Página 1 dos resultados de 5446 itens digitais encontrados em 0.015 segundos

ASAP: an automated system for scientific literature search in pubmed using web agentes

Carvalhal, Carlos; Deusdado, Sérgio; Deusdado, Leonel
Fonte: Springer Publicador: Springer
Tipo: conferenceobject
Português
Relevância na Pesquisa
36.82%
In this paper we present ASAP - Automated Search with Agents in PubMed, a web-based service aiming to manage and automate scientific literature search in the PubMed database. The system allows the creation and management of web agents, specifically parameterized thematically and functionally, that automatically and periodically crawl the PubMed database, oriented to search and retrieve relevant results according the requirements provided by the user. The results, containing the publications list retrieved, are emailed to the agent owner weekly during the activity period programmed for the web agent. The ASAP service is devoted to help researchers, especially from the field of biomedicine and bioinformatics, in order to increase their productivity, and can be accessed at: http://esa.ipb.pt/~agentes.

Crawling PubMed with web agents for literature search and alerting services

Carvalhal, Carlos; Deusdado, Sérgio; Deusdado, Leonel
Fonte: Universidade de Salamanca Publicador: Universidade de Salamanca
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
36.82%
In this paper we present ASAP - Automated Search with Agents in PubMed, a web-based service aiming to manage and automate scientific literature search in the PubMed database. The system allows the creation and management of web agents, parameterized thematically and functionally, that crawl the PubMed database autonomously and periodically, aiming to search and retrieve relevant results according the requirements provided by the user. The results, containing the publications list retrieved, are emailed to the agent owner on a weekly basis, during the activity period defined for the web agent. The ASAP service is devoted to help researchers, especially from the field of biomedicine and bioinformatics, in order to increase their productivity, and can be accessed at: http://esa.ipb.pt/~agentes.

A comunicação científica em saúde: uma abordagem semiótica; Scientific communication in health: a semiotic approach

Alvarez, Maria do Carmo Avamilano
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 06/03/2015 Português
Relevância na Pesquisa
26.89%
No cenário da cultura acadêmica e científica em transformação, as bibliotecas indagam os pesquisadores em HIV/aids sobre dificuldades e facilidades na procura de informações. Articulando as disciplinas ciência da informação, saúde pública e semiótica da cultura, este estudo busca analisar o entendimento dos pesquisadores sobre as estratégias de busca de informação técnica e científica nos sistemas bibliográficos. Além disso, identifica os sistemas de signos centrais na semiosfera da cultura e descreve as interações dos pesquisadores com sistemas de informação e bibliotecas, refletindo sobre a comunicação e seus desafios na contemporaneidade. Com base no método semiótico estrutural da Escola de Tártu-Moscou e nos trabalhos de seu maior expoente Iuri Lótman, foram realizadas 25 entrevistas com dois grupos de pesquisa em HIV/aids no Brasil. A diversidade de estratégias do pesquisador sobre a ação de buscar informação científica na contemporaneidade sustenta a dinâmica e a complexidade dos sistemas de signos. As divergências e convergências, traduzidas nas narrativas, explicitam as diferentes linguagens presentes na semiosfera e as tradições de pesquisa. Essas linguagens se transformam, modelizando-se pela variedade de formação acadêmica...

Testing search strategies for systematic reviews in the Medline literature database through PubMed

Volpato, Enilze S. N.; Betini, Marluci; El Dib, Regina
Fonte: Wiley-Blackwell Publicador: Wiley-Blackwell
Tipo: Artigo de Revista Científica Formato: 117-120
Português
Relevância na Pesquisa
36.74%
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); BackgroundA high-quality electronic search is essential in ensuring accuracy and completeness in retrieved records for the conducting of a systematic review.ObjectiveWe analysed the available sample of search strategies to identify the best method for searching in Medline through PubMed, considering the use or not of parenthesis, double quotation marks, truncation and use of a simple search or search history.MethodsIn our cross-sectional study of search strategies, we selected and analysed the available searches performed during evidence-based medicine classes and in systematic reviews conducted in the Botucatu Medical School, UNESP, Brazil.ResultsWe analysed 120 search strategies. With regard to the use of phrase searches with parenthesis, there was no difference between the results with and without parenthesis and simple searches or search history tools in 100% of the sample analysed (P = 1.0). The number of results retrieved by the searches analysed was smaller using double quotations marks and using truncation compared with the standard strategy (P = 0.04 and P = 0.08, respectively).ConclusionsThere is no need to use phrase-searching parenthesis to retrieve studies; however...

Topic maps applied to PubMed

Librelotto, Giovani Rubert; Machado, Henrique Tamiosso; Martins, Mirkos; Ferreira, Pedro Gabriel Dias; Ramalho, José Carlos; Henriques, Pedro Rangel
Fonte: Extreme Markup Languages 2007 Publicador: Extreme Markup Languages 2007
Tipo: info:eu-repo/semantics/conferenceobject
Publicado em //2007 Português
Relevância na Pesquisa
36.89%
This paper presents a topic map approach to PubMed in order to create a knowledge representation for this information system. PubMed is a free search engine that gives very full coverage of the related biomedical sciences. With more than 17 millions of citations since 1865, PubMed users have several problems to find the papers desired. So, it is necessary to organize these concepts in a semantic network. To achieve this objective, we use the Metamorphosis system, choosing the keywords from MeSH ontology. This way, we obtain an ontological index for PubMed, making easier to find specific papers.

Generating semantic networks to the PubMed

Librelotto, Giovani Rubert; Martins, Mirkos; Machado, Henrique Tamiosso; Vizzotto, Juliana; Ramalho, José Carlos; Henriques, Pedro Rangel
Tipo: info:eu-repo/semantics/conferenceobject
Publicado em 14/02/2008 Português
Relevância na Pesquisa
36.89%
This paper presents a topic map approach to PubMed in order to create a knowledge representation for this information system. PubMed is a free search engine that gives very full coverage of the related biomedical sciences. With more than 17 millions of citations since 1865, PubMed users have several problems to find the papers desired. So, it is necessary to organize these concepts in a semantic network. To achieve this objective, we use the Metamorphosis system, choosing the keywords from MeSH ontology. This way, we obtain an ontological index for PubMed, making easier to find specific papers.

Radiotherapy, cancer and some anatomical structures related with the pelvic floor: an evaluation of the scientific literature

Santos-Filho,Sebastião David; Presta,Giuseppe Antonio; Paoli,Severo de; Missailids,Sotiris; Fonseca,Adenilson de Souza da; Bernardo-Filho,Mario
Fonte: Instituto de Tecnologia do Paraná - Tecpar Publicador: Instituto de Tecnologia do Paraná - Tecpar
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/12/2008 Português
Relevância na Pesquisa
26.82%
Radiotherapy is a cancer treatment that uses high-energy X-rays or other types of ionizing radiation to try to kill the cancer cells in various organs/tissues. PubMed is a database used as a tool in various publications. The aim of this work was to evaluate, in the PubMed, the number of publications (NP) in radiotherapy and cancer in various organs related to the pelvic floor as well as brachytherapy. The searches were performed (August 2008) in the PubMed (http://www.pubmed.com) using the words: (i) radiotherapy (RT) or cancer (CA), (ii) RT and CA, (iii) RT and CA and prostate, RT and CA and testis, RT and CA and breast, RT and CA and kidneys, RT and CA and vulva, RT and CA and vagina, RT and CA and penis, RT and CA and uterus, RT and CA and ovary, RT and CA and bladder, and RT and CA and urethra. A search using brachytherapy was also performed. The NP in each subject was determined and was 2178635 to CA and about 9% of them are related with RT. The NP in RT and CA and breast or prostate is bigger than for the other organs, whereas brachytherapy is mainly cited in the studies about CA of prostate, bladder and breast. In conclusion, our findings demonstrate the importance of radiation therapy studies in the cancer of several organs. This information is crucial in understanding the field and demonstrates areas of significant progress or existing gaps of research in radiotherapy treatment of various cancers of the pelvis. Furthermore...

Prostate cancer, treatment modalities and complications: an evaluation of the scientific literature

Santos-Filho,Sebastião David; Missailids,Sotiris; Fonseca,Adenilson de Souza da; Bernardo-Filho,Mario
Fonte: Instituto de Tecnologia do Paraná - Tecpar Publicador: Instituto de Tecnologia do Paraná - Tecpar
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/12/2008 Português
Relevância na Pesquisa
26.82%
Prostate (PR) cancer (CA) is one of the most common malignant neoplasms in men all over the world. In general, if prostate cancer (PC) is detected early, treatment usually involves either surgical removal of the prostate or radiotherapy (RT). Hormone Therapy (HT) or chemotherapy (CH) is the preferred treatment for more advanced cases of PC or if CA spreads beyond the PT. A number of complications, such as urinary incontinence (IU) or erectile dysfunction (ED), can be associated with some modalities of treatment of the PC. The aim of this work is to evaluate, in PubMed, the number of publications related with prostate cancer and the main modalities of treatment, as well as some clinical complications. The searches were performed in PubMed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi) in the period 1950 to 2008 using the words: (i) CA, (ii) CA and PR or penis or testis, (iii) CA and PR and RT, CA and PR and surgery (SU), CA and PR and CH and, CA and PR and HT and (iv) CA and PR and RT and IU or ED, CA and PR and SU and IU or ED, CA and PR and CH and IU or ED and, CA and PR and HT and CH and IU or ED, and (V) PC and the same modalities of treatment. The data was obtained on July 20th, 2008. PC, as expected has been cited extensively and surgery has been identified as the most widely referenced modality of treatment. Furthermore...

A Review of Scientific Papers About Head and Neck Cancers

Paoli,Severo de; Fonseca,Adenilson de Souza da; Paoli,Flávia de; Geller,Mauro; Presta,Giuseppe Antonio; Santos-Filho,Sebastião David; Bernardo-Filho,Mário
Fonte: Instituto de Tecnologia do Paraná - Tecpar Publicador: Instituto de Tecnologia do Paraná - Tecpar
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/12/2008 Português
Relevância na Pesquisa
26.74%
Head and neck cancer is one of the 10 most frequent cancers worldwide, with an estimated 500000 new cases diagnosed annually. Treatment of head and neck cancers require a multidisciplinary approach due their complexity and the functional and esthetic alterations that cancer can cause. The interest of the scientific community in a specific subject can be evaluated by analyzing of the number and the quality of published papers on the topic. The information obtained from PubMed (www.ncbi.nlm.nih.gov/sites/entrez) has been used as a tool in various publications to aid the evaluation of the scientific interest in specific research areas The aim of this work is to evaluate, using PubMed, the scientific interest in studies of head and neck cancer treatments such as radiotherapy, chemotherapy and surgery. The searches were performed on PubMed for publications from the period of 1949 to 2008 using the search terms "head and neck cancer" and "surgery" or "radiotherapy" or "chemotherapy". The number of publications per year was determined in each search. The percentage of publications was also calculated for each subject in each year. An interest factor in a subject (IFS) was also determined. The number of publications was higher for surgery than chemotherapy or radiotherapy. The calculated 1964 IFS for surgery was 14.79...

PubMed Informer: Monitoring MEDLINE/PubMed through E-mail Alerts, SMS, PDA downloads and RSS feeds

Muin, Michael; Fontelo, Paul; Ackerman, Michael
Fonte: American Medical Informatics Association Publicador: American Medical Informatics Association
Tipo: text
Publicado em //2005 Português
Relevância na Pesquisa
26.82%
PubMed Informer is a Web-based monitoring tool for topics of interest from MEDLINE/PubMed primarily designed for healthcare professionals. Five tracking methods are available: Web access, e-mail, Short Message Service (SMS), PDA downloads and RSS feeds. PubMed Informer delivers focused search updates and specific information to users with varying information-seeking practices.

PubMed QUEST: The PubMed Query Search Tool. An informatics tool to aid cancer centers and cancer investigators in searching the PubMed databases

Hanauer, David A.; Chinnaiyan, Arul M.
Fonte: Libertas Academica Publicador: Libertas Academica
Tipo: text
Publicado em 12/02/2007 Português
Relevância na Pesquisa
26.93%
Searching PubMed for citations related to a specific cancer center or group of authors can be labor-intensive. We have created a tool, PubMed QUEST, to aid in the rapid searching of PubMed for publications of interest. It was designed by taking into account the needs of entire cancer centers as well as individual investigators. The experience of using the tool by our institution’s cancer center administration and investigators has been favorable and we believe it could easily be adapted to other institutions. Use of the tool has identified limitations of automated searches for publications based on an author’s name, especially for common names. These limitations could likely be solved if the PubMed database assigned a unique identifier to each author.

Understanding PubMed® user search behavior through log analysis

Islamaj Dogan, Rezarta; Murray, G. Craig; Névéol, Aurélie; Lu, Zhiyong
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: text
Português
Relevância na Pesquisa
26.89%
This article reports on a detailed investigation of PubMed users’ needs and behavior as a step toward improving biomedical information retrieval. PubMed is providing free service to researchers with access to more than 19 million citations for biomedical articles from MEDLINE and life science journals. It is accessed by millions of users each day. Efficient search tools are crucial for biomedical researchers to keep abreast of the biomedical literature relating to their own research. This study provides insight into PubMed users’ needs and their behavior. This investigation was conducted through the analysis of one month of log data, consisting of more than 23 million user sessions and more than 58 million user queries. Multiple aspects of users’ interactions with PubMed are characterized in detail with evidence from these logs. Despite having many features in common with general Web searches, biomedical information searches have unique characteristics that are made evident in this study. PubMed users are more persistent in seeking information and they reformulate queries often. The three most frequent types of search are search by author name, search by gene/protein, and search by disease. Use of abbreviation in queries is very frequent. Factors such as result set size influence users’ decisions. Analysis of characteristics such as these plays a critical role in identifying users’ information needs and their search habits. In turn...

Finding Query Suggestions for PubMed

Lu, Zhiyong; Wilbur, W. John; McEntyre, Johanna R; Iskhakov, Alexey; Szilagyi, Lee
Fonte: American Medical Informatics Association Publicador: American Medical Informatics Association
Tipo: text
Português
Relevância na Pesquisa
26.82%
It is common for PubMed users to repeatedly modify their queries (search terms) before retrieving documents relevant to their information needs. To assist users in reformulating their queries, we report the implementation and usage analysis of a new component in PubMed called Related Queries, which automatically produces query suggestions in response to the original user’s input. The proposed method is based on query log analysis and focuses on finding popular queries that contain the initial user search term with a goal of helping users describe their information needs in a more precise manner. This work has been integrated into PubMed since January 2009. Automatic assessment using clickthrough data show that each day, the new feature is used consistently between 6% and 10% of the time when it is shown, suggesting that it has quickly become a popular new feature in PubMed.

Enhancing search efficiency by means of a search filter for finding all studies on animal experimentation in PubMed

Hooijmans, Carlijn R; Tillema, Alice; Leenaars, Marlies; Ritskes-Hoitinga, Merel
Fonte: Royal Society of Medicine Press Publicador: Royal Society of Medicine Press
Tipo: text
Publicado em /07/2010 Português
Relevância na Pesquisa
26.89%
Collecting and analysing all available literature before starting an animal experiment is important and it is indispensable when writing a systematic review (SR) of animal research. Writing such review prevents unnecessary duplication of animal studies and thus unnecessary animal use (Reduction). One of the factors currently impeding the production of ‘high-quality’ SRs in laboratory animal science is the fact that searching for all available literature concerning animal experimentation is rather difficult. In order to diminish these difficulties, we developed a search filter for PubMed to detect all publications concerning animal studies. This filter was compared with the method most frequently used, the PubMed Limit: Animals, and validated further by performing two PubMed topic searches. Our filter performs much better than the PubMed limit: it retrieves, on average, 7% more records. Other important advantages of our filter are that it also finds the most recent records and that it is easy to use. All in all, by using our search filter in PubMed, all available literature concerning animal studies on a specific topic can easily be found and assessed, which will help in increasing the scientific quality and thereby the ethical validity of animal experiments.

Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

Srikrishna, Devabhaktuni; Coram, Marc A.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: text
Publicado em 14/09/2011 Português
Relevância na Pesquisa
26.89%
Author-supplied citations are a fraction of the related literature for a paper. The “related citations” on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed “related citations.” We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers...

Combining PubMed Knowledge and EHR Data to Develop a Weighted Bayesian Network for Pancreatic Cancer Prediction

Zhao, Di; Weng, Chunhua
Tipo: text
Português
Relevância na Pesquisa
26.82%
In this paper, we propose a novel method that combines PubMed knowledge and Electronic Health Records to develop a weighted Bayesian Network Inference (BNI) model for pancreatic cancer prediction. We selected 20 common risk factors associated with pancreatic cancer and used PubMed knowledge to weigh the risk factors. A keyword-based algorithm was developed to extract and classify PubMed abstracts into three categories that represented positive, negative, or neutral associations between each risk factor and pancreatic cancer. Then we designed a weighted BNI model by adding the normalized weights into a conventional BNI model. We used this model to extract the EHR values for patients with or without pancreatic cancer, which then enabled us to calculate the prior probabilities for the 20 risk factors in the BNI. The software iDiagnosis was designed to use this weighted BNI model for predicting pancreatic cancer. In an evaluation using a case-control dataset, the weighted BNI model significantly outperformed the conventional BNI and two other classifiers (k-Nearest Neighbor and Support Vector Machine). We conclude that the weighted BNI using PubMed knowledge and EHR data shows remarkable accuracy improvement over existing representative methods for pancreatic cancer prediction.

Finding Translational Science Publications in MEDLINE/PubMed with Translational Science Filters

Fontelo, Paul; Liu, Fang
Tipo: text
Português
Relevância na Pesquisa
26.82%
Translational Science Search (http://tscience.nlm.nih.gov) is a Web application for finding MEDLINE/PubMed journal articles that are regarded by their authors as novel, promising, or may have potential clinical application. A set of “translational” filters and related terms was created by reviewing journal articles published in clinical and translational science journals. Through E-Utilities, a user’s query and translational science (TS) filters are submitted to PubMed, and then the retrieved PubMed citations are matched with a database of MeSH terms (for disease conditions) and RxNorm (for interventions) to locate the search term, translational filters found, and associated interventions in the title and abstract. An algorithm ranks the Interventions and Conditions, and then highlights them in the results page for quick reading and evaluation. Using previously searched terms and standard formulas, the Precision and Recall of Translational Science Search (TSS) were 0.99 and 0.47, compared to 0.58 and 1.0 for PubMed Entrez, respectively.

Materia Socio Medica is Indexed in Pubmed and Archived in PubMed Central

Masic, Izet
Fonte: AVICENA, d.o.o., Sarajevo Publicador: AVICENA, d.o.o., Sarajevo
Tipo: text
Publicado em //2013 Português
Relevância na Pesquisa
26.82%
Materia Socio Medica Journal has been accepted for archiving in PubMed Central from 2011. The journal started in 1993 as offi cial journal of Social Medicine Association of B&H. During last 3 years Mat Soc Med has included in almost all femous on-line databases (except WoS). All issues of Mat Soc Med published in 2012 are now visible on PubMed/PubMed Central.

Predicting clicks of PubMed articles

Mao, Yuqing; Lu, Zhiyong
Fonte: American Medical Informatics Association Publicador: American Medical Informatics Association
Tipo: text
Publicado em 16/11/2013 Português
Relevância na Pesquisa
26.93%
Predicting the popularity or access usage of an article has the potential to improve the quality of PubMed searches. We can model the click trend of each article as its access changes over time by mining the PubMed query logs, which contain the previous access history for all articles. In this article, we examine the access patterns produced by PubMed users in two years (July 2009 to July 2011). We explore the time series of accesses for each article in the query logs, model the trends with regression approaches, and subsequently use the models for prediction. We show that the click trends of PubMed articles are best fitted with a log-normal regression model. This model allows the number of accesses an article receives and the time since it first becomes available in PubMed to be related via quadratic and logistic functions, with the model parameters to be estimated via maximum likelihood. Our experiments predicting the number of accesses for an article based on its past usage demonstrate that the mean absolute error and mean absolute percentage error of our model are 4.0% and 8.1% lower than the power-law regression model, respectively. The log-normal distribution is also shown to perform significantly better than a previous prediction method based on a human memory theory in cognitive science. This work warrants further investigation on the utility of such a log-normal regression approach towards improving information access in PubMed.

PubstractHelper: A Web-based Text-Mining Tool for Marking Sentences in Abstracts from PubMed Using Multiple User-Defined Keywords

Chen, Chou-Cheng; Ho, Chung-Liang
Fonte: Biomedical Informatics Publicador: Biomedical Informatics
Tipo: text
Publicado em 27/11/2014 Português
Relevância na Pesquisa
26.82%
While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible to increase this efficiency. Some websites use text mining to gather information from the PubMed database; however, they are database-oriented, using pre-defined search keywords while lacking a query interface for user-defined search inputs. We present the PubMed Abstract Reading Helper (PubstractHelper) website which combines text mining and reading assistance for an efficient PubMed search. PubstractHelper can accept a maximum of ten groups of keywords, within each group containing up to ten keywords. The principle behind the text-mining function of PubstractHelper is that keywords contained in the same sentence are likely to be related. PubstractHelper highlights sentences with co-occurring keywords in different colors. The user can download the PMID and the abstracts with color markings to be reviewed later. The PubstractHelper website can help users to identify relevant publications based on the presence of related keywords, which should be a handy tool for their research.