searching for query words within sentences rather than the whole article. It uses sentence-level concurrence as a statistical surrogate for the existence of relationship between the words. It also estimates a relevance score and sorts the results on this basis, thus shifting irrelevant articles lower down the list. In two case studies, we demonstrate that the most relevant articles appear at the top of the Relemed results, while this is not necessarily the case with a PubMed search. We have also shown that a Relemed search includes not only all the articles retrieved by PubMed, but potentially additional relevant articles, due to the extended 'automatic term mapping' and text-word searching features implemented in Relemed. Conclusion By using sentence

  15. 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…

  16. 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…

  17. 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

  18. 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.

  19. Optimal Aide Security Information Search (OASIS)

    DTIC Science & Technology

    2005-03-01

    Fetch Technologies (referred to as the Fetch tool) has some potential applicability in network security domains. The tool works very well with static web pages...evaluation of the Fetch tool be conducted to determine the areas of information in the network security domain that use static web pages for extraction

  20. 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.

  1. 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

  2. Biomedical and health informatics education and research at the Information Technology Institute in Egypt.

    PubMed

    Hussein, R; Khalifa, A

    2011-01-01

    During the last decade, Egypt has experienced a revolution in the field of Information and Communication Technology (ICT) that has had a corresponding impact on the field of healthcare. Since 1993, the Information Technology Institute (ITI) has been leading the development of the Information Technology (IT) professional training and education in Egypt to produce top quality IT professionals who are considered now the backbone of the IT revolution in Egypt. For the past five years, ITI has been adopting the objective of building high caliber health professionals who can effectively serve the ever-growing information society. Academic links have been established with internationally renowned universities, e.g., Oregon Health and Science University (OHSU) in US, University of Leipzig in Germany, in addition those with the Egyptian Fellowship Board in order to enrich ITI Medical Informatics Education and Research. The ITI Biomedical and Health Informatics (BMHI) education and training programs target fresh graduates as well as life-long learners. Therefore, the program's learning objectives are framed within the context of the four specialization tracks: Healthcare Management (HCM), Biomedical Informatics Research (BMIR), Bioinformatics Professional (BIP), and Healthcare Professional (HCP). The ITI BMHI research projects tackle a wide-range of current challenges in this field, such as knowledge management in healthcare, providing tele-consultation services for diagnosis and treatment of infectious diseases for underserved regions in Egypt, and exploring the cultural and educational aspects of Nanoinformatics. Since 2006, ITI has been positively contributing to develop the discipline of BMHI in Egypt in order to support improved healthcare services.

  3. Personal Information Search on Mobile Devices

    DTIC Science & Technology

    2007-09-01

    comparable features and capabilities. They have a microprocessor , read only memory (ROM), random access memory (RAM), a communication module, a...fails, the information in the RAM can be lost [19]. Modern mobile phones are generally equipped with system level microprocessors , which cut down on...or stereo , as well as for playing computer games, recording survey responses, and GPS (Global Positioning System) receivers. Newer PDAs also have

  4. Quantifying the informativeness for biomedical literature summarization: An itemset mining method.

    PubMed

    Moradi, Milad; Ghadiri, Nasser

    2017-07-01

    Automatic text summarization tools can help users in the biomedical domain to access information efficiently from a large volume of scientific literature and other sources of text documents. In this paper, we propose a summarization method that combines itemset mining and domain knowledge to construct a concept-based model and to extract the main subtopics from an input document. Our summarizer quantifies the informativeness of each sentence using the support values of itemsets appearing in the sentence. To address the concept-level analysis of text, our method initially maps the original document to biomedical concepts using the Unified Medical Language System (UMLS). Then, it discovers the essential subtopics of the text using a data mining technique, namely itemset mining, and constructs the summarization model. The employed itemset mining algorithm extracts a set of frequent itemsets containing correlated and recurrent concepts of the input document. The summarizer selects the most related and informative sentences and generates the final summary. We evaluate the performance of our itemset-based summarizer using the Recall-Oriented Understudy for Gisting Evaluation (ROUGE) metrics, performing a set of experiments. We compare the proposed method with GraphSum, TexLexAn, SweSum, SUMMA, AutoSummarize, the term-based version of the itemset-based summarizer, and two baselines. The results show that the itemset-based summarizer performs better than the compared methods. The itemset-based summarizer achieves the best scores for all the assessed ROUGE metrics (R-1: 0.7583, R-2: 0.3381, R-W-1.2: 0.0934, and R-SU4: 0.3889). We also perform a set of preliminary experiments to specify the best value for the minimum support threshold used in the itemset mining algorithm. The results demonstrate that the value of this threshold directly affects the accuracy of the summarization model, such that a significant decrease can be observed in the performance of summarization due to

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Asking Better Questions: How Presentation Formats Influence Information Search.

    PubMed

    Wu, Charley M; Meder, Björn; Filimon, Flavia; Nelson, Jonathan D

    2017-03-20

    While the influence of presentation formats have been widely studied in Bayesian reasoning tasks, we present the first systematic investigation of how presentation formats influence information search decisions. Four experiments were conducted across different probabilistic environments, where subjects (N = 2,858) chose between 2 possible search queries, each with binary probabilistic outcomes, with the goal of maximizing classification accuracy. We studied 14 different numerical and visual formats for presenting information about the search environment, constructed across 6 design features that have been prominently related to improvements in Bayesian reasoning accuracy (natural frequencies, posteriors, complement, spatial extent, countability, and part-to-whole information). The posterior variants of the icon array and bar graph formats led to the highest proportion of correct responses, and were substantially better than the standard probability format. Results suggest that presenting information in terms of posterior probabilities and visualizing natural frequencies using spatial extent (a perceptual feature) were especially helpful in guiding search decisions, although environments with a mixture of probabilistic and certain outcomes were challenging across all formats. Subjects who made more accurate probability judgments did not perform better on the search task, suggesting that simple decision heuristics may be used to make search decisions without explicitly applying Bayesian inference to compute probabilities. We propose a new take-the-difference (TTD) heuristic that identifies the accuracy-maximizing query without explicit computation of posterior probabilities. (PsycINFO Database Record

  10. Career Planning and Job Searching in the Information Age.

    ERIC Educational Resources Information Center

    Lorenzen, Elizabeth A., Ed.

    1996-01-01

    This volume's topics include librarian role and ethical issues in Internet searching, strategies for locating career resources on the Internet and World Wide Web, career information for "Generation X" and for alumni, collaboration between libraries and university career services, career information gophers, and electronic privacy and…

  11. Personalisation of Generic Library Search Results Using Student Enrolment Information

    ERIC Educational Resources Information Center

    Alaofi, Marwah; Rumantir, Grace

    2015-01-01

    This research explores the application of implicit personalisation techniques in information retrieval in the context of education. Motivated by the large and ever-growing volume of resources in digital libraries, coupled with students' limited experience in searching for these resources, particularly in translating their information needs into…

  12. Personalisation of Generic Library Search Results Using Student Enrolment Information

    ERIC Educational Resources Information Center

    Alaofi, Marwah; Rumantir, Grace

    2015-01-01

    This research explores the application of implicit personalisation techniques in information retrieval in the context of education. Motivated by the large and ever-growing volume of resources in digital libraries, coupled with students' limited experience in searching for these resources, particularly in translating their information needs into…

  13. Level Search Schemes for Information Filtering and Retrieval.

    ERIC Educational Resources Information Center

    Zhang, Xiaoyan; Berry, Michael W.; Raghavan, Padma

    2001-01-01

    Discusses latent semantic indexing (LSI); considers the high cost associated with the singular value decomposition (SVD) of the large term-by-document matrix that becomes a barrier for its application to scalable information retrieval; and shows that information filtering using level search techniques can reduce the SVD computation cost for LSI.…

  14. Level Search Schemes for Information Filtering and Retrieval.

    ERIC Educational Resources Information Center

    Zhang, Xiaoyan; Berry, Michael W.; Raghavan, Padma

    2001-01-01

    Discusses latent semantic indexing (LSI); considers the high cost associated with the singular value decomposition (SVD) of the large term-by-document matrix that becomes a barrier for its application to scalable information retrieval; and shows that information filtering using level search techniques can reduce the SVD computation cost for LSI.…

  15. 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…

  16. 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.

  17. 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.

  18. Quality of anaesthesia-related information accessed via Internet searches.

    PubMed

    Caron, S; Berton, J; Beydon, L

    2007-08-01

    We conducted a study to examine the quality and stability of information available from the Internet on four anaesthesia-related topics. In January 2006, we searched using four key words (porphyria, scleroderma, transfusion risk, and epidural analgesia risk) with five search engines (Google, HotBot, AltaVista, Excite, and Yahoo). We used a published scoring system (NetScoring) to evaluate the first 15 sites identified by each of these 20 searches. We also used a simple four-point scale to assess the first 100 sites in the Google search on one of our four topics ('epidural analgesia risk'). In November 2006, we conducted a second evaluation, using three search engines (Google, AltaVista, and Yahoo) with 14 synonyms for 'epidural analgesia risk'. The five search engines performed similarly. NetScoring scores were lower for transfusion risk (P < 0.001). One or more high-quality sites was identified consistently among the first 15 sites in each search. Quality scored using the simple scale correlated closely with medical content and design by NetScoring and with the number of references (P < 0.05). Synonyms of 'epidural analgesia risk' yielded similar results. The quality of accessed information improved somewhat over the 11 month period with Yahoo and AltaVista, but declined with Google. The Internet is a valuable tool for obtaining medical information, but the quality of websites varies between different topics. A simple rating scale may facilitate the quality scoring on individual websites. Differences in precise search terms used for a given topic did not appear to affect the quality of the information obtained.

  19. A biomedical informatics perspective on human factors - How human factors influence information technology adoption.

    PubMed

    Meyer, R

    2011-01-01

    to select and summarize excellent research published in 2010 in the field of bio-medical informatics human factors. we attempt to derive a synthetic overview of the activity and new trends in this field, from a selection of worldwide research papers published during 2010. this year again, healthcare information technology (HIT) adoption occupies a central role in the field and leads to research focused mainly on measuring impact and factors influencing it. One of the selected papers especially dissects the anatomy of a nationwide personal electronic health record adoption failure. Due to the vast and increasing amount of excellent works, choosing the best papers in human factors is a challenge. More and more the published work takes into account fundamental principles expressed in Grudin's Laws, one form of which is: "When those who beneût from a technology are not those who do the work, then the technology is likely to fail or be subverted.".

  20. [Evidence-based medicine. 2. Research of clinically relevant biomedical information. Gruppo Italiano per la Medicina Basata sulle Evidenze--GIMBE].

    PubMed

    Cartabellotta, A

    1998-05-01

    Evidence-based Medicine is a product of the electronic information age and there are several databases useful for practice it--MEDLINE, EMBASE, specialized compendiums of evidence (Cochrane Library, Best Evidence), practice guidelines--most of them free available through Internet, that offers a growing number of health resources. Because searching best evidence is a basic step to practice Evidence-based Medicine, this second review (the first one has been published in the issue of March 1998) has the aim to provide physicians tools and skills for retrieving relevant biomedical information. Therefore, we discuss about strategies for managing information overload, analyze characteristics, usefulness and limits of medical databases and explain how to use MEDLINE in day-to-day clinical practice.

  1. Learning to rank diversified results for biomedical information retrieval from multiple features

    PubMed Central

    2014-01-01

    Background Different from traditional information retrieval (IR), promoting diversity in IR takes consideration of relationship between documents in order to promote novelty and reduce redundancy thus to provide diversified results to satisfy various user intents. Diversity IR in biomedical domain is especially important as biologists sometimes want diversified results pertinent to their query. Methods A combined learning-to-rank (LTR) framework is learned through a general ranking model (gLTR) and a diversity-biased model. The former is learned from general ranking features by a conventional learning-to-rank approach; the latter is constructed with diversity-indicating features added, which are extracted based on the retrieved passages' topics detected using Wikipedia and ranking order produced by the general learning-to-rank model; final ranking results are given by combination of both models. Results Compared with baselines BM25 and DirKL on 2006 and 2007 collections, the gLTR has 0.2292 (+16.23% and +44.1% improvement over BM25 and DirKL respectively) and 0.1873 (+15.78% and +39.0% improvement over BM25 and DirKL respectively) in terms of aspect level of mean average precision (Aspect MAP). The LTR method outperforms gLTR on 2006 and 2007 collections with 4.7% and 2.4% improvement in terms of Aspect MAP. Conclusions The learning-to-rank method is an efficient way for biomedical information retrieval and the diversity-biased features are beneficial for promoting diversity in ranking results. PMID:25560088

  2. 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.

  3. Learning to rank diversified results for biomedical information retrieval from multiple features.

    PubMed

    Wu, Jiajin; Huang, Jimmy; Ye, Zheng

    2014-01-01

    Different from traditional information retrieval (IR), promoting diversity in IR takes consideration of relationship between documents in order to promote novelty and reduce redundancy thus to provide diversified results to satisfy various user intents. Diversity IR in biomedical domain is especially important as biologists sometimes want diversified results pertinent to their query. A combined learning-to-rank (LTR) framework is learned through a general ranking model (gLTR) and a diversity-biased model. The former is learned from general ranking features by a conventional learning-to-rank approach; the latter is constructed with diversity-indicating features added, which are extracted based on the retrieved passages' topics detected using Wikipedia and ranking order produced by the general learning-to-rank model; final ranking results are given by combination of both models. Compared with baselines BM25 and DirKL on 2006 and 2007 collections, the gLTR has 0.2292 (+16.23% and +44.1% improvement over BM25 and DirKL respectively) and 0.1873 (+15.78% and +39.0% improvement over BM25 and DirKL respectively) in terms of aspect level of mean average precision (Aspect MAP). The LTR method outperforms gLTR on 2006 and 2007 collections with 4.7% and 2.4% improvement in terms of Aspect MAP. The learning-to-rank method is an efficient way for biomedical information retrieval and the diversity-biased features are beneficial for promoting diversity in ranking results.

  4. Mobility and health information searches - a Swedish perspective.

    PubMed

    Eklund, Ann-Marie

    2013-01-01

    Today the first point of contact between a patient and health care is often an internet health portal - not a human. There is also a trend towards increased use of mobile devices for internet searching. We present a study of the use of mobile vs non-mobile devices when accessing the main Swedish official health portal. Our findings indicate that there is a difference in not only when people search for health information, but also the type of information searched for using different devices. We conclude that further analysis is needed to understand these differences, and consequently that the same portal solution may not suit both mobile and non-mobile health information seekers.

  5. Global search demand for varicose vein information on the internet.

    PubMed

    El-Sheikha, Joseph

    2015-09-01

    Changes in internet search trends can provide healthcare professionals detailed information on prevalence of disease and symptoms. Chronic venous disease, more commonly known as varicose veins, is a common symptomatic disease among the adult population. This study aims to measure the change in global search demand for varicose vein information using Google over the past 8 years. The Google Trends instrument was used to measure the change in demand for the use of the local name for varicose veins in several countries across the world between January 2006 and December 2012. The measurements were normalised onto a scale relative to the largest volume of search requests received during a designated time and geographical location. Comparison of national levels of private healthcare and healthcare spending per capita to search demand was also undertaken using Organisation for Economic Co-operation and development economic measurements. Global interest has increased significantly, with linear regression demonstrating a 3.72% year-on-year increase in demand over the 8-year time period (r(2 )= 0.385, p < 0.001). Annual demand significantly increased in the northern hemisphere (p < 0.001 Friedman) yet decreased in the southern hemisphere (p < 0.001 Friedman). Significant seasonality was observed, with warmer months experiencing greater search demand compared to cooler winter months (<0.001 Kruskal-Wallis). National levels of private healthcare did not appear to correlate in search demand (r(2 )= 0.120 p = 0.306). Healthcare spending per capita did not relate to search demand (r(2 )= 0.450 p = 0.077). There is increasing demand for information about varicose veins on the internet, especially during the warmer months of the year. Online search demand does not appear to be related to healthcare spending. © The Author(s) 2014.

  6. The ethics of physicians' web searches for patients' information.

    PubMed

    Genes, Nicholas; Appel, Jacob

    2015-01-01

    When physicians search the web for personal information about their patients, others have argued that this undermines patients' trust, and the physician-patient relationship in general. We add that this practice also places other relationships at risk, and could jeopardize a physician's career. Yet there are also reports of web searches that have unambiguously helped in the care of patients, suggesting circumstances in which a routine search of the web could be beneficial. We advance the notion that, just as nonverbal cues and unsolicited information can be useful in clinical decision making, so too can online information from patients. As electronic records grow more voluminous and span more types of data, searching these resources will become a clinical skill, to be used judiciously and with care--just as evaluating the literature is, today. But to proscribe web searches of patients' information altogether is as nonsensical as disregarding findings from physical exams-instead, what's needed are guidelines for when to look and how to evaluate what's uncovered, online.

  7. Why not just Google it? An assessment of information literacy skills in a biomedical science curriculum.

    PubMed

    Kingsley, Karl; Galbraith, Gillian M; Herring, Matthew; Stowers, Eva; Stewart, Tanis; Kingsley, Karla V

    2011-04-25

    Few issues in higher education are as fundamental as the ability to search for, evaluate, and synthesize information. The need to develop information literacy, the process of finding, retrieving, organizing, and evaluating the ever-expanding collection of online information, has precipitated the need for training in skill-based competencies in higher education, as well as medical and dental education. The current study evaluated the information literacy skills of first-year dental students, consisting of two, consecutive dental student cohorts (n = 160). An assignment designed to evaluate information literacy skills was conducted. In addition, a survey of student online search engine or database preferences was conducted to identify any significant associations. Subsequently, an intervention was developed, based upon the results of the assessment and survey, to address any deficiencies in information literacy. Nearly half of students (n = 70/160 or 43%) missed one or more question components that required finding an evidence-based citation. Analysis of the survey revealed a significantly higher percentage of students who provided incorrect responses (n = 53/70 or 75.7%) reported using Google as their preferred online search method (p < 0.01). In contrast, a significantly higher percentage of students who reported using PubMed (n = 39/45 or 86.7%) were able to provide correct responses (p < 0.01). Following a one-hour intervention by a health science librarian, virtually all students were able to find and retrieve evidence-based materials for subsequent coursework. This study confirmed that information literacy among this student population was lacking and that integration of modules within the curriculum can help students to filter and establish the quality of online information, a critical component in the training of new health care professionals. Furthermore, incorporation of these modules early in the curriculum may be of significant value to other dental

  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. 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

  10. Searching for suicide-related information on Chinese websites.

    PubMed

    Chen, Ying-Yeh; Hung, Galen Chin-Lun; Cheng, Qijin; Tsai, Chi-Wei; Wu, Kevin Chien-Chang

    2017-09-01

    Growing concerns about cyber-suicide have prompted many studies on suicide information available on the web. However, very few studies have considered non-English websites. We aimed to analyze online suicide-related information accessed through Chinese-language websites. We used Taiwan's two most popular search engines (Google and Yahoo) to explore the results returned from six suicide-related search terms in March 2016. The first three pages listing the results from each search were analyzed and rated based on the attitude towards suicide (pro-suicide, anti-suicide, neutral/mixed, not a suicide site, or error). Comparisons across different search terms were also performed. In all, 375 linked webpages were included; 16.3% of the webpages were pro-suicide and 41.3% were anti-suicide. The majority of the pro-suicide sites were user-generated webpages (96.7%). Searches using the keywords 'ways to kill yourself' (31.7%) and 'painless suicide' (28.3%) generated much larger numbers of harmful webpages than the term 'suicide' (4.3%). We conclude that collaborative efforts with internet service providers and search engines to improve the ranking of anti-suicide webpages and websites and implement online suicide reporting guidelines are highly encouraged. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Meeting Report from the Second “Minimum Information for Biological and Biomedical Investigations” (MIBBI) workshop

    PubMed Central

    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

  12. Online consumer search strategies for smoking-cessation information.

    PubMed

    Cobb, Nathan K

    2010-03-01

    For many Americans, the Internet has become a primary mechanism for locating information on healthcare and treatment options, including tobacco addiction. Detailed information on this behavior could inform design decisions for next-generation cessation interventions, but very little is known about how consumers search or what resources they locate. A subset of a publicly available, anonymized record of the search behavior of 650,000 individuals over 3 months in 2006 was analyzed. Smoking cessation-related queries were extracted and coded via manual identification of terms and by back-identifying terms by matching them to the websites ultimately visited. Destination sites were coded as to whether or not they originated from a professional source based on the literature and known healthcare organizations. A total of 628 individuals (0.10%) made 1106 cessation-related searches during the observation period. Of these, 76% resulted in the individual reaching a website; professional sites were reached by only 34% of searchers. Complementary or alternative therapies were popular, with 10% of individuals searching for "laser" therapy. A concerning disconnect exists between consumer demand (as demonstrated by search behavior) and the sites produced by researchers and health professionals. This "demand gap" may contribute to low overall participation rates and hamper the potential impact of such systems. Further research is needed to link online consumer preferences to intervention design decisions. 2010 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

  13. The effects of preference for information on consumers' online health information search behavior.

    PubMed

    Zhang, Yan

    2013-11-26

    Preference for information is a personality trait that affects people's tendency to seek information in health-related situations. Prior studies have focused primarily on investigating its impact on patient-provider communication and on the implications for designing information interventions that prepare patients for medical procedures. Few studies have examined its impact on general consumers' interactions with Web-based search engines for health information or the implications for designing more effective health information search systems. This study intends to fill this gap by investigating the impact of preference for information on the search behavior of general consumers seeking health information, their perceptions of search tasks (representing information needs), and user experience with search systems. Forty general consumers who had previously searched for health information online participated in the study in our usability lab. Preference for information was measured using Miller's Monitor-Blunter Style Scale (MBSS) and the Krantz Health Opinion Survey-Information Scale (KHOS-I). Each participant completed four simulated health information search tasks: two look-up (fact-finding) and two exploratory. Their behaviors while interacting with the search systems were automatically logged and ratings of their perceptions of tasks and user experience with the systems were collected using Likert-scale questionnaires. The MBSS showed low reliability with the participants (Monitoring subscale: Cronbach alpha=.53; Blunting subscale: Cronbach alpha=.35). Thus, no further analyses were performed based on the scale. KHOS-I had sufficient reliability (Cronbach alpha=.77). Participants were classified into low- and high-preference groups based on their KHOS-I scores. The high-preference group submitted significantly shorter queries when completing the look-up tasks (P=.02). The high-preference group made a significantly higher percentage of parallel movements in query

  14. The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services

    PubMed Central

    Phillips, Joshua; Chilukuri, Ram; Fragoso, Gilberto; Warzel, Denise; Covitz, Peter A

    2006-01-01

    Background Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. Results The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key

  15. The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.

    PubMed

    Phillips, Joshua; Chilukuri, Ram; Fragoso, Gilberto; Warzel, Denise; Covitz, Peter A

    2006-01-06

    Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for

  16. Asking Better Questions: How Presentation Formats Influence Information Search

    ERIC Educational Resources Information Center

    Wu, Charley M.; Meder, Björn; Filimon, Flavia; Nelson, Jonathan D.

    2017-01-01

    While the influence of presentation formats have been widely studied in Bayesian reasoning tasks, we present the first systematic investigation of how presentation formats influence information search decisions. Four experiments were conducted across different probabilistic environments, where subjects (N = 2,858) chose between 2 possible search…

  17. 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…

  18. 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…

  19. 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…

  20. 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…

  1. 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…

  2. 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…

  3. 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.

  4. 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…

  5. Searching electronically for information on transcultural nursing and health subjects.

    PubMed

    Andrews, Margaret; Burr, Jennifer; Janetos, Deborah H

    2004-07-01

    With the proliferation of electronic resources available to search for subjects related to transcultural nursing and health, nurses must keep abreast of computer-based tools that enable them to quickly and efficiently obtain information on a variety of topics. This article provides suggestions for narrowing and focusing a search on transcultural nursing and related subjects using important research databases such as Medline and Cumulative Index to Nursing and Allied Health Literature (CINAHL). Information about additional useful databases such as Educational Resources Information Center (ERIC) and Psychological Abstracts (PsycINFO) is also provided. In the article, selected examples of Internet sites of interest in transcultural nursing and health are identified and described in brief annotations. Web sites for U.S. government agencies, organizations, and commercial groups that concern transcultural nursing and health care are cited. Global transcultural health and nursing Internet resources also are included.

  6. 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.

  7. 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

  8. Why not just Google it? An assessment of information literacy skills in a biomedical science curriculum

    PubMed Central

    2011-01-01

    Background Few issues in higher education are as fundamental as the ability to search for, evaluate, and synthesize information. The need to develop information literacy, the process of finding, retrieving, organizing, and evaluating the ever-expanding collection of online information, has precipitated the need for training in skill-based competencies in higher education, as well as medical and dental education. Methods The current study evaluated the information literacy skills of first-year dental students, consisting of two, consecutive dental student cohorts (n = 160). An assignment designed to evaluate information literacy skills was conducted. In addition, a survey of student online search engine or database preferences was conducted to identify any significant associations. Subsequently, an intervention was developed, based upon the results of the assessment and survey, to address any deficiencies in information literacy. Results Nearly half of students (n = 70/160 or 43%) missed one or more question components that required finding an evidence-based citation. Analysis of the survey revealed a significantly higher percentage of students who provided incorrect responses (n = 53/70 or 75.7%) reported using Google as their preferred online search method (p < 0.01). In contrast, a significantly higher percentage of students who reported using PubMed (n = 39/45 or 86.7%) were able to provide correct responses (p < 0.01). Following a one-hour intervention by a health science librarian, virtually all students were able to find and retrieve evidence-based materials for subsequent coursework. Conclusions This study confirmed that information literacy among this student population was lacking and that integration of modules within the curriculum can help students to filter and establish the quality of online information, a critical component in the training of new health care professionals. Furthermore, incorporation of these modules early in the curriculum may be of

  9. eClims: An Extensible and Dynamic Integration Framework for Biomedical Information Systems.

    PubMed

    Savonnet, Marinette; Leclercq, Eric; Naubourg, Pierre

    2016-11-01

    Biomedical information systems (BIS) require consideration of three types of variability: data variability induced by new high throughput technologies, schema or model variability induced by large scale studies or new fields of research, and knowledge variability resulting from new discoveries. Beyond data heterogeneity, managing variabilities in the context of BIS requires extensible and dynamic integration process. In this paper, we focus on data and schema variabilities and we propose an integration framework based on ontologies, master data, and semantic annotations. The framework addresses issues related to: 1) collaborative work through a dynamic integration process; 2) variability among studies using an annotation mechanism; and 3) quality control over data and semantic annotations. Our approach relies on two levels of knowledge: BIS-related knowledge is modeled using an application ontology coupled with UML models that allow controlling data completeness and consistency, and domain knowledge is described by a domain ontology, which ensures data coherence. A system build with the eClims framework has been implemented and evaluated in the context of a proteomic platform.

  10. Ethics Review Committee approval and informed consent: an analysis of biomedical publications originating from Sri Lanka

    PubMed Central

    Sumathipala, Athula; Siribaddana, Sisira; Hewege, Suwin; Lekamwattage, Manura; Athukorale, Manjula; Siriwardhana, Chesmal; Murray, Joanna; Prince, Martin

    2008-01-01

    Background International guidelines on research have focused on protecting research participants. Ethical Research Committee (ERC) approval and informed consent are the cornerstones. Externally sponsored research requires approval through ethical review in both the host and the sponsoring country. This study aimed to determine to what extent ERC approval and informed consent procedures are documented in locally and internationally published human subject research carried out in Sri Lanka. Methods We obtained ERC approval in Sri Lanka and the United Kingdom. Theses from 1985 to 2005 available at the Postgraduate Institute of Medicine (PGIM) library affiliated to the University of Colombo were scrutinised using checklists agreed in consultation with senior research collaborators. A Medline search was carried out with MeSH major and minor heading 'Sri Lanka' as the search term for international publications originating in Sri Lanka during 1999 to 2004. All research publications from CMJ during 1999 to 2005 were also scrutinized. Results Of 291 theses, 34% documented ERC approvals and 61% documented obtaining consent. From the international journal survey, 250 publications originated from Sri Lanka of which only 79 full text original research publications could be accessed electronically. Of these 38% documented ERC approval and 39% documented obtaining consent. In the Ceylon Medical Journal 36% documented ERC approval and 37% documented obtaining consent. Conclusion Only one third of the publications scrutinized recorded ERC approval and procurement of informed consent. However, there is a positive trend in documenting these ethical requirements in local postgraduate research and in the local medical journal. PMID:18267015

  11. Specialized medical search-engines are no better than general search-engines in sourcing consumer information about androgen deficiency.

    PubMed

    Ilic, D; Bessell, T L; Silagy, C A; Green, S

    2003-03-01

    The Internet provides consumers with access to online health information; however, identifying relevant and valid information can be problematic. Our objectives were firstly to investigate the efficiency of search-engines, and then to assess the quality of online information pertaining to androgen deficiency in the ageing male (ADAM). Keyword searches were performed on nine search-engines (four general and five medical) to identify website information regarding ADAM. Search-engine efficiency was compared by percentage of relevant websites obtained via each search-engine. The quality of information published on each website was assessed using the DISCERN rating tool. Of 4927 websites searched, 47 (1.44%) and 10 (0.60%) relevant websites were identified by general and medical search-engines respectively. The overall quality of online information on ADAM was poor. The quality of websites retrieved using medical search-engines did not differ significantly from those retrieved by general search-engines. Despite the poor quality of online information relating to ADAM, it is evident that medical search-engines are no better than general search-engines in sourcing consumer information relevant to ADAM.

  12. Information Seeking and Mediated Searching. Part 4. Cognitive Styles in Information Seeking.

    ERIC Educational Resources Information Center

    Ford, Nigel; Wilson, T. D.; Foster, Allen; Ellis, David; Spink, Amanda

    2002-01-01

    Tested hypotheses linking global/analytic cognitive styles and aspects of researchers' problem-solving and related information-seeking behavior, based on a longitudinal study conducted in the United Sates and the United Kingdom that investigated the processes of mediated information retrieval searching during human information-seeking processes.…

  13. 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

  14. Active learning-based information structure analysis of full scientific articles and two applications for biomedical literature review.

    PubMed

    Guo, Yufan; Silins, Ilona; Stenius, Ulla; Korhonen, Anna

    2013-06-01

    Techniques that are capable of automatically analyzing the information structure of scientific articles could be highly useful for improving information access to biomedical literature. However, most existing approaches rely on supervised machine learning (ML) and substantial labeled data that are expensive to develop and apply to different sub-fields of biomedicine. Recent research shows that minimal supervision is sufficient for fairly accurate information structure analysis of biomedical abstracts. However, is it realistic for full articles given their high linguistic and informational complexity? We introduce and release a novel corpus of 50 biomedical articles annotated according to the Argumentative Zoning (AZ) scheme, and investigate active learning with one of the most widely used ML models-Support Vector Machines (SVM)-on this corpus. Additionally, we introduce two novel applications that use AZ to support real-life literature review in biomedicine via question answering and summarization. We show that active learning with SVM trained on 500 labeled sentences (6% of the corpus) performs surprisingly well with the accuracy of 82%, just 2% lower than fully supervised learning. In our question answering task, biomedical researchers find relevant information significantly faster from AZ-annotated than unannotated articles. In the summarization task, sentences extracted from particular zones are significantly more similar to gold standard summaries than those extracted from particular sections of full articles. These results demonstrate that active learning of full articles' information structure is indeed realistic and the accuracy is high enough to support real-life literature review in biomedicine. The annotated corpus, our AZ classifier and the two novel applications are available at http://www.cl.cam.ac.uk/yg244/12bioinfo.html

  15. Sequential pattern mining for discovering gene interactions and their contextual information from biomedical texts.

    PubMed

    Cellier, Peggy; Charnois, Thierry; Plantevit, Marc; Rigotti, Christophe; Crémilleux, Bruno; Gandrillon, Olivier; Kléma, Jiří; Manguin, Jean-Luc

    2015-01-01

    Discovering gene interactions and their characterizations from biological text collections is a crucial issue in bioinformatics. Indeed, text collections are large and it is very difficult for biologists to fully take benefit from this amount of knowledge. Natural Language Processing (NLP) methods have been applied to extract background knowledge from biomedical texts. Some of existing NLP approaches are based on handcrafted rules and thus are time consuming and often devoted to a specific corpus. Machine learning based NLP methods, give good results but generate outcomes that are not really understandable by a user. We take advantage of an hybridization of data mining and natural language processing to propose an original symbolic method to automatically produce patterns conveying gene interactions and their characterizations. Therefore, our method not only allows gene interactions but also semantics information on the extracted interactions (e.g., modalities, biological contexts, interaction types) to be detected. Only limited resource is required: the text collection that is used as a training corpus. Our approach gives results comparable to the results given by state-of-the-art methods and is even better for the gene interaction detection in AIMed. Experiments show how our approach enables to discover interactions and their characterizations. To the best of our knowledge, there is few methods that automatically extract the interactions and also associated semantics information. The extracted gene interactions from PubMed are available through a simple web interface at https://bingotexte.greyc.fr/. The software is available at https://bingo2.greyc.fr/?q=node/22.

  16. Impact of French 'Comités de Protection des Personnes' on the readability of informed consent documents (ICD) in biomedical research: more information, but not better information.

    PubMed

    Paris, Adeline; Cracowski, Jean-Luc; Maison, Patrick; Radauceanu, Anca; Cornu, Catherine; Hommel, Marc

    2005-06-01

    Information is the keystone to the participation of subjects in biomedical research. Clear comprehension of the informed consent documents (ICDs) is primordial and a necessary requirement is that they are readable. While submission of a protocol to a French 'Comités de Protection des Personnes' (CPP) is a mandatory step with regard to the French legislation on biomedical research, no published data are available concerning its influence on ICDs readability. The aim of our study was to determine the impact of French CPP on the readability of ICDs, using lexico-syntactic readability indexes and ICDs from four clinical research centres and one clinical research unit. Twenty-five ICDs were analysed. The Flesch score was not modified after CPP review, while the Cordial score was significantly lower [from 4 (1-14) to 1 (1-13), P = 0.014]. The information was longer and more complex following CPP review. No protocol characteristics had any impact on the variation before and after review for either the Flesch or the Cordial indexes, nor on the number of syllables per word. Changes in the total number of words before and after review varied considerably between study centre, supporting heterogeneity of CPP review. Since August 2004, French CPP have to study the intelligibility of ICDs in addition to the scientific and ethic aspects of a research. We show that their current reviews do not increase the readability, while increasing the length of ICDs.

  17. 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…

  18. 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…

  19. Institute for Scientific Information-indexed biomedical journals of Saudi Arabia. Their performance from 2007-2014.

    PubMed

    Rohra, Dileep K; Rohra, Vikram K; Cahusac, Peter

    2016-11-01

    To compare the journal impact factor (JIF) and Eigenfactor score (ES) of Institute for Scientific Information (ISI)-indexed biomedical journals published from the Kingdom of Saudi Arabia (KSA) over the last 8 years. Methods: This is a retrospective study, conducted at Alfaisal University, Riyadh, KSA from January to March 2016. The Journal Citation Reports of ISI Web of Knowledge were accessed, and 6 Saudi biomedical journals were included for analysis. Results: All Saudi journals have improved their IF compared with their baseline. However, the performance of the Journal of Pharmaceutical Sciences and Neurosciences has been exceptionally good. The biggest improvement in percent growth in JIF was seen in the Saudi Pharmaceutical Journal (approximately 887%) followed by Neurosciences (approximately 462%). Interestingly, the ES of all biomedical journals, except Saudi Journal of Gastroenterology and Saudi Medical Journal, increased over the years. The greatest growth in ES (more than 5 fold) was noted for Neurosciences and Saudi Pharmaceutical Journal. Conclusion: This study shows that the overall quality of all Saudi biomedical journals has improved in the last 8 years.

  20. 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

  1. 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

  2. Information spread of emergency events: path searching on social networks.

    PubMed

    Dai, Weihui; Hu, Hongzhi; Wu, Tunan; Dai, Yonghui

    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.

  3. A Probabilistic Approach to Information Retrieval in Systems with Boolean Search Request Formulations.

    ERIC Educational Resources Information Center

    Radecki, Tadeusz

    1982-01-01

    Outlines an approach to information retrieval which integrates the existing theory of probabilistic retrieval into a practical methodology based on Boolean searches. Basic concepts, search methodology, and examples of Boolean searching are noted. Twenty-six sources are appended. (EJS)

  4. Foraging for Information in the EHR: The Search for Adherence Related Information by Mental Health Clinicians

    PubMed Central

    Gibson, Bryan; Butler, Jorie; Zirkle, Maryan; Hammond, Kenric; Weir, Charlene

    2016-01-01

    In this project we sought to qualitatively describe clinician’s search for information related to the complex construct of adherence. Nineteen think aloud observations and semi-structured interviews were conducted with mental health providers as they prepared for a patient visit. The transcripts were coded according to constructs from information foraging theory (information goal, patch, scent, enrichment, and opportunity cost). The search strategies uncovered were complicated: provider’s searches were sometimes multi-staged (e.g. a search of the EHR led to further enquiry when interviewing the patient), and involved multiple ‘patches’ (i.e. data from the EHR, the patient and other providers were all sought out). In addition, some information that providers considered relevant to understand adherence related questions was non-obvious (e.g. the absence of specific information was considered a useful cue). Providers’ information search strategies for complex constructs are at times non-intuitive; implications for the design of EHR summarization tools are discussed. PMID:28269856

  5. 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.

  6. Expertise, visual search, and information pick-up in squash.

    PubMed

    Abernethy, B

    1990-01-01

    The visual search characteristics of expert and novice squash players were compared in two experiments. In the first experiment subjects were required to predict the forthcoming direction and force of an opponent's stroke from a film display. This film display was designed to simulate the normal display available to the defending player in squash and involved the use of variable temporal cut-offs to force the subjects to use advance cues in their prediction. Systematic differences in the information pick-up of the experts and novices were observed on the film task but these differences were achieved with only relatively minor between-group variations in visual search strategy. In the second experiment, set in the natural field setting, no expert-novice differences in either fixation distribution, order, or duration were observed on a comparable prediction task. This provided further support for the conclusion that the limiting factor in the perceptual performance of the novices is not an inappropriate search strategy but rather an inability to make full use of the information available from fixated display features. Some practical implications of these findings for the squash coach and player are considered.

  7. 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…

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

    PubMed

    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.

  9. 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

  10. The Effects of Preference for Information on Consumers’ Online Health Information Search Behavior

    PubMed Central

    2013-01-01

    Background Preference for information is a personality trait that affects people’s tendency to seek information in health-related situations. Prior studies have focused primarily on investigating its impact on patient-provider communication and on the implications for designing information interventions that prepare patients for medical procedures. Few studies have examined its impact on general consumers’ interactions with Web-based search engines for health information or the implications for designing more effective health information search systems. Objective This study intends to fill this gap by investigating the impact of preference for information on the search behavior of general consumers seeking health information, their perceptions of search tasks (representing information needs), and user experience with search systems. Methods Forty general consumers who had previously searched for health information online participated in the study in our usability lab. Preference for information was measured using Miller’s Monitor-Blunter Style Scale (MBSS) and the Krantz Health Opinion Survey-Information Scale (KHOS-I). Each participant completed four simulated health information search tasks: two look-up (fact-finding) and two exploratory. Their behaviors while interacting with the search systems were automatically logged and ratings of their perceptions of tasks and user experience with the systems were collected using Likert-scale questionnaires. Results The MBSS showed low reliability with the participants (Monitoring subscale: Cronbach alpha=.53; Blunting subscale: Cronbach alpha=.35). Thus, no further analyses were performed based on the scale. KHOS-I had sufficient reliability (Cronbach alpha=.77). Participants were classified into low- and high-preference groups based on their KHOS-I scores. The high-preference group submitted significantly shorter queries when completing the look-up tasks (P=.02). The high-preference group made a significantly higher

  11. The development of a quality-and-multimedia-based health web information searching tool.

    PubMed

    Chang, Hui-Jou; Chang, Polun

    2009-01-01

    People have not been satisfied with the search tools of web health information. We built a prototype easy-to-use web information searching tool by using multimedia techniques, combined with the emphasis of result presentation and content quality information. Instead of traditional search methods, we provide quality and webpage source information of websites for people to get useful information, and present search result by graphs and animations for people to get better user experience.

  12. Electrophysiological measurement of information flow during visual search.

    PubMed

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

    2016-04-01

    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.

  13. Information asymmetry and search in the market for physicians' services.

    PubMed

    Rochaix, L

    1989-03-01

    This paper offers an integrated approach to the physician-patient interaction based on the notion of a conditional demand function where the physician 'proposes' and the patient 'disposes'. The model specifies the information asymmetry between the physician and the patient mainly in terms of a differential in uncertainty about the patient's health status. An imperfect agency may result, leading some physicians to recommend more (less) treatment than the patient would have chosen, had the patient been fully informed. But patients are shown to exert pressure on their physician by potentially seeking a second opinion. In effect, patients' search for an adequate treatment becomes an ex ante monitoring technique, which induces physicians to act as 'better agents'. We further show, by means of a simulation, that it is enough for a small number of patients to be well informed for this result to hold.

  14. 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)…

  15. 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)…

  16. [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.

  17. Log analysis to understand medical professionals' image searching behaviour.

    PubMed

    Tsikrika, Theodora; Müller, Henning; Kahn, Charles E

    2012-01-01

    This paper reports on the analysis of the query logs of a visual medical information retrieval system that provides access to radiology resources. Our analysis shows that, despite sharing similarities with general Web search and also with biomedical text search, query formulation and query modification when searching for visual biomedical information have unique characteristics that need to be taken into account in order to enhance the effectiveness of the search support offered by such systems. Typical information needs of medical professionals searching radiology resources are also identified with the goal to create realistic search tasks for a medical image retrieval evaluation benchmark.

  18. 75 FR 25239 - Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-07

    ... invited to review the literature search results and submit additional information to EPA. Literature... From the Federal Register Online via the Government Publishing Office ENVIRONMENTAL PROTECTION AGENCY Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches for...

  19. 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

  20. Re-ranking with context for high-performance biomedical information retrieval.

    PubMed

    Yin, Xiaoshi; Huang, Jimmy Xiangji; Li, Zhoujun

    2012-01-01

    In this paper, we present a context-sensitive approach to re-ranking retrieved documents for further improving the effectiveness of high-performance biomedical literature retrieval systems. For each topic, a two-dimensional positive context is learnt from the top N retrieved documents and a group of negative contexts are learnt from the last N' documents in initial retrieval ranked list. The contextual space contains lexical context and conceptual context. The probabilities that retrieved documents are generated within the contextual space are then computed for document re-ranking. Empirical evaluation on the TREC Genomics full-text collection and three high-performance biomedical literature retrieval runs demonstrates that the context-sensitive re-ranking approach yields better retrieval performance.

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

    PubMed

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

    2010-01-01

    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 of an

  2. The impact of information skills training on independent literature searching activity and requests for mediated literature searches.

    PubMed

    Addison, John; Glover, Steven William; Thornton, Christine

    2010-09-01

    Most NHS library services routinely offer both mediated searches and information skills training sessions to their users. We analyse the impact of these two services on the amount of literature searching demonstrated by users of hospital- based library services in the north-west of England. Data for (1) mediated literature searches, (2) number of library users attending information skills training sessions, (3) amount of library staff time devoted to information skills training, and (4) number of Athens-authenticated log-ins to databases were obtained from statistical returns for 2007, and analysed for significant correlations. There was evidence of quite strong correlations between the two measures of training activity and the number of mediated literature searches performed by library staff. There was weaker evidence of correlation between training activity and total literature searching activity. Attending training sessions may make some library users aware of the difficulty of complex literature searches and actually reduce their confidence to perform their own complex searches independently. The relationships between information skills training, mediated literature searches, and independent literature searching activity remain complex.

  3. 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)

  4. 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)

  5. The National Institutes of Health's Biomedical Translational Research Information System (BTRIS): design, contents, functionality and experience to date.

    PubMed

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

    2014-12-01

    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.

  6. 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.

  7. The roles of biomedical maintenance branch, automation management & informatics departments throughout a clinical information systems's life cycle.

    PubMed

    Williams, D; Beebe, M E; Levin, B L

    1994-01-01

    The introduction of new technology, such as a Clinical Information System (CIS), requires hospitals to re-evaluate the roles of the Biomedical Maintenance Branch, Automation Management, and Informatics departments. This paper describes the process a 400-bed hospital underwent to resolve role ambiguity among the three activities. The institution's goal was to reach an optimal solution to using the resources offered by each activity through redrawing lines of responsibilities. This experience demonstrated that relationships among departments are dynamic and vary depending on the stage of the CIS life cycle.

  8. 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

  9. How much information? East Asian and North American cultural products and information search performance.

    PubMed

    Wang, Huaitang; Masuda, Takahiko; Ito, Kenichi; Rashid, Marghalara

    2012-12-01

    Literature in cultural psychology suggests that compared with North Americans, East Asians prefer context-rich cultural products (e.g., paintings and photographs). The present article further examines the preferred amount of information in cultural products produced by East Asians and North Americans (Study 1: Society for Personality and Social Psychology conference posters; Study 2: government and university portal pages). The authors found that East Asians produced more information-rich products than did North Americans. Study 3 further examined people's information search speed when identifying target objects on mock webpages containing large amounts of information. The results indicated that East Asians were faster than North Americans in dealing with information on mock webpages with large amounts of information. Finally, the authors found that there were cultural differences as well as similarities in functional and aesthetic preferences regarding styles of information presentation. The interplay between cultural products and skills for accommodating to the cultural products is discussed.

  10. Migrant information, job search and the remigration decision.

    PubMed

    Herzog Hwj; Schlottmann, A M

    1983-07-01

    "Labor force migration poses two important questions for the economist. The first concerns the nature, magnitude and direction of labor force response to perceived earnings differentials over space. The latter and more complex question concerns the effectiveness, or efficiency, of this response--namely migration--and other market mechanisms in reducing these earnings differentials over time." Both questions are addressed in this paper "by examining relationships among: (1) quality of information obtained prior to a move, (2) search duration at the migration destination, and (3) the likelihood of subsequent (perhaps corrective) remigration." These relationships are analyzed using the human capital model of migration-remigration and data from the 1970 U.S. census.

  11. 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

  12. [Human rights. Right to health. Right to health information. The Venezuelan biomedical journals].

    PubMed

    Stegemann, Herbert

    2013-06-01

    Venezuelan Biomedical journals have been confronting, for several years, a gradual decline both, from the standpoint of their management and in the quality of their editorial content. At its highest level, Venezuela had about sixty different titles. But irregular financial support, as well as the lack of a clear official policy, regarding these scientific activities, were some of the reasons that have contributed to this decline. Several recent Venezuelan and international documents provide an important legal support for the design of new official policies and government responsibilities. There is now a valid opportunity to profit from new tools to evaluate and improve the quality of our scientific and editorial activities.

  13. 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' outcomes...

  14. 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 Search...

  15. The Information-Seeking Practices of Engineers: Searching for Documents as Well as for People.

    ERIC Educational Resources Information Center

    Hertzum, Morten; Pejtersen, Annelise Mark

    2000-01-01

    Investigates engineers' information-seeking practices based on case studies in two organizations. Results show engineers search for documents to find people, search for people to get documents, and interact socially to get information without engaging in explicit searches. Discusses the design task and how computer systems could support searches…

  16. 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…

  17. Secure information embedding into 1D biomedical signals based on SPIHT.

    PubMed

    Rubio, Oscar J; Alesanco, Alvaro; García, José

    2013-08-01

    This paper proposes an encoding system for 1D biomedical signals that allows embedding metadata and provides security and privacy. The design is based on the analysis of requirements for secure and efficient storage, transmission and access to medical tests in e-health environment. This approach uses the 1D SPIHT algorithm to compress 1D biomedical signals with clinical quality, metadata embedding in the compressed domain to avoid extra distortion, digital signature to implement security and attribute-level encryption to support Role-Based Access Control. The implementation has been extensively tested using standard electrocardiogram and electroencephalogram databases (MIT-BIH Arrhythmia, MIT-BIH Compression and SCCN-EEG), demonstrating high embedding capacity (e.g. 3 KB in resting ECGs, 200 KB in stress tests, 30 MB in ambulatory ECGs), short delays (2-3.3s in real-time transmission) and compression of the signal (by ≃3 in real-time transmission, by ≃5 in offline operation) despite of the embedding of security elements and metadata to enable e-health services.

  18. Searching the Internet for information on prostate cancer screening: an assessment of quality.

    PubMed

    Ilic, Dragan; Risbridger, Gail; Green, Sally

    2004-07-01

    To identify how on-line information relating to prostate cancer screening (PCS) is best sourced, whether through general, medical, or meta-search engines, and to assess the quality of that information. Websites providing information about PCS were searched across 15 search engines representing three distinct types: general, medical, and meta-search engines. The quality of on-line information was assessed using the DISCERN quality assessment tool. Quality performance characteristics were analyzed by performing Mann-Whitney U tests. Search engine efficiency was measured by each search query as a percentage of the relevant websites included for analysis from the total returned and analyzed by performing Kruskal-Wallis analysis of variance. Of 6690 websites reviewed, 84 unique websites were identified as providing information relevant to PCS. General and meta-search engines were significantly more efficient at retrieving relevant information on PCS compared with medical search engines. The quality of information was variable, with most of a poor standard. Websites that provided referral links to other resources and a citation of evidence provided a significantly better quality of information. In contrast, websites offering a direct service were more likely to provide a significantly poorer quality of information. The current lack of a clear consensus on guidelines and recommendation in published data is also reflected by the variable quality of information found on-line. Specialized medical search engines were no more likely to retrieve relevant, high-quality information than general or meta-search engines.

  19. 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.

  20. 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.

  1. 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)

  2. 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)

  3. Exploring antecedents of consumer satisfaction and repeated search behavior on e-health information.

    PubMed

    Lee, Yun Jung; Park, Jungkun; Widdows, Richard

    2009-03-01

    E-health information has become an important resource for people seeking health information. Even though many studies have been conducted to examine the quality of e-health information, only a few studies have explored the effects of the information seekers' motivations on the perceived quality of e-health information. There is even less information about repeated searches for e-health information after the users' initial experience of e-health information use. Using an online survey of information seekers, 252 e-health information users' responses were collected. The research examines the relationship among motivation, perceived quality, satisfaction, and intention to repeat-search e-health information. The results identify motivations to search e-health information and confirm the relationship among motivation, perceived quality dimensions, and satisfaction and intention to repeat searches for e-health information.

  4. A Bayesian network coding scheme for annotating biomedical information presented to genetic counseling clients.

    PubMed

    Green, Nancy

    2005-04-01

    We developed a Bayesian network coding scheme for annotating biomedical content in layperson-oriented clinical genetics documents. The coding scheme supports the representation of probabilistic and causal relationships among concepts in this domain, at a high enough level of abstraction to capture commonalities among genetic processes and their relationship to health. We are using the coding scheme to annotate a corpus of genetic counseling patient letters as part of the requirements analysis and knowledge acquisition phase of a natural language generation project. This paper describes the coding scheme and presents an evaluation of intercoder reliability for its tag set. In addition to giving examples of use of the coding scheme for analysis of discourse and linguistic features in this genre, we suggest other uses for it in analysis of layperson-oriented text and dialogue in medical communication.

  5. 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

  6. Using Internet search engines to obtain medical information: a comparative study.

    PubMed

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

    2012-05-16

    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. To compare major Internet search engines in their usability of obtaining medical and health information. 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. 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 results highly overlapped between the

  7. 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-launcher/launcher.html > ).

  8. 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.

  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. 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…

  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. The Development of an Information Search and Recording System for Research and Development Organizations.

    ERIC Educational Resources Information Center

    Fitch, Judith Preuss; And Others

    This paper explains the development of an Information Search and Recording System (ISRS) for research and development organizations which require an efficient method of locating and recording stored information, including literature searches by staff members. The system will enable staff members to: (1) locate stored information by use of a…

  14. 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,…

  15. 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

  16. 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.

  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. Information Seeking and Mediated Searching. Part 5. User-Intermediary Interaction.

    ERIC Educational Resources Information Center

    Ellis, David; Wilson, T. D.; Ford, Nigel; Foster, Allen; Lam, H. M.; Burton, R.; Spink, Amanda

    2002-01-01

    Describes studies conducted at the University of Sheffield that explored the variables during mediated online search interaction. Discuses aspects of the mediated search process, including user satisfaction; relevant information sources; and interaction measures derived from search logs and tape transcripts, and related interaction measures.…

  19. 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…

  20. 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...

  1. 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 2...

  2. 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 2...

  3. 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...

  4. 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

  5. BioSimplify: an open source sentence simplification engine to improve recall in automatic biomedical information extraction.

    PubMed

    Jonnalagadda, Siddhartha; Gonzalez, Graciela

    2010-11-13

    BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification for improving human readability). The model is based on a "shot-gun" approach that produces many different (simpler) versions of the original sentence by combining variants of its constituent elements. This tool is optimized for processing biomedical scientific literature such as the abstracts indexed in PubMed. We tested our tool on its impact to the task of PPI extraction and it improved the f-score of the PPI tool by around 7%, with an improvement in recall of around 20%. The BioSimplify tool and test corpus can be downloaded from https://biosimplify.sourceforge.net.

  6. Confirming Preferences or Collecting Data? Information Search Strategies and Romantic Partner Selection

    PubMed Central

    Hennessy, Michael; Fishbein, Martin; Curtis, Brenda; Barrett, Daniel W.

    2010-01-01

    This article investigates two kinds of information search strategies in the context of selecting romantic partners. Confirmatory searching occurs when people ask for more information about a romantic partner in order to validate or confirm their assessment. Balanced searches are characterized by a search for risk information for partners rated as attractive and for attractiveness information about partners rated as risky in order to attain a more complete evaluation. A factorial survey computer program randomly constructed 5 types of partner descriptions and college-age respondents evaluated nine descriptions in terms of both health risk and romantic attractiveness outcomes. The results show little evidence of balanced search strategies: for all vignette types the respondents searched for attractiveness information. Regression analysis of the search outcomes showed no difference between males and females in the desire for attractiveness or risk information, the amount of additional information desired, or the proportion of descriptions for which more information was desired. However, an attractive physical appearance did increase the amount of additional information desired and the proportion of vignettes for which more information was desired. The results were generally inconsistent with a balanced search hypothesis; a better characterization of the respondents' strategy might be “confirmatory bias.” PMID:18350465

  7. Data management integration for biomedical core facilities

    NASA Astrophysics Data System (ADS)

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

    2007-03-01

    We present the design, development, and pilot-deployment experiences of MIMI, a web-based, Multi-modality Multi-Resource Information Integration environment for biomedical core facilities. This is an easily customizable, web-based software tool that integrates scientific and administrative support for a biomedical core facility involving a common set of entities: researchers; projects; equipments and devices; support staff; services; samples and materials; experimental workflow; large and complex data. With this software, one can: register users; manage projects; schedule resources; bill services; perform site-wide search; archive, back-up, and share data. With its customizable, expandable, and scalable characteristics, MIMI not only provides a cost-effective solution to the overarching data management problem of biomedical core facilities unavailable in the market place, but also lays a foundation for data federation to facilitate and support discovery-driven research.

  8. Finding and accessing diagrams in biomedical publications.

    PubMed

    Kuhn, Tobias; Luong, ThaiBinh; Krauthammer, Michael

    2012-01-01

    Complex relationships in biomedical publications are often communicated by diagrams such as bar and line charts, which are a very effective way of summarizing and communicating multi-faceted data sets. Given the ever-increasing amount of published data, we argue that the precise retrieval of such diagrams is of great value for answering specific and otherwise hard-to-meet information needs. To this end, we demonstrate the use of advanced image processing and classification for identifying bar and line charts by the shape and relative location of the different image elements that make up the charts. With recall and precisions of close to 90% for the detection of relevant figures, we discuss the use of this technology in an existing biomedical image search engine, and outline how it enables new forms of literature queries over biomedical relationships that are represented in these charts.

  9. Finding and Accessing Diagrams in Biomedical Publications

    PubMed Central

    Kuhn, Tobias; Luong, ThaiBinh; Krauthammer, Michael

    2012-01-01

    Complex relationships in biomedical publications are often communicated by diagrams such as bar and line charts, which are a very effective way of summarizing and communicating multi-faceted data sets. Given the ever-increasing amount of published data, we argue that the precise retrieval of such diagrams is of great value for answering specific and otherwise hard-to-meet information needs. To this end, we demonstrate the use of advanced image processing and classification for identifying bar and line charts by the shape and relative location of the different image elements that make up the charts. With recall and precisions of close to 90% for the detection of relevant figures, we discuss the use of this technology in an existing biomedical image search engine, and outline how it enables new forms of literature queries over biomedical relationships that are represented in these charts. PMID:23304318

  10. 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

  11. [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.

  12. 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

  13. Neural integration of top-down spatial and feature-based information in visual search.

    PubMed

    Egner, Tobias; Monti, Jim M P; Trittschuh, Emily H; Wieneke, Christina A; Hirsch, Joy; Mesulam, M-Marsel

    2008-06-11

    Visual search is aided by previous knowledge regarding distinguishing features and probable locations of a sought-after target. However, how the human brain represents and integrates concurrent feature-based and spatial expectancies to guide visual search is currently not well understood. Specifically, it is not clear whether spatial and feature-based search information is initially represented in anatomically segregated regions, nor at which level of processing expectancies regarding target features and locations may be integrated. To address these questions, we independently and parametrically varied the degree of spatial and feature-based (color) cue information concerning the identity of an upcoming visual search target while recording blood oxygenation level-dependent (BOLD) responses in human subjects. Search performance improved with the amount of spatial and feature-based cue information, and cue-related BOLD responses showed that, during preparation for visual search, spatial and feature cue information were represented additively in shared frontal, parietal, and cingulate regions. These data show that representations of spatial and feature-based search information are integrated in source regions of top-down biasing and oculomotor planning before search onset. The purpose of this anticipatory integration could lie with the generation of a "top-down salience map," a search template of primed target locations and features. Our results show that this role may be served by the intraparietal sulcus, which additively integrated a spatially specific activation gain in relation to spatial cue information with a spatially global activation gain in relation to feature cue information.

  14. Development and evaluation of a prototype search engine to meet public health information needs.

    PubMed

    Keeling, Jonathan W; Turner, Anne M; Allen, Eileen E; Rowe, Steven A; Merrill, Jacqueline A; Liddy, Elizabeth D; Turtle, Howard R

    2011-01-01

    Grey literature is information not available through commercial publishers. It is a sizable and valuable information source for public health (PH) practice but because documents are not formally indexed the information is difficult to locate. Public Health Information Search (PHIS) was developed to address this problem. NLP techniques were used to create informative document summaries for an extensive collection of grey literature on PH topics. The system was evaluated with PH workers using the critical incident technique in a two stage field evaluation to assess effectiveness in comparison with Google. Document summaries were found to be both helpful and accurate. Increased document collection size and enhanced result rankings improved search effectiveness from 28% to 55%. PHIS would work best in conjunction with Google or another broad coverage Web search engine when searching for documents and reports as opposed to local health data and primary disease information. PHIS could enhance both the quality and quantity of PH search results.

  15. Problematic internet use and internet searches for medical information: the role of health anxiety.

    PubMed

    Fergus, Thomas A; Dolan, Sara L

    2014-12-01

    Individuals frequently use the Internet to search for medical information. For some individuals, repeated searches for medical information on the Internet exacerbate health anxiety. Researchers have termed this phenomenon "cyberchondria" and have suggested that cyberchondria might relate to the excessive use of the Internet for other purposes as well. The present study examined associations among Internet searches for medical information, health anxiety, and problematic Internet use (PIU) using a large sample of medically healthy community adults located in the United States (N=430). As predicted, respondents who experienced increased health anxiety following Internet searches for medical information reported significantly greater PIU than respondents for whom such searches either had no impact on or decreased their health anxiety. This effect was not attributable to the frequency of health-related online searching behavior or negative affect. Conceptual and therapeutic implications are discussed.

  16. [Online literature searches--a new dimension in mastering the information avalanche? A demonstration using examples].

    PubMed

    Zass, E

    1982-06-01

    Several examples of online literature searches in the Chemical Abstracts, Science Citation Index, and Biological Abstracts data bases are discussed to demonstrate that online searching is a powerful and very useful tool for retrieving information faster and more efficiently than before. This article attempts to stimulate scientists to familiarize themselves with this new technique and gain some personal experience, because online searching for information will probably become indispensable in scientific research and teaching in the near future.

  17. 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…

  18. 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…

  19. 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.

  20. 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…

  1. Which Occupational Analysis Technique: Critical Incident, DACUM, and/or Information Search?

    ERIC Educational Resources Information Center

    Willett, Jan; Hermann, Graham

    1989-01-01

    In a study of competencies needed by secondary school teachers, the comparative effectiveness of three occupational analysis techniques was examined. It was found that DACUM and Information Search were equally effective, and critical incident was less effective. It was considered that both DACUM and Information Search needed to be used to obtain…

  2. 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…

  3. 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…

  4. 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)…

  5. Information Search as an Indication of Rationality in Student Choice of Higher Education

    ERIC Educational Resources Information Center

    Menon, Maria E.

    2004-01-01

    This paper investigates the degree of information search that precedes the choice of a private third-level educational institution in Cyprus. Information search is used as an indication of rationality in order to provide a test for the economic approach to the explanation of human behaviour. A survey was conducted among 120 college students in the…

  6. 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…

  7. Target-present guessing as a function of target prevalence and accumulated information in visual search.

    PubMed

    Peltier, Chad; Becker, Mark W

    2017-02-09

    Target prevalence influences visual search behavior. At low target prevalence, miss rates are high and false alarms are low, while the opposite is true at high prevalence. Several models of search aim to describe search behavior, one of which has been specifically intended to model search at varying prevalence levels. The multiple decision model (Wolfe & Van Wert, Current Biology, 20(2), 121--124, 2010) posits that all searches that end before the observer detects a target result in a target-absent response. However, researchers have found very high false alarms in high-prevalence searches, suggesting that prevalence rates may be used as a source of information to make "educated guesses" after search termination. Here, we further examine the ability for prevalence level and knowledge gained during visual search to influence guessing rates. We manipulate target prevalence and the amount of information that an observer accumulates about a search display prior to making a response to test if these sources of evidence are used to inform target present guess rates. We find that observers use both information about target prevalence rates and information about the proportion of the array inspected prior to making a response allowing them to make an informed and statistically driven guess about the target's presence.

  8. Using the iHOP information resource to mine the biomedical literature on genes, proteins, and chemical compounds.

    PubMed

    Hoffmann, Robert

    2007-12-01

    The iHOP (Information Hyperlinked over Proteins) resource employs sophisticated text-mining methods to assist researchers in their quest for information on specific genes and proteins, their physical interactions and regulatory relationships, their relevance in pathologies, and their interactions with chemical compounds. iHOP parses thousands of PubMed documents every day and collects information specific to thousands of different biological molecules. Rather than providing long lists of entire abstracts upon keyword searches, iHOP selectively retrieves information that is specific to genes and proteins, and summarizes their interactions and functions. In iHOP, with genes and proteins acting as hyperlinks between sentences and abstracts, a large part of the PubMed knowledgebase becomes a giant navigable information network. (c) 2007 by John Wiley & Sons, Inc.

  9. 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

  10. Evaluating the process of online health information searching: a qualitative approach to exploring consumer perspectives.

    PubMed

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

    2014-10-07

    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. 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. 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. 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. 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 aimed at accommodating diverse populations

  11. Study of Query Expansion Techniques and Their Application in the Biomedical Information Retrieval

    PubMed Central

    Rivas, A. R.; Iglesias, E. L.; Borrajo, L.

    2014-01-01

    Information Retrieval focuses on finding documents whose content matches with a user query from a large document collection. As formulating well-designed queries is difficult for most users, it is necessary to use query expansion to retrieve relevant information. Query expansion techniques are widely applied for improving the efficiency of the textual information retrieval systems. These techniques help to overcome vocabulary mismatch issues by expanding the original query with additional relevant terms and reweighting the terms in the expanded query. In this paper, different text preprocessing and query expansion approaches are combined to improve the documents initially retrieved by a query in a scientific documental database. A corpus belonging to MEDLINE, called Cystic Fibrosis, is used as a knowledge source. Experimental results show that the proposed combinations of techniques greatly enhance the efficiency obtained by traditional queries. PMID:24723793

  12. Study of query expansion techniques and their application in the biomedical information retrieval.

    PubMed

    Rivas, A R; Iglesias, E L; Borrajo, L

    2014-01-01

    Information Retrieval focuses on finding documents whose content matches with a user query from a large document collection. As formulating well-designed queries is difficult for most users, it is necessary to use query expansion to retrieve relevant information. Query expansion techniques are widely applied for improving the efficiency of the textual information retrieval systems. These techniques help to overcome vocabulary mismatch issues by expanding the original query with additional relevant terms and reweighting the terms in the expanded query. In this paper, different text preprocessing and query expansion approaches are combined to improve the documents initially retrieved by a query in a scientific documental database. A corpus belonging to MEDLINE, called Cystic Fibrosis, is used as a knowledge source. Experimental results show that the proposed combinations of techniques greatly enhance the efficiency obtained by traditional queries.

  13. 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

  14. Development of health information search engine based on metadata and ontology.

    PubMed

    Song, Tae-Min; Park, Hyeoun-Ae; Jin, Dal-Lae

    2014-04-01

    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. 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. 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. Health information search engine based on metadata and ontology will provide reliable health information to both information producer and information consumers.

  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. Online games: a novel approach to explore how partial information influences human random searches

    NASA Astrophysics Data System (ADS)

    Martínez-García, Ricardo; Calabrese, Justin M.; López, Cristóbal

    2017-01-01

    Many natural processes rely on optimizing the success ratio of a search process. We use an experimental setup consisting of a simple online game in which players have to find a target hidden on a board, to investigate how the rounds are influenced by the detection of cues. We focus on the search duration and the statistics of the trajectories traced on the board. The experimental data are explained by a family of random-walk-based models and probabilistic analytical approximations. If no initial information is given to the players, the search is optimized for cues that cover an intermediate spatial scale. In addition, initial information about the extension of the cues results, in general, in faster searches. Finally, strategies used by informed players turn into non-stationary processes in which the length of e ach displacement evolves to show a well-defined characteristic scale that is not found in non-informed searches.

  17. Online games: a novel approach to explore how partial information influences human random searches.

    PubMed

    Martínez-García, Ricardo; Calabrese, Justin M; López, Cristóbal

    2017-01-06

    Many natural processes rely on optimizing the success ratio of a search process. We use an experimental setup consisting of a simple online game in which players have to find a target hidden on a board, to investigate how the rounds are influenced by the detection of cues. We focus on the search duration and the statistics of the trajectories traced on the board. The experimental data are explained by a family of random-walk-based models and probabilistic analytical approximations. If no initial information is given to the players, the search is optimized for cues that cover an intermediate spatial scale. In addition, initial information about the extension of the cues results, in general, in faster searches. Finally, strategies used by informed players turn into non-stationary processes in which the length of e ach displacement evolves to show a well-defined characteristic scale that is not found in non-informed searches.

  18. Online games: a novel approach to explore how partial information influences human random searches

    PubMed Central

    Martínez-García, Ricardo; Calabrese, Justin M.; López, Cristóbal

    2017-01-01

    Many natural processes rely on optimizing the success ratio of a search process. We use an experimental setup consisting of a simple online game in which players have to find a target hidden on a board, to investigate how the rounds are influenced by the detection of cues. We focus on the search duration and the statistics of the trajectories traced on the board. The experimental data are explained by a family of random-walk-based models and probabilistic analytical approximations. If no initial information is given to the players, the search is optimized for cues that cover an intermediate spatial scale. In addition, initial information about the extension of the cues results, in general, in faster searches. Finally, strategies used by informed players turn into non-stationary processes in which the length of e ach displacement evolves to show a well-defined characteristic scale that is not found in non-informed searches. PMID:28059115

  19. 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…

  20. Developing an Information Commitment Survey for Assessing Students' Web Information Searching Strategies and Evaluative Standards for Web Materials

    ERIC Educational Resources Information Center

    Wu, Ying-Tien; Tsai, Chin-Chung

    2007-01-01

    The idea of "information commitments" refers to both learners' online searching strategies and the evaluative standards that students use to assess the accuracy and usefulness of information in web-based learning environments. Based upon the results of a pioneering and qualitative study on information commitments, this study aimed to develop an…

  1. 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

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

    PubMed

    Dwairy, Mai; Dowell, Anthony C; Stahl, Jean-Claude

    2011-08-23

    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. 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. 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%. 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 time. As predicted by foraging theory, GPs

  3. 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…

  4. 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…

  5. 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…

  6. 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…

  7. Computer Supported Cooperative Work in Information Search and Retrieval.

    ERIC Educational Resources Information Center

    Twidale, Michael B.; Nichols, David M.

    1998-01-01

    Considers how research in collaborative technologies can inform research and development in library and information science. Topics include computer supported collaborative work; shared drawing; collaborative writing; MUDs; MOOs; workflow; World Wide Web; collaborative learning; computer mediated communication; ethnography; evaluation; remote…

  8. 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

  9. Information content and analysis methods for multi-modal high-throughput biomedical data.

    PubMed

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

    2014-03-21

    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.

  10. 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

  11. 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.

  12. Biomedical Imaging,

    DTIC Science & Technology

    precision required from the task. This report details the technologies in surface and subsurface imaging systems for research and commercial applications. Biomedical imaging, Anthropometry, Computer imaging.

  13. Guide to the Use of Information. Question Negotiation, Search Delivery, Search Evaluation.

    ERIC Educational Resources Information Center

    Kansas State Dept. of Education, Topeka.

    This guide to the use of information reviews the development of Kansas Project Communicate from 1972-1976, and the Kansas State Department of Education (KSDE) computerized information service (KEDDS), which serves as the resource component of the information dissemination system. KEDDS (Kansas Educational Dissemination Diffusion system) is…

  14. The price of information: Increased inspection costs reduce the confirmation bias in visual search.

    PubMed

    Rajsic, Jason; Wilson, Daryl E; Pratt, Jay

    2017-01-31

    In visual search, there is a confirmation bias such that attention is biased towards stimuli that match a target template, which has been attributed to covert costs of updating the templates that guide search [Rajsic, Wilson, & Pratt, 2015. Confirmation bias in visual search. Journal of Experimental Psychology: Human Perception and Performance. Advance online publication. doi: 10.1037/xhp0000090 ]. In order to provide direct evidence for this speculation, the present study increased the cost of inspections in search by using gaze- and mouse-contingent searches, which restrict the manner in which information in search displays can be accrued, and incur additional motor costs (in the case of mouse-contingent searches). In a fourth experiment, we rhythmically mask elements in the search display to induce temporal inspection costs. Our results indicated that confirmation bias is indeed attenuated when inspection costs are increased. We conclude that confirmation bias results from the low-cost strategy of matching information to a single, concrete visual template, and that more sophisticated guidance strategies will be used when sufficiently beneficial. This demonstrates that search guidance itself comes at a cost, and that the form of guidance adopted in a given search depends on a comparison between guidance costs and the expected benefits of their implementation.

  15. 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

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

    PubMed

    McClymont, Hoda; Gow, Jeff; Perry, Chad

    2014-01-01

    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? 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. 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. 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.

  18. 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

  19. 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.…

  20. The Library, Information, and Institutional Outcomes: Searching in a Time of Change.

    ERIC Educational Resources Information Center

    Brittingham, Barbara

    1997-01-01

    Describes how the University of Rhode Island conducted its search for a newly configured position of Vice Provost for Information and Dean of University Libraries. Discusses the search committee members, the two professional "cultures" representing libraries and academic computing, degree requirements, job responsibilities and…

  1. End User Search Systems: Access to Library and Information Science Literature.

    ERIC Educational Resources Information Center

    LaBorie, Tim; Garson, Ken

    1988-01-01

    This study investigated the usefulness of end user systems to library and information science students. Seventeen volunteers were offered free searching on BRS/After Dark and DIALOG's Knowledge Index. The search itself, postsearch questionnaire, and completed research papers were analyzed for databases used, cost and time online, and precision.…

  2. 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…

  3. 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…

  4. 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…

  5. 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.…

  6. 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

  7. A biomedical information system for retrieval and manipulation of NHANES data.

    PubMed

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

    2013-01-01

    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, recoded, 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.

  8. 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

  9. What do web-use skill differences imply for online health information searches?

    PubMed

    Feufel, Markus A; Stahl, S Frederica

    2012-06-13

    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. 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. 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. 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 confirm their health-related opinions

  10. Language preferences on websites and in Google searches for human health and food information.

    PubMed

    Singh, Punam Mony; Wight, Carly A; Sercinoglu, Olcan; Wilson, David C; Boytsov, Artem; Raizada, Manish N

    2007-06-28

    While it is known that the majority of pages on the World Wide Web are in English, little is known about the preferred language of users searching for health information online. (1) To help global and domestic publishers, for example health and food agencies, to determine the need for translation of online information from English into local languages. (2) To help these agencies determine which language(s) they should select when publishing information online in target nations and for target subpopulations within nations. To estimate the percentage of Web publishers that translate their health and food websites, we measured the frequency at which domain names retrieved by Google overlap for language translations of the same health-related search term. To quantify language choice of searchers from different countries, Google provided estimates of the rate at which its search engine was queried in six languages relative to English for the terms "avian flu," "tuberculosis," "schizophrenia," and "maize" (corn) from January 2004 to April 2006. The estimate was based on a 20% sample of all Google queries from 227 nations. We estimate that 80%-90% of health- and food-related institutions do not translate their websites into multiple languages, even when the information concerns pandemic disease such as avian influenza. Although Internet users are often well-educated, there was a strong preference for searching for health and food information in the local language, rather than English. For "avian flu," we found that only 1% of searches in non-English-speaking nations were in English, whereas for "tuberculosis" or "schizophrenia," about 4%-40% of searches in non-English countries employed English. A subset of searches for health information presumably originating from immigrants occurred in their native tongue, not the language of the adopted country. However, Spanish-language online searches for "avian flu," "schizophrenia," and "maize/corn" in the United States occurred

  11. Biomedical Imaging

    NASA Astrophysics Data System (ADS)

    MacPherson, Emma

    This chapter builds on the basic principles of THz spectroscopy and explains how they can be applied to biomedical systems as well as the motivation for doing so. Sample preparation techniques and measurement methods for biomedical samples are described in detail. Examples of medical applications investigated hitherto including breast cancer and skin cancer are also presented.

  12. Corrigendum: Information Search in Decisions From Experience: Do Our Patterns of Sampling Foreshadow Our Decisions?

    PubMed

    2017-09-01

    Original article: Hills, T. T., & Hertwig, R. (2010). Information search in decisions from experience: Do our patterns of sampling foreshadow our decisions? Psychological Science, 21, 1787-1792. doi:10.1177/0956797610387443.

  13. Improved informed consent documents for biomedical research do not increase patients’ understanding but reduce enrolment: a study in real settings

    PubMed Central

    Paris, Adeline; Deygas, Béatrice; Cornu, Catherine; Thalamas, Claire; Maison, Patrick; Duale, Christian; Kane, Maty; Hodaj, Enkelejda; Cracowski, Jean-Luc

    2015-01-01

    Aims The aim was to evaluate the comprehension of participants of an improved informed consent document (ICD). Method This was a randomized controlled French multicentre study performed in real conditions. Participants were adult patients undergoing screening for enrolment in biomedical research studies, who agreed to answer a validated questionnaire evaluating objective and subjective comprehension scored from 0 (no comprehension) to 100 (excellent comprehension). Patients were provided either the original ICD or an ICD modified in terms of structure and readability. The primary end point was the score of objective comprehension. The secondary end-points were the enrolment rate in the clinical study and patient characteristics associated with the score of objective comprehension. Results Four hundred and eighty-one patients were included, 241 patients in the original ICD group and 240 patients in the modified ICD group. There was no difference between the two groups for the score of objective comprehension (original ICD 72.7 (95% CI 71.3, 74.1) vs. modified ICD 72.5 (95% CI 71.0, 74.0); P = 0.81). However, the rate of enrolment in the clinical study was lower in the group who received the modified ICD (64.4% (95% CI 58.3, 70.5)) than for the original ICD (73.0% (95% CI 67.4, 78.7)) (P = 0.042). Only female gender and high educational level were associated with a better objective comprehension. Conclusions Improving ICDs had no effect on participants’ understanding, whereas the rate of enrolment was lower in this group. In attempts at improving potential participants’ understanding of clinical research information, efforts and future trials should focus on other ways to improve comprehension. PMID:26147763

  14. Donor conception, secrecy and the search for information.

    PubMed

    Allan, Sonia

    2012-06-01

    Donor conception has historically been shrouded in secrecy. Such secrecy has been underpinned by social views and legal issues concemrning the adults involved in the process--the donor, the recipient parent(s), and, at times, the doctor. However, there is increasing recognition of the need to focus upon donor-conceived people's interests and rights to have identifying and non-identifying information about their donors. This editorial examines issues raised in relation to information release, while also introducing some of the arguments presented by other authors in this Special Issue of the JLM. It also considers recent Australian federal and State government inquiries that have favoured information release and the former Victorian Infertility Treatment Authority's service model to support people in the process of information access and release. While there has been a clear shift to favouring openness and honesty, legislative action is still required to ensure the balancing and realisation of people's interests.

  15. A Study of Organizational Information Search, Acquisition, Storage and Retrieval

    DTIC Science & Technology

    1986-08-01

    literatures associated with the perspectives are described. The perspectives themselves are first contrasted and then, using a communicatins framework... corporation division. This 19 31 (selective distribution greatly reduces the information processing load of the many potential receiving units having...of Management, 11: 75-86. Shields, M.D. 1983. Effects of Information Supply and Demand on Judgment Accuracy: Evidence from Corporate Managers. The

  16. 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.

  17. Do dietary intakes affect search for nutrient information on food labels?

    PubMed

    Lin, Chung-Tung Jordan; Lee, Jonq-Ying; Yen, Steven T

    2004-11-01

    Nutrition labels on food packages are designed to promote and protect public health by providing nutrition information so that consumers can make informed dietary choices. High levels of total fat, saturated fat and cholesterol in diets are linked to increased blood cholesterol levels and a greater risk of heart disease. Therefore, an understanding of consumer use of total fat, saturated fat, and cholesterol information on food labels has important implications for public health and nutrition education. This study explores the association between dietary intakes of these three nutrients and psychological or demographic factors and the search for total fat, saturated fat, and cholesterol information on food labels. Psychology literature suggests a negative association between intakes of these nutrients and probability of search for their information on food labels. Health behavior theories also suggest perceived benefits and costs of using labels and perceived capability of using labels are associated with the search behavior. We estimate the relationship between label information search and its predictors using logistic regressions. Our samples came from the 1994-1996 Continuing Survey of Food Intakes by Individuals and Diet and Health Knowledge Survey conducted by the United States Department of Agriculture. Results suggest that search for total fat, saturated fat, and cholesterol information on food labels is less likely among individuals who consume more of the three nutrients, respectively. The search is also related to perceived benefits and costs of using the label, perceived capability of using the label, knowledge of nutrition and fats, perceived efficacy of diets in reducing the risk of illnesses, perceived importance of nutrition in food shopping, perceived importance of a healthy diet, and awareness of linkage between excessive consumption of the nutrients and health problems. These findings suggest encouraging search of food label information among

  18. An exploration of search patterns and credibility issues among older adults seeking online health information.

    PubMed

    Robertson-Lang, Laura; Major, Sonya; Hemming, Heather

    2011-12-01

    The Internet is an important resource for health information, among younger and older people alike. Unfortunately, there are limitations associated with online health information. Research is needed on the quality of information found online and on whether users are being critical consumers of the information they find. Also, there is a need for research investigating online use among adults aged 65 and over - a rapidly growing demographic of Internet users. The current study presents important descriptive data about the search patterns of older adults seeking online health information, the types of health topics they research, and whether they consider credibility issues when retrieving online health information. A comparison is also made between search strategies used in printed text and hypertext environments. The results, which have implications with respect to credibility issues, highlight the need to increase awareness about critical searching skills among older adult Internet users.

  19. Information overload or search-amplified risk? Set size and order effects on decisions from experience.

    PubMed

    Hills, Thomas T; Noguchi, Takao; Gibbert, Michael

    2013-10-01

    How do changes in choice-set size influence information search and subsequent decisions? Moreover, does information overload influence information processing with larger choice sets? We investigated these questions by letting people freely explore sets of gambles before choosing one of them, with the choice sets either increasing or decreasing in number for each participant (from two to 32 gambles). Set size influenced information search, with participants taking more samples overall, but sampling a smaller proportion of gambles and taking fewer samples per gamble, when set sizes were larger. The order of choice sets also influenced search, with participants sampling from more gambles and taking more samples overall if they started with smaller as opposed to larger choice sets. Inconsistent with information overload, information processing appeared consistent across set sizes and choice order conditions, reliably favoring gambles with higher sample means. Despite the lack of evidence for information overload, changes in information search did lead to systematic changes in choice: People who started with smaller choice sets were more likely to choose gambles with the highest expected values, but only for small set sizes. For large set sizes, the increase in total samples increased the likelihood of encountering rare events at the same time that the reduction in samples per gamble amplified the effect of these rare events when they occurred-what we call search-amplified risk. This led to riskier choices for individuals whose choices most closely followed the sample mean.

  20. Information theory, animal communication, and the search for extraterrestrial intelligence

    NASA Astrophysics Data System (ADS)

    Doyle, Laurance R.; McCowan, Brenda; Johnston, Simon; Hanser, Sean F.

    2011-02-01

    We present ongoing research in the application of information theory to animal communication systems with the goal of developing additional detectors and estimators for possible extraterrestrial intelligent signals. Regardless of the species, for intelligence (i.e., complex knowledge) to be transmitted certain rules of information theory must still be obeyed. We demonstrate some preliminary results of applying information theory to socially complex marine mammal species (bottlenose dolphins and humpback whales) as well as arboreal squirrel monkeys, because they almost exclusively rely on vocal signals for their communications, producing signals which can be readily characterized by signal analysis. Metrics such as Zipf's Law and higher-order information-entropic structure are emerging as indicators of the communicative complexity characteristic of an "intelligent message" content within these animals' signals, perhaps not surprising given these species' social complexity. In addition to human languages, for comparison we also apply these metrics to pulsar signals—perhaps (arguably) the most "organized" of stellar systems—as an example of astrophysical systems that would have to be distinguished from an extraterrestrial intelligence message by such information theoretic filters. We also look at a message transmitted from Earth (Arecibo Observatory) that contains a lot of meaning but little information in the mathematical sense we define it here. We conclude that the study of non-human communication systems on our own planet can make a valuable contribution to the detection of extraterrestrial intelligence by providing quantitative general measures of communicative complexity. Studying the complex communication systems of other intelligent species on our own planet may also be one of the best ways to deprovincialize our thinking about extraterrestrial communication systems in general.

  1. Information Search Behaviors of Indian Farmers: Implications for Extension Services

    ERIC Educational Resources Information Center

    Glendenning, Claire J.; Babu, Suresh C.; Asenso-Okyere, Kwadwo

    2012-01-01

    Purpose: In India, a national survey conducted in 2003 showed that only 40% of farmers accessed extension. But little is known of the characteristics of farmers who did not access extension. However, this understanding is needed in order to target approaches to farmers, who differ in their access and use of information, that is their information…

  2. Information Science and the Martial Arts: Perspectives on Online Searching.

    ERIC Educational Resources Information Center

    Raitt, David I.

    The relatively new discipline of information science has its origins in the West, while the ancient martial arts have their origins in the East. Despite these differences in age and hemisphere, the two disciplines can be shown to possess many conceptual as well as technical similarities which have evolved quite independently of each other. This…

  3. Information Literacy--Don't Search the WWW Without It!

    NASA Astrophysics Data System (ADS)

    Cromer, Donna E.

    2002-04-01

    Physics and astronomy information resources are proliferating at a rapid pace today. The ability to differentiate between the myriad of resources available and to learn to evaluate them is a necessary skill if students are to succeed in college and beyond. This is not a new problem, in fact, yet it has become more urgent with the proliferation of the World Wide Web and the ability of anyone to put up a webpage. Too often students pay little attention to the authority behind a website, and use whatever they find without questioning the source. It is important, then, to include information literacy skills in the curriculum. Physics and astronomy librarians are uniquely qualified to assist in developing these skills. Even better is cooperation and collaboration between the librarian and the teaching faculty. In practice, this works best when any sort of information seeking assignment, including a research paper, is required for a class. Information literacy is defined and discussed, and an outline of an instruction session that could be used in conjunction with a research paper assignment is given.

  4. Information Science and the Martial Arts: Perspectives on Online Searching.

    ERIC Educational Resources Information Center

    Raitt, David I.

    The relatively new discipline of information science has its origins in the West, while the ancient martial arts have their origins in the East. Despite these differences in age and hemisphere, the two disciplines can be shown to possess many conceptual as well as technical similarities which have evolved quite independently of each other. This…

  5. Information Search Behaviors of Indian Farmers: Implications for Extension Services

    ERIC Educational Resources Information Center

    Glendenning, Claire J.; Babu, Suresh C.; Asenso-Okyere, Kwadwo

    2012-01-01

    Purpose: In India, a national survey conducted in 2003 showed that only 40% of farmers accessed extension. But little is known of the characteristics of farmers who did not access extension. However, this understanding is needed in order to target approaches to farmers, who differ in their access and use of information, that is their information…

  6. In Search of Credibility: Pupils' Information Practices in Learning Environments

    ERIC Educational Resources Information Center

    Sundin, Olof; Francke, Helena

    2009-01-01

    Introduction: We aim to create an in-depth understanding of how pupils in upper secondary school negotiate the credibility and authority of information as part of their practices of learning. Particular focus is on the use of user-created resources, such as "Wikipedia", where authorship is collective and/or hard to determine. Method: An…

  7. Capturing deaths not informed to the Ministry of Health: proactive search of deaths in Brazilian municipalities.

    PubMed

    Almeida, Wanessa da Silva de; Szwarcwald, Célia Landmann; Frias, Paulo Germano de; Souza, Paulo Roberto Borges de; Lima, Raquel Barbosa de; Rabello, Dácio de Lyra; Escalante, Juan José Cortez

    2017-01-01

    The proactive search of deaths is a strategy for capturing events that were not informed to the Mortality Information System of Ministry of Health. Its importance to reduce underreporting of deaths and to evaluate the operation of the information system is widely known. To describe the methodology and main findings of the Proactive Search of Deaths, 2013, establishing the contribution of different information sources. The research was carried out in 79 Brazilian municipalities. We investigated several official and unofficial sources of information about deaths of municipality residents. Every information source investigated and all cases found in each source were typed in an on-line panel. The second stage of the research was the confirmation of cases to verify information of year and residence and to complete missing information. For all confirmed cases, we estimated the completeness of death registration and correction factors according to the adequacy level of mortality information. We found 2,265 deaths that were not informed to the Mortality Information System. From those, 49.3% were found in unofficial sources, cemeteries and funeral homes. In some rural municipalities, precarious burial conditions were found in cemeteries in the middle of the forest and no registration of the deceased. Correction factors were inversely associated to the adequacy level of mortality information. The findings confirm the association between level of information adequacy and completeness of death registration, and indicate that the application of the proactive search is an effective method to capture deaths not informed to the Ministry of Health.

  8. 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.

  9. How Parents Search, Interpret, and Evaluate Genetic Information Obtained from the Internet

    PubMed Central

    Roche, Myra I.; Skinner, Debra

    2011-01-01

    This study describes how parents of a child referred for genetic services searched the Internet for information, summarizes how they interpreted and evaluated the information they obtained, and identifies barriers that they encountered. Audio-taped interviews were conducted with 100 ethnically diverse families referred to a pediatric genetics clinic. After transcription, coded text was entered into a software program (QSR N6) for searching and data retrieval. Matrices were created to systematically categorize and compare families’ Internet use. Eighty-three percent of families obtained Internet information about the diagnosis, the clinic visit, and/or treatment and services. Those not conducting searches lacked access, Internet experience, or a diagnostic term and had lower incomes and less education, regardless of ethnicity. Families sought information in preparation for the clinic visit but barriers to obtaining and interpreting relevant information were common. Parents’ Internet searching experiences illustrate common barriers to obtaining and understanding genetic information. Identifying them can help genetic counselors facilitate parents’ searches for relevant information. PMID:18937062

  10. The Twin Cities biomedical consortium.

    PubMed

    Bailey, A S

    1975-07-01

    Twenty-eight health science libraries in the St. Paul-Minneapolis area formed the Twin Cities Biomedical Consortium with the intention of developing a strong network of biomedical libraries in the Twin Cities area. Toward this end, programs were designed to strengthen lines of communication and increase cooperation among local health science libraries; improve access to biomedical information at the local level; and enable the Consortium, as a group, to meet an increasing proportion of its members' needs for biomedical information. Presently, the TCBC comprises libraries in twenty-two hospitals, two county medical societies, one school of nursing, one junior college, and two private corporations.

  11. Study on the Web Information Search Prediction Algorithm

    NASA Astrophysics Data System (ADS)

    Wang, Zhong-Sheng; Cao, Mei

    This paper introduces the methods of tailing after user's browsing action and forecasting users' download action. In order to foresee user's download action, when user is applying for a web page at browser, the query string based on hierarchical information directory, which is presented to database server, is recorded. When these query strings have been processed with certain algorithm, user's interested strength level to certain product can be obtained.

  12. Evaluating medical student searches of MEDLINE for evidence-based information: process and application of results.

    PubMed

    Burrows, S C; Tylman, V

    1999-10-01

    To evaluate the adequacy of the MEDLINE instruction routinely given to all entering medical students at the University of Miami School of Medicine and the ability of students to search effectively for and retrieve evidence-based information for clinical decision making by the end of their third-year. The authors developed and implemented a strategy for evaluating the search strategies and articles selected by third-year students, who participated in the Objective Structured Clinical Examination (OSCE) in June 1996, 1997, and 1998, and reviewed the literature on evidence-based medicine and evaluation of medical student searches. A mean of 5% of the students' search strategies and a mean of 26% of articles selected were ranked "excellent" or "good"; a mean of 26% of search strategies were ranked "fair" and a mean of 69% were ranked "poor"; and a mean of 22% of articles selected were ranked "fair" and a mean of 52% were ranked "poor" based on the strategy developed to evaluate student searches. Evaluating medical student searches for evidence-based information is an effective way of evaluating students' searching proficiency, and, in turn, the adequacy of the instruction they receive. Based on the results of the OSCE test, the school of medicine expanded the library's educational role and the library implemented major changes in the training program. Information on evidence-based medicine is now incorporated into the MEDLINE instruction. Library faculty evaluate the required searches performed by students for evidence-based information during their first and second years; 30% of students are identified for follow-up, individualized instruction based on the evaluation; and a new case-based curriculum has been proposed with a fourteen-week problem-based learning (PBL) block. These developments are timely in light of the evidence-based competencies recently published by the Association of American Medical Colleges.

  13. Evaluating medical student searches of MEDLINE for evidence-based information: process and application of results.

    PubMed Central

    Burrows, S C; Tylman, V

    1999-01-01

    OBJECTIVE: To evaluate the adequacy of the MEDLINE instruction routinely given to all entering medical students at the University of Miami School of Medicine and the ability of students to search effectively for and retrieve evidence-based information for clinical decision making by the end of their third-year. METHODOLOGY: The authors developed and implemented a strategy for evaluating the search strategies and articles selected by third-year students, who participated in the Objective Structured Clinical Examination (OSCE) in June 1996, 1997, and 1998, and reviewed the literature on evidence-based medicine and evaluation of medical student searches. RESULTS: A mean of 5% of the students' search strategies and a mean of 26% of articles selected were ranked "excellent" or "good"; a mean of 26% of search strategies were ranked "fair" and a mean of 69% were ranked "poor"; and a mean of 22% of articles selected were ranked "fair" and a mean of 52% were ranked "poor" based on the strategy developed to evaluate student searches. CONCLUSIONS: Evaluating medical student searches for evidence-based information is an effective way of evaluating students' searching proficiency, and, in turn, the adequacy of the instruction they receive. Based on the results of the OSCE test, the school of medicine expanded the library's educational role and the library implemented major changes in the training program. Information on evidence-based medicine is now incorporated into the MEDLINE instruction. Library faculty evaluate the required searches performed by students for evidence-based information during their first and second years; 30% of students are identified for follow-up, individualized instruction based on the evaluation; and a new case-based curriculum has been proposed with a fourteen-week problem-based learning (PBL) block. These developments are timely in light of the evidence-based competencies recently published by the Association of American Medical Colleges. PMID

  14. Search for Information-Bearing Components in Neural Data

    PubMed Central

    Hu, Meng; Liang, Hualou

    2014-01-01

    Multivariate empirical mode decomposition (MEMD) is an important extension of EMD, suitable for processing multichannel data. It can adaptively decompose multivariate data into a set of intrinsic mode functions (IMFs) that are matched both in number and in frequency scale. This method is thus holds great potential for the analysis of multi- channel neural recordings as it is capable of ensuring all the intrinsic oscillatory modes are aligned not only across channels, but also across trials. Given a plethora of IMFs derived by MEMD, a question of significant interest is how to identify which IMFs contain information, and which IMFs are noise. Existing methods that exploit the dyadic filter bank structure of white noise decomposition are insufficient since the IMFs do not always adhere to the presumed dyadic relationship. Here we propose a statistical procedure to identify information-bearing IMFs, which is built upon MEMD that allows adding noise as separate channels to serve as a reference to facilitate IMF identification. In this procedure, Wasserstein distance is used to measure the similarity between the reference IMF and that from data. Simulations are performed to validate the method. Local field potentials from cortex of monkeys while performing visual tasks are used for demonstration. PMID:24932596

  15. Optimal information transmission in organizations: search and congestion

    SciTech Connect

    Arenas, A.; Cabrales, A.; Danon, L.; Diaz-Guilera, A.; Guimera, R.; Vega-Redondo, F.

    2008-01-01

    We propose a stylized model of a problem-solving organization whose internal communication structure is given by a fixed network. Problems arrive randomly anywhere in this network and must find their way to their respective specialized solvers by relying on local information alone. The organization handles multiple problems simultaneously. For this reason, the process may be subject to congestion. We provide a characterization of the threshold of collapse of the network and of the stock of floating problems (or average delay) that prevails below that threshold. We build upon this characterization to address a design problem: the determination of what kind of network architecture optimizes performance for any given problem arrival rate. We conclude that, for low arrival rates, the optimal network is very polarized (i.e. star-like or centralized), whereas it is largely homogeneous (or decentralized) for high arrival rates. These observations are in line with a common transformation experienced by information-intensive organizations as their work flow has risen in recent years.

  16. Understanding vaccination resistance: vaccine search term selection bias and the valence of retrieved information.

    PubMed

    Ruiz, Jeanette B; Bell, Robert A

    2014-10-07

    Dubious vaccination-related information on the Internet leads some parents to opt out of vaccinating their children. To determine if negative, neutral and positive search terms retrieve vaccination information that differs in valence and confirms searchers' assumptions about vaccination. A content analysis of first-page Google search results was conducted using three negative, three neutral, and three positive search terms for the concepts "vaccine," "vaccination," and "MMR"; 84 of the 90 websites retrieved met inclusion requirements. Two coders independently and reliably coded for the presence or absence of each of 15 myths about vaccination (e.g., "vaccines cause autism"), statements that countered these myths, and recommendations for or against vaccination. Data were analyzed using descriptive statistics. Across all websites, at least one myth was perpetuated on 16.7% of websites and at least one myth was countered on 64.3% of websites. The mean number of myths perpetuated on websites retrieved with negative, neutral, and positive search terms, respectively, was 1.93, 0.53, and 0.40. The mean number of myths countered on websites retrieved with negative, neutral, and positive search terms, respectively, was 3.0, 3.27, and 2.87. Explicit recommendations regarding vaccination were offered on 22.6% of websites. A recommendation against vaccination was more often made on websites retrieved with negative search terms (37.5% of recommendations) than on websites retrieved with neutral (12.5%) or positive (0%) search terms. The concerned parent who seeks information about the risks of childhood immunizations will find more websites that perpetuate vaccine myths and recommend against vaccination than the parent who seeks information about the benefits of vaccination. This suggests that search term valence can lead to online information that supports concerned parents' misconceptions about vaccines. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. Biomedical Telectrodes

    NASA Technical Reports Server (NTRS)

    Shepherd, C. K.

    1989-01-01

    Compact transmitters eliminate need for wires to monitors. Biomedical telectrode is small electronic package that attaches to patient in manner similar to small adhesive bandage. Patient wearing biomedical telectrodes moves freely, without risk of breaking or entangling wire connections. Especially beneficial to patients undergoing electrocardiographic monitoring in intensive-care units in hospitals. Eliminates nuisance of coping with wire connections while dressing and going to toilet.

  18. Opportunity for information search and the effect of false heart rate feedback.

    PubMed

    Barefoot, John C; Straub, Ronald B

    2005-01-01

    The role of information search in the attribution of physiological states was investigated by manipulating the subject's opportunity for information search following the presentation of false information about his heart-rate reactions to photographs of female nudes. Consistent with the self-persuasion hypothesis proposed by Valins, the rated attractiveness of the slides was not affected by the false heart-rate feedback for those subjects who were prevented from visually searching the slides. Those subjects who had ample opportunity to view the slides rated those slides accompanied by false information of a heart-rate change as more attractive than those slides which were not paired with a change in heart rate.

  19. Information Searching across the Curriculum: Literacy Skills for the 90s and Beyond.

    ERIC Educational Resources Information Center

    Harada, Violet H.; Nakamura, Margaret

    1994-01-01

    In 1991, a partnership of three public schools in Hawaii received an Elementary and Secondary Education Act grant to develop a K-12 information skills curriculum and purchase electronic resources. Discusses installing the hardware and software, creating the information search framework, and developing the K-12 guide. Evaluates the two year project…

  20. Exploring gender differences in information search among domestic vistors to Yellow Mountain and Guilin, PRC

    Treesearch

    Hui Xie; Jigang Bao; Duarte B. Morais

    2007-01-01

    In the dynamic global environment of today, understanding how consumers acquire information is important at the micro level for marketing management decisions and at the macro level for public policy decisions. Gender has been identified as a factor influencing information search and other meaningful consumer behavior constructs. Therefore, understanding gender...

  1. Information Retrieval Strategies of Millennial Undergraduate Students in Web and Library Database Searches

    ERIC Educational Resources Information Center

    Porter, Brandi

    2009-01-01

    Millennial students make up a large portion of undergraduate students attending colleges and universities, and they have a variety of online resources available to them to complete academically related information searches, primarily Web based and library-based online information retrieval systems. The content, ease of use, and required search…

  2. Need for Cognition and Active Information Search in Small Student Groups

    ERIC Educational Resources Information Center

    Curseu, Petru Lucian

    2011-01-01

    In a sample of 213 students organized in 44 groups this study tests the impact of need for cognition on active information search by using a multilevel analysis. The results show that group members with high need for cognition seek more advice in task related issues than those with low need for cognition and this pattern of information exchange is…

  3. Learning centred approach for developing the electronic information search processes of students.

    PubMed

    Shanahan, Madeleine

    2009-11-01

    Undergraduate students of the twenty-first century are widely regarded as 'technologically savvy' and have embraced the electronic information world. The literature, however, describes undergraduate students as using a limited range of electronic information sources and not critically evaluating the information they retrieve from internet searches. The aim was to evaluate a purposefully designed intervention that sought to expand the information search and evaluation practices of undergraduate students. The intervention scaffolded an independent learning activity in the form of a group-based project. Survey methodology was used to collect data from student pre- and post-intervention for two cohorts of students who undertook the intervention in 2005 and 2006 involving a total of 71 students. Percentages were used to describe survey findings and chi-square analysis and Fisher's exact test examined differences between groups. Questionnaires were completed by 59 students (response rate 83%) pre-intervention and 49 students (response rate 69%) post-intervention. Post-intervention there were positive and statistically significant differences in database searching behaviour (p = 0.000), use of Google Scholar (p = 0.035) and number of criteria used to evaluate information retrieved from the internet (p = 0.000) by students. By positively reshaping the electronic information search and evaluation practices of students we are helping students to find informed information sources as they engage in independent learning activities at university and as future health professionals.

  4. An Observational Study of How Young People Search for Online Sexual Health Information

    ERIC Educational Resources Information Center

    Buhi, Eric R.; Daley, Ellen M.; Fuhrmann, Hollie J.; Smith, Sarah A.

    2009-01-01

    Little is known about the quality of online sexual health information, how young people access the Internet to answer their sexual health questions, or an individual's ability to sort through myriad sources for accurate information. Objective: The purpose of this study was to determine how college students search for online sexual health…

  5. Searching from the Heart: The Interplay between Emotions and Customization in Online Health Information Seeking

    ERIC Educational Resources Information Center

    Myrick, Jessica Gall

    2013-01-01

    The prospect of a threat to one's health or an opportunity for improved health can spark emotional reactions--the fear of an illness or the hope of a healthier life. People are increasingly turning to the Internet to search for information related to such health issues. However, the dizzying amount of online health information--some of it of…

  6. Need for Cognition and Active Information Search in Small Student Groups

    ERIC Educational Resources Information Center

    Curseu, Petru Lucian

    2011-01-01

    In a sample of 213 students organized in 44 groups this study tests the impact of need for cognition on active information search by using a multilevel analysis. The results show that group members with high need for cognition seek more advice in task related issues than those with low need for cognition and this pattern of information exchange is…

  7. Information Retrieval Strategies of Millennial Undergraduate Students in Web and Library Database Searches

    ERIC Educational Resources Information Center

    Porter, Brandi

    2009-01-01

    Millennial students make up a large portion of undergraduate students attending colleges and universities, and they have a variety of online resources available to them to complete academically related information searches, primarily Web based and library-based online information retrieval systems. The content, ease of use, and required search…

  8. An Observational Study of How Young People Search for Online Sexual Health Information

    ERIC Educational Resources Information Center

    Buhi, Eric R.; Daley, Ellen M.; Fuhrmann, Hollie J.; Smith, Sarah A.

    2009-01-01

    Little is known about the quality of online sexual health information, how young people access the Internet to answer their sexual health questions, or an individual's ability to sort through myriad sources for accurate information. Objective: The purpose of this study was to determine how college students search for online sexual health…

  9. Searching from the Heart: The Interplay between Emotions and Customization in Online Health Information Seeking

    ERIC Educational Resources Information Center

    Myrick, Jessica Gall

    2013-01-01

    The prospect of a threat to one's health or an opportunity for improved health can spark emotional reactions--the fear of an illness or the hope of a healthier life. People are increasingly turning to the Internet to search for information related to such health issues. However, the dizzying amount of online health information--some of it of…

  10. Students' Self-Regulated Learning, Online Information Evaluative Standards and Online Academic Searching Strategies

    ERIC Educational Resources Information Center

    Tseng, Sheng-Chau; Liang, Jyh-Chong; Tsai, Chin-Chung

    2014-01-01

    Online information searching strategies (OISS) used by students can be viewed as a key indicator in online learning environments. Therefore, developments in their OISS may also involve variables such as self-regulated learning (SRL) and online information evaluative standards (OIES). Three instruments, an OISS, a SRL and an OIES were used to…

  11. Chinese Internet Searches Provide Inaccurate and Misleading Information to Epilepsy Patients

    PubMed Central

    Liu, Jian-Ming; Xu, Ru-Xiang; Hu, Yong-Sheng; Ren, Lian-Kun; Qiao, Hui; Ding, Hu; Liu, Zhi-Liang

    2015-01-01

    Background: Most patients with epilepsy want to learn as much as possible about the disease, and many have turned to the internet for information. Patients are likely to use information obtained from the internet to control their epilepsy, but little is known about the accuracy of this information. In this survey, we have assessed the feasibility and usability of internet-based interventions for the treatment of epilepsy. Methods: Data were collected from an internet search. Different search terms were used to obtain general information on epilepsy together with information about medication, types of epilepsy, treatment, women's health, and other information. The accuracy of the information was evaluated by a group of experts. Results: A total of 1320 web pages were assessed. The majority were websites related to health. A large number (80.2%) of web pages contained content related to the search term. A significant number of web pages 450/1058 (42.5%) claimed to provide information from a credible source; however, only 206/1058 (19.5%) of the information was accurate and complete; 326/1058 (30.8%) was accurate but incomplete; 328/1058 (31.0%) was correct but nonstandard, and 198/1058 (18.8%) was inaccurate. The authenticity of the information was not significantly different between the two search engines (χ2 = 0.009, P = 0.924). No significant difference was observed in the information obtained from a specialist or nonspecialist source (χ2 = 7.538, P = 0.057). There was also no correlation between the quality of the information and the priority (χ2 = 6.880, P = 0.076). Conclusions: Searching for information about epilepsy on the internet is convenient, but the information provided is not reliable. Too much information is inaccurate or for advertisement purposes, and it is difficult for patients to find the useful information. Turning to the internet for medical knowledge may be harmful. Physicians should be aware that their patients may search for information on

  12. Chinese Internet Searches Provide Inaccurate and Misleading Information to Epilepsy Patients.

    PubMed

    Liu, Jian-Ming; Xu, Ru-Xiang; Hu, Yong-Sheng; Ren, Lian-Kun; Qiao, Hui; Ding, Hu; Liu, Zhi-Liang

    2015-12-20

    Most patients with epilepsy want to learn as much as possible about the disease, and many have turned to the internet for information. Patients are likely to use information obtained from the internet to control their epilepsy, but little is known about the accuracy of this information. In this survey, we have assessed the feasibility and usability of internet-based interventions for the treatment of epilepsy. Data were collected from an internet search. Different search terms were used to obtain general information on epilepsy together with information about medication, types of epilepsy, treatment, women's health, and other information. The accuracy of the information was evaluated by a group of experts. A total of 1320 web pages were assessed. The majority were websites related to health. A large number (80.2%) of web pages contained content related to the search term. A significant number of web pages 450/1058 (42.5%) claimed to provide information from a credible source; however, only 206/1058 (19.5%) of the information was accurate and complete; 326/1058 (30.8%) was accurate but incomplete; 328/1058 (31.0%) was correct but nonstandard, and 198/1058 (18.8%) was inaccurate. The authenticity of the information was not significantly different between the two search engines (χ2 = 0.009, P = 0.924). No significant difference was observed in the information obtained from a specialist or nonspecialist source (χ2 = 7.538, P = 0.057). There was also no correlation between the quality of the information and the priority (χ2 = 6.880, P = 0.076). Searching for information about epilepsy on the internet is convenient, but the information provided is not reliable. Too much information is inaccurate or for advertisement purposes, and it is difficult for patients to find the useful information. Turning to the internet for medical knowledge may be harmful. Physicians should be aware that their patients may search for information on the internet and guide them to safe

  13. Using internet search engines and library catalogs to locate toxicology information.

    PubMed

    Wukovitz, L D

    2001-01-12

    The increasing importance of the Internet demands that toxicologists become aquainted with its resources. To find information, researchers must be able to effectively use Internet search engines, directories, subject-oriented websites, and library catalogs. The article will explain these resources, explore their benefits and weaknesses, and identify skills that help the researcher to improve search results and critically evaluate sources for their relevancy, validity, accuracy, and timeliness.

  14. Information-seeking behaviour for epilepsy: an infodemiological study of searches for Wikipedia articles.

    PubMed

    Brigo, Francesco; Otte, Willem M; Igwe, Stanley C; Ausserer, Harald; Nardone, Raffaele; Tezzon, Frediano; Trinka, Eugen

    2015-12-01

    Millions of people worldwide use the internet daily as a source of health information. Wikipedia is a popular free online encyclopaedia used by patients and physicians to search for health-related information. Our aim was to evaluate information-seeking behaviour of English-speaking internet users searching Wikipedia for articles related to epilepsy and epileptic seizures. Using Wiki Trends, which provides quantitative information on daily viewing of articles, data on global search queries for Wikipedia articles related to epilepsy and seizures were analysed. The daily Wikipedia article views on syncope, psychogenic non-epileptic seizures, migraine, and multiple sclerosis served as comparative data. The period of analysis covered was from January 2008 to December 2014. Overall, the Wikipedia article "epilepsy and driving" was found to be more frequently visited than the articles "epilepsy and employment" or "epilepsy in children". Since January 2008, the Wikipedia article "multiple sclerosis" was more often visited compared to the articles "epilepsy", "syncope", "psychogenic non-epileptic seizures" or "migraine"; the article "epilepsy" ranked 3,779 and was less frequently visited than "multiple sclerosis", ranked at 571, in traffic on Wikipedia. The highest peak in search volume for the article "epilepsy" coincided with the news of a celebrity having seizures. Fears and worries about epileptic seizures, their impact on driving and employment, and news about celebrities with epilepsy might be major determinants in searching Wikipedia for information.

  15. Online health information search: what struggles and empowers the users? Results of an online survey.

    PubMed

    Pletneva, Natalia; Vargas, Alejandro; Kalogianni, Konstantina; Boyer, Célia

    2012-01-01

    The most popular mean of searching for online health content is a general search engine for all domains of interest. Being general implies on one hand that the search engine is not tailored to the needs which are particular to the medical and on another hand that health domain and health-specific queries may not always return adequate and adapted results. The aim of our study was to identify difficulties and preferences in online health information search encountered by members of the general public. The survey in four languages was online from the 9th of March until the 27th of April, 2011. 385 answers were collected, representing mostly the opinions of highly educated users, mostly from France and Spain. The most important characteristics of a search engine are relevance and trustworthiness of results. The results currently retrieved do not fulfil these requirements. The ideal representation of the information will be a categorization of the results into different groups. Medical dictionaries/thesauruses, suggested relevant topics, image searches and spelling corrections are regarded as helpful tools. There is a need to work towards better customized solutions which provide users with the trustworthy information of high quality specific to his/her case in a user-friendly environment which would eventually lead to making appropriate health decisions.

  16. A comparison of information functions and search strategies for sensor planning in target classification.

    PubMed

    Zhang, Guoxian; Ferrari, Silvia; Cai, Chenghui

    2012-02-01

    This paper investigates the comparative performance of several information-driven search strategies and decision rules using a canonical target classification problem. Five sensor models are considered: one obtained from classical estimation theory and four obtained from Bernoulli, Poisson, binomial, and mixture-of-binomial distributions. A systematic approach is presented for deriving information functions that represent the expected utility of future sensor measurements from mutual information, Rènyi divergence, Kullback-Leibler divergence, information potential, quadratic entropy, and the Cauchy-Schwarz distance. The resulting information-driven strategies are compared to direct-search, alert-confirm, task-driven (TS), and log-likelihood-ratio (LLR) search strategies. Extensive numerical simulations show that quadratic entropy typically leads to the most effective search strategy with respect to correct-classification rates. In the presence of prior information, the quadratic-entropy-driven strategy also displays the lowest rate of false alarms. However, when prior information is absent or very noisy, TS and LLR strategies achieve the lowest false-alarm rates for the Bernoulli, mixture-of-binomial, and classical sensor models.

  17. Information search in health care decision-making: a study of word-of-mouth and internet information users.

    PubMed

    Snipes, Robin L; Ingram, Rhea; Jiang, Pingjun

    2005-01-01

    This paper investigates how individual consumers may differ in their information search behavior in health care decision-making. Results indicate that most consumers still use word-of-mouth as a primary information source for health care decisions. However, usage of the Internet is increasing. The results of this study indicate that consumers who are most likely to use the Internet for health care information are single, younger, and less educated, whereas consumers who are most likely to use word-of-mouth are middle-aged, married, with higher income and higher education. Surprisingly, no significant gender difference was found in information search behavior for health care decision-making. The results also suggest that consumers with the highest tendency to use word-of-mouth are also the lowest users of the Internet in health care decision-making. Implications of these findings are discussed.

  18. The Separate Spheres of Online Health: Gender, Parenting, and Online Health Information Searching in the Information Age

    ERIC Educational Resources Information Center

    Stern, Michael J.; Cotten, Shelia R.; Drentea, Patricia

    2012-01-01

    The objective of this article is to explore how parental status, gender, and their interaction influence a variety of aspects of searching for online health information. Drawing on nationally representative survey data, the results show that in a number of ways parenting and gender have separate but significant influences on the following: online…

  19. What is biomedical informatics?

    PubMed

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

    2010-02-01

    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.

  20. 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

  1. What do patients search for when seeking clinical trial information online?

    PubMed

    Patel, Chintan O; Garg, Vivek; Khan, Sharib A

    2010-11-13

    The Internet has become a common source for consumers to seek health information across a wide range of topics including searching for clinical trials. However, not much is known about what consumers search for in relation to clinical trials and how they formulate their search queries. In this study, we use log file data from TrialX.com, a consumer-centric website that provides clinical trial information to ascertain patterns in consumer queries. We analyzed semantic patterns in the queries by mapping query keywords to the UMLS Semantic Types and performed a manual evaluation of user paths. We found that the queries can be grouped into combinations of information needs related to condition, location and treatment. The results also suggested that the consumers using longer search queries with multiple Semantic Types are more likely to take action to participate in clinical trials. The study provides early insights that can be used to inform changes in website content and information display to improve clinical trials information seeking.

  2. Online Information Searches and Help Seeking for Mental Health Problems in Urban China.

    PubMed

    Chen, Juan; Zhu, Shizhan

    2016-07-01

    In recent years, the Internet has emerged as an alternative information source on mental health problems. Yet, the profile of the typical Internet help seeker is to be determined. Based on data from a household survey of 2558 Beijing residents, the study investigates online information searches and help seeking for mental health problems. Multinomial logistic regressions are estimated for respondents' access to the Internet, and mental-health-related information searches and help seeking on the Internet for the whole community sample and the most psychologically distressed subsample. The study identifies a digital divide in online help seeking for mental health issues based on age, migration and hukou status, and socio-economic factors. Youth and high socio-economic status are significant predictors of Internet access and use. Among the whole community sample, rural-to-urban migrants are less likely to have access to the Internet and search information or seek help online. Among the most psychologically distressed subsample, urban-to-urban migrants are significantly more likely to have access to the Internet and search information or seek help online. Given the shortage of mental health professionals in China, online information dissemination and guided self-help, if properly designed, could offer a means to reach large numbers of individuals in a cost-effective manner.

  3. How does searching for health information on the Internet affect individuals' demand for health care services?

    PubMed

    Suziedelyte, Agne

    2012-11-01

    The emergence of the Internet made health information, which previously was almost exclusively available to health professionals, accessible to the general public. Access to health information on the Internet is likely to affect individuals' health care related decisions. The aim of this analysis is to determine how health information that people obtain from the Internet affects their demand for health care. I use a novel data set, the U.S. Health Information National Trends Survey (2003-07), to answer this question. The causal variable of interest is a binary variable that indicates whether or not an individual has recently searched for health information on the Internet. Health care utilization is measured by an individual's number of visits to a health professional in the past 12 months. An individual's decision to use the Internet to search for health information is likely to be correlated to other variables that can also affect his/her demand for health care. To separate the effect of Internet health information from other confounding variables, I control for a number of individual characteristics and use the instrumental variable estimation method. As an instrument for Internet health information, I use U.S. state telecommunication regulations that are shown to affect the supply of Internet services. I find that searching for health information on the Internet has a positive, relatively large, and statistically significant effect on an individual's demand for health care. This effect is larger for the individuals who search for health information online more frequently and people who have health care coverage. Among cancer patients, the effect of Internet health information seeking on health professional visits varies by how long ago they were diagnosed with cancer. Thus, the Internet is found to be a complement to formal health care rather than a substitute for health professional services. Copyright © 2012 Elsevier Ltd. All rights reserved.

  4. Integrating the humanities in the education of health professionals: implications for search and retrieval of information.

    PubMed

    Polson, Robert G; Farmer, Elizabeth S

    2002-03-01

    This article examines the increasing use of the humanities in the education of health professionals and posits that the approach may be of use in teaching health professionals information search and retrieval skills. However little evidence exists to support the educational effectiveness of using the humanities. This lack of evidence raises concerns about the costs of financing this approach to learning. These costs include the issue of copyright which cannot be ignored. While the humanities might provide a more attractive approach to teaching information search and retrieval skills, further research is needed to justify the costs of this approach to learning in more general terms and urgent attention to.

  5. Semantic biomedical resource discovery: a Natural Language Processing framework.

    PubMed

    Sfakianaki, Pepi; Koumakis, Lefteris; Sfakianakis, Stelios; Iatraki, Galatia; Zacharioudakis, Giorgos; Graf, Norbert; Marias, Kostas; Tsiknakis, Manolis

    2015-09-30

    A plethora of publicly available biomedical resources do currently exist and are constantly increasing at a fast rate. In parallel, specialized repositories are been developed, indexing numerous clinical and biomedical tools. The main drawback of such repositories is the difficulty in locating appropriate resources for a clinical or biomedical decision task, especially for non-Information Technology expert users. In parallel, although NLP research in the clinical domain has been active since the 1960s, progress in the development of NLP applications has been slow and lags behind progress in the general NLP domain. The aim of the present study is to investigate the use of semantics for biomedical resources annotation with domain specific ontologies and exploit Natural Language Processing methods in empowering the non-Information Technology expert users to efficiently search for biomedical resources using natural language. A Natural Language Processing engine which can "translate" free text into targeted queries, automatically transforming a clinical research question into a request description that contains only terms of ontologies, has been implemented. The implementation is based on information extraction techniques for text in natural language, guided by integrated ontologies. Furthermore, knowledge from robust text mining methods has been incorporated to map descriptions into suitable domain ontologies in order to ensure that the biomedical resources descriptions are domain oriented and enhance the accuracy of services discovery. The framework is freely available as a web application at ( http://calchas.ics.forth.gr/ ). For our experiments, a range of clinical questions were established based on descriptions of clinical trials from the ClinicalTrials.gov registry as well as recommendations from clinicians. Domain experts manually identified the available tools in a tools repository which are suitable for addressing the clinical questions at hand, either

  6. 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

  7. A Semidefinite Programming Based Search Strategy for Feature Selection with Mutual Information Measure.

    PubMed

    Naghibi, Tofigh; Hoffmann, Sarah; Pfister, Beat

    2015-08-01

    Feature subset selection, as a special case of the general subset selection problem, has been the topic of a considerable number of studies due to the growing importance of data-mining applications. In the feature subset selection problem there are two main issues that need to be addressed: (i) Finding an appropriate measure function than can be fairly fast and robustly computed for high-dimensional data. (ii) A search strategy to optimize the measure over the subset space in a reasonable amount of time. In this article mutual information between features and class labels is considered to be the measure function. Two series expansions for mutual information are proposed, and it is shown that most heuristic criteria suggested in the literature are truncated approximations of these expansions. It is well-known that searching the whole subset space is an NP-hard problem. Here, instead of the conventional sequential search algorithms, we suggest a parallel search strategy based on semidefinite programming (SDP) that can search through the subset space in polynomial time. By exploiting the similarities between the proposed algorithm and an instance of the maximum-cut problem in graph theory, the approximation ratio of this algorithm is derived and is compared with the approximation ratio of the backward elimination method. The experiments show that it can be misleading to judge the quality of a measure solely based on the classification accuracy, without taking the effect of the non-optimum search strategy into account.

  8. Algorithm for shortest path search in Geographic Information Systems by using reduced graphs.

    PubMed

    Rodríguez-Puente, Rafael; Lazo-Cortés, Manuel S

    2013-01-01

    The use of Geographic Information Systems has increased considerably since the eighties and nineties. As one of their most demanding applications we can mention shortest paths search. Several studies about shortest path search show the feasibility of using graphs for this purpose. Dijkstra's algorithm is one of the classic shortest path search algorithms. This algorithm is not well suited for shortest path search in large graphs. This is the reason why various modifications to Dijkstra's algorithm have been proposed by several authors using heuristics to reduce the run time of shortest path search. One of the most used heuristic algorithms is the A* algorithm, the main goal is to reduce the run time by reducing the search space. This article proposes a modification of Dijkstra's shortest path search algorithm in reduced graphs. It shows that the cost of the path found in this work, is equal to the cost of the path found using Dijkstra's algorithm in the original graph. The results of finding the shortest path, applying the proposed algorithm, Dijkstra's algorithm and A* algorithm, are compared. This comparison shows that, by applying the approach proposed, it is possible to obtain the optimal path in a similar or even in less time than when using heuristic algorithms.

  9. Language Preferences on Websites and in Google Searches for Human Health and Food Information

    PubMed Central

    Singh, Punam Mony; Wight, Carly A; Sercinoglu, Olcan; Wilson, David C; Boytsov, Artem

    2007-01-01

    Background While it is known that the majority of pages on the World Wide Web are in English, little is known about the preferred language of users searching for health information online. Objectives (1) To help global and domestic publishers, for example health and food agencies, to determine the need for translation of online information from English into local languages. (2) To help these agencies determine which language(s) they should select when publishing information online in target nations and for target subpopulations within nations. Methods To estimate the percentage of Web publishers that translate their health and food websites, we measured the frequency at which domain names retrieved by Google overlap for language translations of the same health-related search term. To quantify language choice of searchers from different countries, Google provided estimates of the rate at which its search engine was queried in six languages relative to English for the terms “avian flu,” “tuberculosis,” “schizophrenia,” and “maize” (corn) from January 2004 to April 2006. The estimate was based on a 20% sample of all Google queries from 227 nations. Results We estimate that 80%-90% of health- and food-related institutions do not translate their websites into multiple languages, even when the information concerns pandemic disease such as avian influenza. Although Internet users are often well-educated, there was a strong preference for searching for health and food information in the local language, rather than English. For “avian flu,” we found that only 1% of searches in non-English-speaking nations were in English, whereas for “tuberculosis” or “schizophrenia,” about 4%-40% of searches in non-English countries employed English. A subset of searches for health information presumably originating from immigrants occurred in their native tongue, not the language of the adopted country. However, Spanish-language online searches for “avian flu

  10. Accessing Suicide-Related Information on the Internet: A Retrospective Observational Study of Search Behavior

    PubMed Central

    2013-01-01

    Background The Internet’s potential impact on suicide is of major public health interest as easy online access to pro-suicide information or specific suicide methods may increase suicide risk among vulnerable Internet users. Little is known, however, about users’ actual searching and browsing behaviors of online suicide-related information. Objective To investigate what webpages people actually clicked on after searching with suicide-related queries on a search engine and to examine what queries people used to get access to pro-suicide websites. Methods A retrospective observational study was done. We used a web search dataset released by America Online (AOL). The dataset was randomly sampled from all AOL subscribers’ web queries between March and May 2006 and generated by 657,000 service subscribers. Results We found 5526 search queries (0.026%, 5526/21,000,000) that included the keyword "suicide". The 5526 search queries included 1586 different search terms and were generated by 1625 unique subscribers (0.25%, 1625/657,000). Of these queries, 61.38% (3392/5526) were followed by users clicking on a search result. Of these 3392 queries, 1344 (39.62%) webpages were clicked on by 930 unique users but only 1314 of those webpages were accessible during the study period. Each clicked-through webpage was classified into 11 categories. The categories of the most visited webpages were: entertainment (30.13%; 396/1314), scientific information (18.31%; 240/1314), and community resources (14.53%; 191/1314). Among the 1314 accessed webpages, we could identify only two pro-suicide websites. We found that the search terms used to access these sites included “commiting suicide with a gas oven”, “hairless goat”, “pictures of murder by strangulation”, and “photo of a severe burn”. A limitation of our study is that the database may be dated and confined to mainly English webpages. Conclusions Searching or browsing suicide-related or pro-suicide webpages was

  11. 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.

  12. Biomedical nanotechnology.

    PubMed

    Hurst, Sarah J

    2011-01-01

    This chapter summarizes the roles of nanomaterials in biomedical applications, focusing on those highlighted in this volume. A brief history of nanoscience and technology and a general introduction to the field are presented. Then, the chemical and physical properties of nanostructures that make them ideal for use in biomedical applications are highlighted. Examples of common applications, including sensing, imaging, and therapeutics, are given. Finally, the challenges associated with translating this field from the research laboratory to the clinic setting, in terms of the larger societal implications, are discussed.

  13. Internet search term affects the quality and accuracy of online information about developmental hip dysplasia.

    PubMed

    Fabricant, Peter D; Dy, Christopher J; Patel, Ronak M; Blanco, John S; Doyle, Shevaun M

    2013-06-01

    The recent emphasis on shared decision-making has increased the role of the Internet as a readily accessible medical reference source for patients and families. However, the lack of professional review creates concern over the quality, accuracy, and readability of medical information available to patients on the Internet. Three Internet search engines (Google, Yahoo, and Bing) were evaluated prospectively using 3 difference search terms of varying sophistication ("congenital hip dislocation," "developmental dysplasia of the hip," and "hip dysplasia in children"). Sixty-three unique Web sites were evaluated by each of 3 surgeons (2 fellowship-trained pediatric orthopaedic attendings and 1 orthopaedic chief resident) for quality and accuracy using a set of scoring criteria based on the AAOS/POSNA patient education Web site. The readability (literacy grade level) of each Web site was assessed using the Fleisch-Kincaid score. There were significant differences noted in quality, accuracy, and readability of information depending on the search term used. The search term "developmental dysplasia of the hip" provided higher quality and accuracy compared with the search term "congenital hip dislocation." Of the 63 total Web sites, 1 (1.6%) was below the sixth grade reading level recommended by the NIH for health education materials and 8 (12.7%) Web sites were below the average American reading level (eighth grade). The quality and accuracy of information available on the Internet regarding developmental hip dysplasia significantly varied with the search term used. Patients seeking information about DDH on the Internet may not understand the materials found because nearly all of the Web sites are written at a level above that recommended for publically distributed health information. Physicians should advise their patients to search for information using the term "developmental dysplasia of the hip" or, better yet, should refer patients to Web sites that they have

  14. Patient-targeted googling: the ethics of searching online for patient information.

    PubMed

    Clinton, Brian K; Silverman, Benjamin C; Brendel, David H

    2010-01-01

    With the growth of the Internet, psychiatrists can now search online for a wide range of information about patients. Psychiatrists face challenges of maintaining professional boundaries with patients in many circumstances, but little consideration has been given to the practice of searching online for information about patients, an act we refer to as patient-targeted Googling (PTG). Psychiatrists are not the only health care providers who can investigate their patients online, but they may be especially likely to engage in PTG because of the unique relationships involved in their clinical practice. Before searching online for a patient, psychiatrists should consider such factors as the intention of searching, the anticipated effect of gaining information online, and its potential value or risk for the treatment. The psychiatrist is obligated to act in a way that respects the patient's best interests and that adheres to professional ethics. In this article, we propose a pragmatic model for considering PTG that focuses on practical results of searches and that aims to minimize the risk of exploiting patients. We describe three cases of PTG, highlighting important ethical dilemmas in multiple practice settings. Each case is discussed from the standpoint of the pragmatic model.

  15. How Students Evaluate Information and Sources when Searching the World Wide Web for Information

    ERIC Educational Resources Information Center

    Walraven, Amber; Brand-Gruwel, Saskia; Boshuizen, Henny P. A.

    2009-01-01

    The World Wide Web (WWW) has become the biggest information source for students while solving information problems for school projects. Since anyone can post anything on the WWW, information is often unreliable or incomplete, and it is important to evaluate sources and information before using them. Earlier research has shown that students have…

  16. How Students Evaluate Information and Sources when Searching the World Wide Web for Information

    ERIC Educational Resources Information Center

    Walraven, Amber; Brand-Gruwel, Saskia; Boshuizen, Henny P. A.

    2009-01-01

    The World Wide Web (WWW) has become the biggest information source for students while solving information problems for school projects. Since anyone can post anything on the WWW, information is often unreliable or incomplete, and it is important to evaluate sources and information before using them. Earlier research has shown that students have…

  17. Searching the internet for health information about bipolar disorder: some cautionary issues.

    PubMed

    Monteith, Scott; Glenn, Tasha; Bauer, Michael

    2013-01-01

    Adults routinely use the Internet as a source of health information. Patients with bipolar disorder and caregivers should be encouraged to increase their knowledge of this complex illness, including through the Internet. However, patients, caregivers, and physicians should be aware of potential perils when searching the Internet for health information, including loss of privacy, quality of web site content, and Internet scams. This review summarizes these cautionary issues. The digital divide remains and includes a lack of technical skills and competency in searching and appraising web sites, in addition to limited access to the Internet. Physicians should provide patients with a list of trustworthy web sites and a brief printed handout on concerns related to searching the Internet. More studies of the use of the Internet by patients with bipolar disorder are needed.

  18. Searching online and Web-based resources for information on natural products used as drugs.

    PubMed Central

    Stone, V L; Fishman, D L; Frese, D B

    1998-01-01

    Finding and evaluating information on natural products used as drugs can present challenges to the information professional. In this study, eight databases including resources retrieved on the Web were compared for relevancy and uniqueness. Ten reference questions related to natural products used as drugs were searched in the latest three year file of a number of databases, including MEDLINE, International Pharmaceutical Abstracts, and EMBASE/Excerpta Medica. In addition, the Web was searched for relevant Internet sites using the Alta Vista search engine. EMBASE/Excerpta Medica retrieved the largest number of relevant citations for four of the ten questions. MEDLINE, the Health Reference Center, and Alta Vista each retrieved the largest numbers in two questions. Overall, the standard medical databases were the first choice for the health professional and for many lay people because of their more extensive indexing and coverage of authoritative journals. PMID:9803295

  19. Incidence of online health information search: a useful proxy for public health risk perception.

    PubMed

    Liang, Bo; Scammon, Debra L

    2013-06-17

    Internet users use search engines to look for information online, including health information. Researchers in medical informatics have found a high correlation of the occurrence of certain search queries and the incidence of certain diseases. Consumers' search for information about diseases is related to current health status with regard to a disease and to the social environments that shape the public's attitudes and behaviors. This study aimed to investigate the extent to which public health risk perception as demonstrated by online information searches related to a health risk can be explained by the incidence of the health risk and social components of a specific population's environment. Using an ecological perspective, we suggest that a population's general concern for a health risk is formed by the incidence of the risk and social (eg, media attention) factors related with the risk. We constructed a dataset that included state-level data from 32 states on the incidence of the flu; a number of social factors, such as media attention to the flu; private resources, such as education and health insurance coverage; public resources, such as hospital beds and primary physicians; and utilization of these resources, including inpatient days and outpatient visits. We then explored whether online information searches about the flu (seasonal and pandemic flu) can be predicted using these variables. We used factor analysis to construct indexes for sets of social factors (private resources, public resources). We then applied panel data multiple regression analysis to exploit both time-series and cross-sectional variation in the data over a 7-year period. Overall, the results provide evidence that the main effects of independent variables-the incidence of the flu (P<.001); social factors, including media attention (P<.001); private resources, including life quality (P<.001) and health lifestyles (P=.009); and public resources, such as hospital care utilization (P=.008

  20. Improvement of the comprehension of written information given to healthy volunteers in biomedical research: a single-blind randomized controlled study.

    PubMed

    Paris, Adeline; Nogueira da Gama Chaves, Daniel; Cornu, Catherine; Maison, Patrick; Salvat-Mélis, Muriel; Ribuot, Christophe; Brandt, Christian; Bosson, Jean-Luc; Hommel, Marc; Cracowski, Jean-Luc

    2007-04-01

    Writing an informed consent form (ICF) for biomedical research is a difficult task. We conducted a multicenter single-blind randomized controlled trial to identify whether a working group or the systematic improvement in lexico-syntactic readability or an association of the two could increase the comprehension of the written information given to healthy volunteers enrolled in biomedical research. Participants were randomized to read one of four versions of the ICF: unchanged ICF (A), ICF with systematic lexico-syntactic readability improvement (B), ICF modified by a working group (C), and ICF modified by the working group followed by systematic lexico-syntactic improvement (D). The primary end-point was the objective comprehension score at day 0 for each study group. The scores of objective comprehension at day 0 were statistically different between the four study groups (anovaP = 0.020). The pairwise analysis showed an improvement in the working group vs. the unchanged group (P = 0.003), and a tendency to improvement in the group who read the ICF modified using lexico-syntactic readability and in the group who read the ICF modified using the two methods (P = 0.020 and 0.027 respectively). We conducted a two-way anova to identify some characteristics of the population which could explain this score. There was a significant interaction between the type of informed consent document (ICD) and the gender. Improving the ICD in phase I biomedical research leads to better comprehension, whether the method used is systematic lexico-syntactic improvement or a review by a working group. The improvement is specifically observed in men compared with women. Conversely, while both methods diverge in their effect on lexico-syntactic readability, their association is not mandatory. We suggest that in all phase I clinical trials, the ICF be improved by either method.

  1. 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.

  2. A biomedical engineer's library.

    PubMed

    Webster, J G

    1982-01-01

    A survey resulted in a list of the 101 textbooks used by 62 biomedical engineering educational programs. A second list shows the textbooks used by each school. A third list shows the 27 textbooks used at two or more schools and the number of times each is used. This selected compilation should be useful to (a) biomedical engineering curriculum committees considering program revision, (b) teachers considering course revision, (c) university and industrial librarians updating their collections, (d) individuals building a personal library, and (e) students desiring information about the emphasis of various educational programs.

  3. Text Mining in Biomedical Domain with Emphasis on Document Clustering

    PubMed Central

    2017-01-01

    Objectives With the exponential increase in the number of articles published every year in the biomedical domain, there is a need to build automated systems to extract unknown information from the articles published. Text mining techniques enable the extraction of unknown knowledge from unstructured documents. Methods This paper reviews text mining processes in detail and the software tools available to carry out text mining. It also reviews the roles and applications of text mining in the biomedical domain. Results Text mining processes, such as search and retrieval of documents, pre-processing of documents, natural language processing, methods for text clustering, and methods for text classification are described in detail. Conclusions Text mining techniques can facilitate the mining of vast amounts of knowledge on a given topic from published biomedical research articles and draw meaningful conclusions that are not possible otherwise. PMID:28875048

  4. Text Mining in Biomedical Domain with Emphasis on Document Clustering.

    PubMed

    Renganathan, Vinaitheerthan

    2017-07-01

    With the exponential increase in the number of articles published every year in the biomedical domain, there is a need to build automated systems to extract unknown information from the articles published. Text mining techniques enable the extraction of unknown knowledge from unstructured documents. This paper reviews text mining processes in detail and the software tools available to carry out text mining. It also reviews the roles and applications of text mining in the biomedical domain. Text mining processes, such as search and retrieval of documents, pre-processing of documents, natural language processing, methods for text clustering, and methods for text classification are described in detail. Text mining techniques can facilitate the mining of vast amounts of knowledge on a given topic from published biomedical research articles and draw meaningful conclusions that are not possible otherwise.

  5. Information is in the eye of the beholder: Seeking information on the MMR vaccine through an Internet search engine.

    PubMed

    Yom-Tov, Elad; Fernandez-Luque, Luis

    2014-01-01

    Vaccination campaigns are one of the most important and successful public health programs ever undertaken. People who want to learn about vaccines in order to make an informed decision on whether to vaccinate are faced with a wealth of information on the Internet, both for and against vaccinations. In this paper we develop an automated way to score Internet search queries and web pages as to the likelihood that a person making these queries or reading those pages would decide to vaccinate. We apply this method to data from a major Internet search engine, while people seek information about the Measles, Mumps and Rubella (MMR) vaccine. We show that our method is accurate, and use it to learn about the information acquisition process of people. Our results show that people who are pro-vaccination as well as people who are anti-vaccination seek similar information, but browsing this information has differing effect on their future browsing. These findings demonstrate the need for health authorities to tailor their information according to the current stance of users.

  6. Information is in the eye of the beholder: Seeking information on the MMR vaccine through an Internet search engine

    PubMed Central

    Yom-Tov, Elad; Fernandez-Luque, Luis

    2014-01-01

    Vaccination campaigns are one of the most important and successful public health programs ever undertaken. People who want to learn about vaccines in order to make an informed decision on whether to vaccinate are faced with a wealth of information on the Internet, both for and against vaccinations. In this paper we develop an automated way to score Internet search queries and web pages as to the likelihood that a person making these queries or reading those pages would decide to vaccinate. We apply this method to data from a major Internet search engine, while people seek information about the Measles, Mumps and Rubella (MMR) vaccine. We show that our method is accurate, and use it to learn about the information acquisition process of people. Our results show that people who are pro-vaccination as well as people who are anti-vaccination seek similar information, but browsing this information has differing effect on their future browsing. These findings demonstrate the need for health authorities to tailor their information according to the current stance of users. PMID:25954435

  7. Search Wide, Dig Deep: Literature Searching for Qualitative Research. An Analysis of the Publication Formats and Information Sources Used for Four Systematic Reviews in Public Health

    ERIC Educational Resources Information Center

    Stansfield, Claire; Brunton, Ginny; Rees, Rebecca

    2014-01-01

    Background: When literature searching for systematic reviews, it is good practice to search widely across different information sources. Little is known about the contributions of different publication formats (e.g. journal article and book chapter) and sources, especially for studies of people's views. Method: Studies from four reviews spanning…

  8. Search Wide, Dig Deep: Literature Searching for Qualitative Research. An Analysis of the Publication Formats and Information Sources Used for Four Systematic Reviews in Public Health

    ERIC Educational Resources Information Center

    Stansfield, Claire; Brunton, Ginny; Rees, Rebecca

    2014-01-01

    Background: When literature searching for systematic reviews, it is good practice to search widely across different information sources. Little is known about the contributions of different publication formats (e.g. journal article and book chapter) and sources, especially for studies of people's views. Method: Studies from four reviews spanning…

  9. Searching ClinicalTrials.gov and the International Clinical Trials Registry Platform to inform systematic reviews: what are the optimal search approaches?

    PubMed

    Glanville, Julie M; Duffy, Steven; McCool, Rachael; Varley, Danielle

    2014-07-01

    Since 2005, International Committee of Medical Journal Editors (ICMJE) member journals have required that clinical trials be registered in publicly available trials registers before they are considered for publication. The research explores whether it is adequate, when searching to inform systematic reviews, to search for relevant clinical trials using only public trials registers and to identify the optimal search approaches in trials registers. A search was conducted in ClinicalTrials.gov and the International Clinical Trials Registry Platform (ICTRP) for research studies that had been included in eight systematic reviews. Four search approaches (highly sensitive, sensitive, precise, and highly precise) were performed using the basic and advanced interfaces in both resources. On average, 84% of studies were not listed in either resource. The largest number of included studies was retrieved in ClinicalTrials.gov and ICTRP when a sensitive search approach was used in the basic interface. The use of the advanced interface maintained or improved sensitivity in 16 of 19 strategies for Clinicaltrials.gov and 8 of 18 for ICTRP. No single search approach was sensitive enough to identify all studies included in the 6 reviews. Trials registers cannot yet be relied upon as the sole means to locate trials for systematic reviews. Trials registers lag behind the major bibliographic databases in terms of their search interfaces. For systematic reviews, trials registers and major bibliographic databases should be searched. Trials registers should be searched using sensitive approaches, and both the registers consulted in this study should be searched.

  10. An Analysis of Undergraduate Students' Search Behaviors in an Information Literacy Class

    ERIC Educational Resources Information Center

    Chen, Hsin-Liang

    2009-01-01

    The purpose of this project was to investigate how students' search strategies changed over the course of a semester-long information literacy class. Data collection included four different paper questionnaires corresponding to course content in the spring 2008 semester. Seventy-seven participants completed the questionnaires and course work in…

  11. Constructing Preference from Experience: The Endowment Effect Reflected in External Information Search

    ERIC Educational Resources Information Center

    Pachur, Thorsten; Scheibehenne, Benjamin

    2012-01-01

    People often attach a higher value to an object when they own it (i.e., as seller) compared with when they do not own it (i.e., as buyer)--a phenomenon known as the "endowment effect". According to recent cognitive process accounts of the endowment effect, the effect is due to differences between sellers and buyers in information search.…

  12. 77 FR 41784 - Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-16

    ... From the Federal Register Online via the Government Publishing Office ENVIRONMENTAL PROTECTION AGENCY Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches for... or email. The http://www.regulations.gov Web site is an ``anonymous access'' system, which means...

  13. 75 FR 76982 - Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-10

    ... From the Federal Register Online via the Government Publishing Office ENVIRONMENTAL PROTECTION AGENCY Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches for... Web site is an ``anonymous access'' system, which means EPA will not know your identity or...

  14. 77 FR 20817 - Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-06

    ... From the Federal Register Online via the Government Publishing Office ENVIRONMENTAL PROTECTION AGENCY Integrated Risk Information System (IRIS); Announcement of Availability of Literature Searches for....regulations.gov or email. The http://www.regulations.gov Web site is an ``anonymous access'' system,...

  15. An Information-Theoretic-based Evolutionary Approach for the Dynamic Search Path Planning Problem

    DTIC Science & Technology

    2014-05-01

    action outcomes/observations as exogenous events, to timely adjust search path plans using coevolution . The approach takes advantage of objective...an information-theoretic framework. Path planning ultimately results from the coevolution of two populations of “plan” individuals describing a

  16. Information Storage and Retrieval. Reports on Analysis, Search, and Iterative Retrieval.

    ERIC Educational Resources Information Center

    Salton, Gerard

    As the fourteenth report in a series describing research in automatic information storage and retrieval, this document covers work carried out on the SMART project for approximately one year (summer 1967 to summer 1968). The document is divided into four main parts: (1) SMART systems design, (2) analysis and search experiments, (3) user feedback…

  17. 78 FR 13624 - Proposed Information Collection; Comment Request; Age Search Service

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-02-28

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF COMMERCE U.S. Census Bureau Proposed Information Collection; Comment Request; Age Search Service AGENCY: U.S. Census... the Paperwork Reduction Act of 1995, Public Law 104-13 (44 U.S.C. 3506(c)(2)(A)). DATES: To ensure...

  18. Differences between Novice and Experienced Users in Searching Information on the World Wide Web.

    ERIC Educational Resources Information Center

    Lazonder, Ard W.; Biemans, Harm J. A.; Wopereis, Iwan G. J. H.

    2000-01-01

    Describes a study conducted in the Netherlands that examined the effect of a user's World Wide Web experience on the search process, which consists of locating an appropriate Web site and retrieving relevant information from that site. Discusses implications for training and supporting student searchers and proposes future research. (Author/LRW)

  19. Participatory Learning through Behavioral and Cognitive Engagements in an Online Collective Information Searching Activity

    ERIC Educational Resources Information Center

    Lin, Chia-Ching; Tsai, Chin-Chung

    2012-01-01

    This study aimed to investigate the relationships between college students' behavioral and cognitive engagements while performing an online collective information searching (CIS) activity. The activity aimed to assist the students in utilizing a social bookmarking application to exploit the Internet in a collective manner. A group of 101 college…

  20. Information Storage and Retrieval. Reports on Analysis, Search, and Iterative Retrieval.

    ERIC Educational Resources Information Center

    Salton, Gerard

    As the fourteenth report in a series describing research in automatic information storage and retrieval, this document covers work carried out on the SMART project for approximately one year (summer 1967 to summer 1968). The document is divided into four main parts: (1) SMART systems design, (2) analysis and search experiments, (3) user feedback…

  1. Quality of Health Information on the Internet for Urolithiasis on the Google Search Engine

    PubMed Central

    Abouassaly, Robert; Lawrentschuk, Nathan

    2016-01-01

    Purpose. To compare the quality of health information on the Internet for keywords related to urolithiasis, to assess for difference in information quality across four main Western languages, and to compare the source of sponsorship in these websites. Methods. Health On the Net (HON) Foundation principles were utilised to determine quality information. Fifteen keywords related to urolithiasis were searched on the Google search engine. The first 150 websites were assessed against the HON principles and the source of sponsorship determined. Results. A total of 8986 websites were analysed. A proportion of HON-accredited websites for individual search terms range between 2.5% and 12.0%. The first 50 websites were more likely to be HON-positive compared to websites 51–100 and 101–150. French websites searched were more likely to be HON-positive whereas German websites were less likely to be HON-positive than English websites. There was no statistically significant difference between the rate of HON-positive English and Spanish websites. The three main website sponsors were from government/educational sources (40.2%), followed by commercial (29.9%) and physician/surgeon sources (18.6%). Conclusions. Health information on most urolithiasis websites was not validated. Nearly one-third of websites in this study have commercial sponsorship. Doctors should recognise the need for more reliable health websites for their patients. PMID:28044076

  2. Rationality, Information Search and Choice in Higher Education: Evidence from Greece

    ERIC Educational Resources Information Center

    Menon, Maria Eliophotou; Saiti, Anna; Socratous, Michalis

    2007-01-01

    The paper presents the findings of a study of the decision-making process which precedes the choice of a university in Greece. Specifically, the degree of rationality exhibited by prospective students is assessed in an attempt to provide a test for the economic approach to the explanation of human behaviour. Information search is used as an…

  3. Participatory Learning through Behavioral and Cognitive Engagements in an Online Collective Information Searching Activity

    ERIC Educational Resources Information Center

    Lin, Chia-Ching; Tsai, Chin-Chung

    2012-01-01

    This study aimed to investigate the relationships between college students' behavioral and cognitive engagements while performing an online collective information searching (CIS) activity. The activity aimed to assist the students in utilizing a social bookmarking application to exploit the Internet in a collective manner. A group of 101 college…

  4. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  5. Quality of Health Information on the Internet for Urolithiasis on the Google Search Engine.

    PubMed

    Chang, Dwayne T S; Abouassaly, Robert; Lawrentschuk, Nathan

    2016-01-01

    Purpose. To compare the quality of health information on the Internet for keywords related to urolithiasis, to assess for difference in information quality across four main Western languages, and to compare the source of sponsorship in these websites. Methods. Health On the Net (HON) Foundation principles were utilised to determine quality information. Fifteen keywords related to urolithiasis were searched on the Google search engine. The first 150 websites were assessed against the HON principles and the source of sponsorship determined. Results. A total of 8986 websites were analysed. A proportion of HON-accredited websites for individual search terms range between 2.5% and 12.0%. The first 50 websites were more likely to be HON-positive compared to websites 51-100 and 101-150. French websites searched were more likely to be HON-positive whereas German websites were less likely to be HON-positive than English websites. There was no statistically significant difference between the rate of HON-positive English and Spanish websites. The three main website sponsors were from government/educational sources (40.2%), followed by commercial (29.9%) and physician/surgeon sources (18.6%). Conclusions. Health information on most urolithiasis websites was not validated. Nearly one-third of websites in this study have commercial sponsorship. Doctors should recognise the need for more reliable health websites for their patients.

  6. The Role of Domain and System Knowledge on Text Comprehension and Information Search in Hypermedia

    ERIC Educational Resources Information Center

    Waniek, Jacqueline; Schafer, Thomas

    2009-01-01

    The goal of this study was to examine the role of domain and system knowledge on learner performance in reading and information search in hypermedia. Previous studies have shown that prior knowledge is an important individual factor for effective hypermedia use. However, current research lacks a full understanding of how these two aspects of prior…

  7. The Future of Information Services in K-12 Schools in Washington State: A Future Search Conference.

    ERIC Educational Resources Information Center

    Baldwin, Margaret

    1995-01-01

    Discusses the process of future search conferences and describes one held to consider the future of school library media centers and information services in the state of Washington. Highlights include participation by students, librarians, teachers, administrators, and others; strategic and participatory planning; and change processes. (LRW)

  8. HelpfulMed: Intelligent Searching for Medical Information over the Internet.

    ERIC Educational Resources Information Center

    Chen, Hsinchun; Lally, Ann M.; Zhu, Bin; Chau, Michael

    2003-01-01

    Discussion of the information needs of medical professionals and researchers focuses on the architecture of a Web portal designed to integrate advanced searching and indexing algorithms, an automatic thesaurus, and self-organizing map technologies to provide searchers with fine-grained results. Reports results of evaluation of spider algorithms…

  9. An Analysis of Undergraduate Students' Search Behaviors in an Information Literacy Class

    ERIC Educational Resources Information Center

    Chen, Hsin-Liang

    2009-01-01

    The purpose of this project was to investigate how students' search strategies changed over the course of a semester-long information literacy class. Data collection included four different paper questionnaires corresponding to course content in the spring 2008 semester. Seventy-seven participants completed the questionnaires and course work in…

  10. Constructing Preference from Experience: The Endowment Effect Reflected in External Information Search

    ERIC Educational Resources Information Center

    Pachur, Thorsten; Scheibehenne, Benjamin

    2012-01-01

    People often attach a higher value to an object when they own it (i.e., as seller) compared with when they do not own it (i.e., as buyer)--a phenomenon known as the "endowment effect". According to recent cognitive process accounts of the endowment effect, the effect is due to differences between sellers and buyers in information search.…

  11. HelpfulMed: Intelligent Searching for Medical Information over the Internet.

    ERIC Educational Resources Information Center

    Chen, Hsinchun; Lally, Ann M.; Zhu, Bin; Chau, Michael

    2003-01-01

    Discussion of the information needs of medical professionals and researchers focuses on the architecture of a Web portal designed to integrate advanced searching and indexing algorithms, an automatic thesaurus, and self-organizing map technologies to provide searchers with fine-grained results. Reports results of evaluation of spider algorithms…

  12. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  13. Rationality, Information Search and Choice in Higher Education: Evidence from Greece

    ERIC Educational Resources Information Center

    Menon, Maria Eliophotou; Saiti, Anna; Socratous, Michalis

    2007-01-01

    The paper presents the findings of a study of the decision-making process which precedes the choice of a university in Greece. Specifically, the degree of rationality exhibited by prospective students is assessed in an attempt to provide a test for the economic approach to the explanation of human behaviour. Information search is used as an…

  14. Proactive Support of Internet Browsing when Searching for Relevant Health Information.

    PubMed

    Rurik, Clas; Zowalla, Richard; Wiesner, Martin; Pfeifer, Daniel

    2015-01-01

    Many people use the Internet as one of the primary sources of health information. This is due to the high volume and easy access of freely available information regarding diseases, diagnoses and treatments. However, users may find it difficult to retrieve information which is easily understandable and does not require a deep medical background. In this paper, we present a new kind of Web browser add-on, in order to proactively support users when searching for relevant health information. Our add-on not only visualizes the understandability of displayed medical text but also provides further recommendations of Web pages which hold similar content but are potentially easier to comprehend.

  15. 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.

  16. The Search for Drug Abuse Information. Drug Abuse Information Research Project (Revised).

    ERIC Educational Resources Information Center

    Hanneman, Gerhard J.; Pet, Marilyn L.

    A large proportion of those who seek drug abuse information from a telephone hotline service have immediate drug information needs, either for themselves or to assist others. Requests for general or pharmacological information are less frequent. Content analysis was applied in a study of telephone calls to a Hartford, Connecticut, "drug abuse…

  17. Search strategies to identify information on adverse effects: a systematic review.

    PubMed

    Golder, Su; Loke, Yoon

    2009-04-01

    The review evaluated studies of electronic database search strategies designed to retrieve adverse effects data for systematic reviews. Studies of adverse effects were located in ten databases as well as by checking references, hand-searching, searching citations, and contacting experts. Two reviewers screened the retrieved records for potentially relevant papers. Five thousand three hundred thirteen citations were retrieved, yielding 19 studies designed to develop or evaluate adverse effect filters, of which 3 met the inclusion criteria. All 3 studies identified highly sensitive search strategies capable of retrieving over 95% of relevant records. However, 1 study did not evaluate precision, while the level of precision in the other 2 studies ranged from 0.8% to 2.8%. Methodological issues in these papers included the relatively small number of records, absence of a validation set of records for testing, and limited evaluation of precision. The results indicate the difficulty of achieving highly sensitive searches for information on adverse effects with a reasonable level of precision. Researchers who intend to locate studies on adverse effects should allow for the amount of resources and time required to conduct a highly sensitive search.

  18. Information-searching behaviors of main and allied health professionals: a nationwide survey in Taiwan.

    PubMed

    Weng, Yi-Hao; Kuo, Ken N; Yang, Chun-Yuh; Lo, Heng-Lien; Shih, Ya-Hui; Chiu, Ya-Wen

    2013-10-01

    There are a variety of resources to obtain health information, but few studies have examined if main and allied health professionals prefer different methods. The current study was to investigate their information-searching behaviours. A constructed questionnaire survey was conducted from January through April 2011 in nationwide regional hospitals of Taiwan. Questionnaires were mailed to main professionals (physicians and nurses) and allied professionals (pharmacists, physical therapists, technicians and others), with 6160 valid returns collected. Among all professional groups, the most commonly used resource for seeking health information was a Web portal, followed by colleague consultations and continuing education. Physicians more often accessed Internet-based professional resources (online databases, electronic journals and electronic books) than the other groups (P < 0.05). In contrast, physical therapists more often accessed printed resources (printed journals and textbooks) than the other specialists (P < 0.05). And nurses, physical therapists and technicians more often asked colleagues and used continuing education than the other groups (P < 0.01). The most commonly used online database was Micromedex for pharmacists and MEDLINE for physicians, technicians and physical therapists. Nurses more often accessed Chinese-language databases rather than English-language databases (P < 0.001). This national survey depicts the information-searching pattern of various health professionals. There were significant differences between and within main and allied health professionals in their information searching. The data provide clinical implications for strategies to promote the accessing of evidence-based information. © 2012 John Wiley & Sons Ltd.

  19. Pharmacovigilance and Biomedical Informatics: A Model for Future Development.

    PubMed

    Beninger, Paul; Ibara, Michael A

    2016-12-01

    The discipline of pharmacovigilance is rooted in the aftermath of the thalidomide tragedy of 1961. It has evolved as a result of collaborative efforts by many individuals and organizations, including physicians, patients, Health Authorities, universities, industry, the World Health Organization, the Council for International Organizations of Medical Sciences, and the International Conference on Harmonisation. Biomedical informatics is rooted in technologically based methodologies and has evolved at the speed of computer technology. The purpose of this review is to bring a novel lens to pharmacovigilance, looking at the evolution and development of the field of pharmacovigilance from the perspective of biomedical informatics, with the explicit goal of providing a foundation for discussion of the future direction of pharmacovigilance as a discipline. For this review, we searched [publication trend for the log10 value of the numbers of publications identified in PubMed] using the key words [informatics (INF), pharmacovigilance (PV), phar-macovigilance þ informatics (PV þ INF)], for [study types] articles published between [1994-2015]. We manually searched the reference lists of identified articles for additional information. Biomedical informatics has made significant contributions to the infrastructural development of pharmacovigilance. However, there has not otherwise been a systematic assessment of the role of biomedical informatics in enhancing the field of pharmacovigilance, and there has been little cross-discipline scholarship. Rapidly developing innovations in biomedical informatics pose a challenge to pharmacovigilance in finding ways to include new sources of safety information, including social media, massively linked databases, and mobile and wearable wellness applications and sensors. With biomedical informatics as a lens, it is evident that certain aspects of pharmacovigilance are evolving more slowly. However, the high levels of mutual interest in

  20. Use of an informed search space maximizes confidence of site-specific assignment of glycoprotein glycosylation.

    PubMed

    Khatri, Kshitij; Klein, Joshua A; Zaia, Joseph

    2017-01-01

    In order to interpret glycopeptide tandem mass spectra, it is necessary to estimate the theoretical glycan compositions and peptide sequences, known as the search space. The simplest way to do this is to build a naïve search space from sets of glycan compositions from public databases and to assume that the target glycoprotein is pure. Often, however, purified glycoproteins contain co-purified glycoprotein contaminants that have the potential to confound assignment of tandem mass spectra based on naïve assumptions. In addition, there is increasing need to characterize glycopeptides from complex biological mixtures. Fortunately, liquid chromatography-mass spectrometry (LC-MS) methods for glycomics and proteomics are now mature and accessible. We demonstrate the value of using an informed search space built from measured glycomes and proteomes to define the search space for interpretation of glycoproteomics data. We show this using α-1-acid glycoprotein (AGP) mixed into a set of increasingly complex matrices. As the mixture complexity increases, the naïve search space balloons and the ability to assign glycopeptides with acceptable confidence diminishes. In addition, it is not possible to identify glycopeptides not foreseen as part of the naïve search space. A search space built from released glycan glycomics and proteomics data is smaller than its naïve counterpart while including the full range of proteins detected in the mixture. This maximizes the ability to assign glycopeptide tandem mass spectra with confidence. As the mixture complexity increases, the number of tandem mass spectra per glycopeptide precursor ion decreases, resulting in lower overall scores and reduced depth of coverage for the target glycoprotein. We suggest use of α-1-acid glycoprotein as a standard to gauge effectiveness of analytical methods and bioinformatics search parameters for glycoproteomics studies. Graphical Abstract Assignment of site specific glycosylation from LC