J Biomed Inform - MeSHy: Mining unanticipated PubMed information using frequencies of occurrences and concurrences of MeSH terms.

Tópicos

{ search(2224) databas(1162) retriev(909) }
{ data(1714) softwar(1251) tool(1186) }
{ extract(1171) text(1153) clinic(932) }
{ use(976) code(926) identifi(902) }
{ drug(1928) target(777) effect(648) }
{ clinic(1479) use(1117) guidelin(835) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ take(945) account(800) differ(722) }
{ state(1844) use(1261) util(961) }
{ activ(1138) subject(705) human(624) }
{ can(981) present(881) function(850) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ implement(1333) system(1263) develop(1122) }
{ method(1969) cluster(1462) data(1082) }
{ can(774) often(719) complex(702) }
{ featur(3375) classif(2383) classifi(1994) }
{ assess(1506) score(1403) qualiti(1306) }
{ concept(1167) ontolog(924) domain(897) }
{ care(1570) inform(1187) nurs(1089) }
{ health(3367) inform(1360) care(1135) }
{ process(1125) use(805) approach(778) }
{ method(2212) result(1239) propos(1039) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ treatment(1704) effect(941) patient(846) }
{ chang(1828) time(1643) increas(1301) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ import(1318) role(1303) understand(862) }
{ visual(1396) interact(850) tool(830) }
{ monitor(1329) mobil(1314) devic(1160) }
{ research(1218) medic(880) student(794) }
{ data(2317) use(1299) case(1017) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ structur(1116) can(940) graph(676) }
{ model(3404) distribut(989) bayesian(671) }
{ imag(1947) propos(1133) code(1026) }
{ system(1976) rule(880) can(841) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ sequenc(1873) structur(1644) protein(1328) }
{ imag(2830) propos(1344) filter(1198) }
{ network(2748) neural(1063) input(814) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ problem(2511) optim(1539) algorithm(950) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ algorithm(1844) comput(1787) effici(935) }
{ method(1557) propos(1049) approach(1037) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ research(1085) discuss(1038) issu(1018) }
{ system(1050) medic(1026) inform(1018) }
{ model(2341) predict(2261) use(1141) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ record(1888) medic(1808) patient(1693) }
{ model(3480) simul(1196) paramet(876) }
{ ehr(2073) health(1662) electron(1139) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ gene(2352) biolog(1181) express(1162) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ time(1939) patient(1703) rate(768) }
{ analysi(2126) use(1163) compon(1037) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ result(1111) use(1088) new(759) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ activ(1452) weight(1219) physic(1104) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

TIVATION: PubMed is the most widely used database of biomedical literature. To the detriment of the user though, the ranking of the documents retrieved for a query is not content-based, and important semantic information in the form of assigned Medical Subject Headings (MeSH) terms is not readily presented or productively utilized. The motivation behind this work was the discovery of unanticipated information through the appropriate ranking of MeSH term pairs and, indirectly, documents. Such information can be useful in guiding novel research and following promising trends.METHODS: A web-based tool, called MeSHy, was developed implementing a mainly statistical algorithm. The algorithm takes into account the frequencies of occurrences, concurrences, and the semantic similarities of MeSH terms in retrieved PubMed documents to create MeSH term pairs. These are then scored and ranked, focusing on their unexpectedly frequent or infrequent occurrences.RESULTS: MeSHy presents results through an online interactive interface facilitating further manipulation through filtering and sorting. The results themselves include the MeSH term pairs, along with MeSH categories, the score, and document IDs, all of which are hyperlinked for convenience. To highlight the applicability of the tool, we report the findings of an expert in the pharmacology field on querying the molecularly-targeted drug imatinib and nutrition-related flavonoids. To the best of our knowledge, MeSHy is the first publicly available tool able to directly provide such a different perspective on the complex nature of published work.IMPLEMENTATION AND AVAILABILITY: Implemented in Perl and served by Apache2 at http://bat.ina.certh.gr/tools/meshy/ with all major browsers supported.

Resumo Limpo

tivat pubm wide use databas biomed literatur detriment user though rank document retriev queri contentbas import semant inform form assign medic subject head mesh term readili present product util motiv behind work discoveri unanticip inform appropri rank mesh term pair indirect document inform can use guid novel research follow promis trendsmethod webbas tool call meshi develop implement main statist algorithm algorithm take account frequenc occurr concurr semant similar mesh term retriev pubm document creat mesh term pair score rank focus unexpect frequent infrequ occurrencesresult meshi present result onlin interact interfac facilit manipul filter sort result includ mesh term pair along mesh categori score document id hyperlink conveni highlight applic tool report find expert pharmacolog field queri molecularlytarget drug imatinib nutritionrel flavonoid best knowledg meshi first public avail tool abl direct provid differ perspect complex natur publish workimplement avail implement perl serv apach httpbatinacerthgrtoolsmeshi major browser support

Resumos Similares

Telemed J E Health - MEDLINE versus EMBASE and CINAHL for telemedicine searches. ( 0,861955316108072 )
AMIA Annu Symp Proc - Evaluation of automated term groupings for detecting anaphylactic shock signals for drugs. ( 0,860727565792759 )
Health Info Libr J - Facilitating access to evidence: Primary Health Care Search Filter. ( 0,859995645926894 )
J Am Med Inform Assoc - Search terms and a validated brief search filter to retrieve publications on health-related values in Medline: a word frequency analysis study. ( 0,847013369242511 )
Int J Health Geogr - HEALTH GeoJunction: place-time-concept browsing of health publications. ( 0,844682503583101 )
J Integr Bioinform - Classification methods for finding articles describing protein-protein interactions in PubMed. ( 0,842095425377662 )
J Integr Bioinform - The LAILAPS search engine: a feature model for relevance ranking in life science databases. ( 0,841219515479785 )
AMIA Annu Symp Proc - Search filter precision can be improved by NOTing out irrelevant content. ( 0,832453941627274 )
J Am Med Inform Assoc - Search filters to identify geriatric medicine in Medline. ( 0,83054126377518 )
Health Info Libr J - Medical literature searches: a comparison of PubMed and Google Scholar. ( 0,827925365892246 )
J. Med. Internet Res. - Retrieving clinical evidence: a comparison of PubMed and Google Scholar for quick clinical searches. ( 0,823547346423787 )
J. Med. Internet Res. - Development and validation of filters for the retrieval of studies of clinical examination from Medline. ( 0,823486000502018 )
J Am Med Inform Assoc - Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters. ( 0,817302220774824 )
J Telemed Telecare - How to improve your PubMed/MEDLINE searches: 1. background and basic searching. ( 0,816023135764385 )
BMC Med Inform Decis Mak - BOSS: context-enhanced search for biomedical objects. ( 0,813055853306806 )
Methods Inf Med - Learning the preferences of physicians for the organization of result lists of medical evidence articles. ( 0,813028956699373 )
Methods Inf Med - Developing topic-specific search filters for PubMed with click-through data. ( 0,811552293897279 )
BMC Med Inform Decis Mak - Glomerular disease search filters for Pubmed, Ovid Medline, and Embase: a development and validation study. ( 0,80785381708377 )
J. Med. Internet Res. - Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews. ( 0,804887671310277 )
Health Info Libr J - Sensitivity and precision of adverse effects search filters in MEDLINE and EMBASE: a case study of fractures with thiazolidinediones. ( 0,804159032853593 )
BMC Med Inform Decis Mak - Boolean versus ranked querying for biomedical systematic reviews. ( 0,802108707332353 )
BMC Med Inform Decis Mak - CDAPubMed: a browser extension to retrieve EHR-based biomedical literature. ( 0,800657200829915 )
J Biomed Inform - On the query reformulation technique for effective MEDLINE document retrieval. ( 0,797796155162907 )
Health Info Libr J - Searching for randomised controlled trials and clinical controlled trials in Thai online bibliographical biomedical databases. ( 0,795956223611519 )
J Integr Bioinform - The LAILAPS search engine: relevance ranking in life science databases. ( 0,794679875891067 )
J Biomed Inform - A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine. ( 0,791295685439741 )
Inform Health Soc Care - Readability of online health information: implications for health literacy. ( 0,788742838922093 )
Health Info Libr J - The performance of adverse effects search filters in MEDLINE and EMBASE. ( 0,786296066852678 )
Health Info Libr J - Assessment of indexing trends with specific and general terms for herbal medicine. ( 0,786067333292609 )
Health Info Libr J - Utilisation of search filters in systematic reviews of prognosis questions. ( 0,785934900113284 )
J. Med. Internet Res. - Definition of Health 2.0 and Medicine 2.0: a systematic review. ( 0,784614612311814 )
Int J Med Inform - An analysis of clinical queries in an electronic health record search utility. ( 0,779086983966937 )
J Integr Bioinform - A query suggestion workflow for life science IR-systems. ( 0,778618009707704 )
J Am Med Inform Assoc - MEDLINE clinical queries are robust when searching in recent publishing years. ( 0,775146861620964 )
AMIA Annu Symp Proc - Does query expansion limit our learning? A comparison of social-based expansion to content-based expansion for medical queries on the internet. ( 0,772814040513941 )
J Med Syst - MIRASS: medical informatics research activity support system using information mashup network. ( 0,768285065623072 )
Int J Med Inform - MEDRank: using graph-based concept ranking to index biomedical texts. ( 0,761303733070912 )
J. Med. Internet Res. - A search engine to access PubMed monolingual subsets: proof of concept and evaluation in French. ( 0,760433495341254 )
BMC Med Inform Decis Mak - Performance evaluation of Unified Medical Language System?'s synonyms expansion to query PubMed. ( 0,760112741573165 )
J. Med. Internet Res. - Using Internet search engines to obtain medical information: a comparative study. ( 0,757873824412468 )
BMC Med Inform Decis Mak - Publication trends of shared decision making in 15 high impact medical journals: a full-text review with bibliometric analysis. ( 0,754391753575777 )
J. Med. Internet Res. - Automatic evidence retrieval for systematic reviews. ( 0,749591330392808 )
J Biomed Inform - Using statistical text mining to supplement the development of an ontology. ( 0,749466073086172 )
AMIA Annu Symp Proc - Query log analysis of an electronic health record search engine. ( 0,746633440017132 )
AMIA Annu Symp Proc - BIOSPIDA: A Relational Database Translator for NCBI. ( 0,746240217625732 )
J Biomed Inform - Development and evaluation of a biomedical search engine using a predicate-based vector space model. ( 0,742948121667003 )
J Am Med Inform Assoc - Improving image retrieval effectiveness via query expansion using MeSH hierarchical structure. ( 0,735768784447146 )
AMIA Annu Symp Proc - Using Co-Authoring and Cross-Referencing Information for MEDLINE Indexing. ( 0,733106415753119 )
J Am Med Inform Assoc - A literature search tool for intelligent extraction of disease-associated genes. ( 0,732517326301571 )
J. Med. Internet Res. - Searching for truth: internet search patterns as a method of investigating online responses to a Russian illicit drug policy debate. ( 0,732154220041219 )
J Biomed Inform - A mutation-centric approach to identifying pharmacogenomic relations in text. ( 0,726095527265328 )
Brief. Bioinformatics - Fast and efficient searching of biological data resources--using EB-eye. ( 0,723403177196708 )
J Biomed Inform - Supporting effective health and biomedical information retrieval and navigation: a novel facet view interface evaluation. ( 0,721995458990391 )
Health Info Libr J - Developing a geographic search filter to identify randomised controlled trials in Africa: finding the optimal balance between sensitivity and precision. ( 0,721255835193569 )
AMIA Annu Symp Proc - An automated approach for ranking journals to help in clinician decision support. ( 0,719481432278825 )
J Am Med Inform Assoc - Directing the public to evidence-based online content. ( 0,715817164081871 )
J Biomed Inform - Improving search over Electronic Health Records using UMLS-based query expansion through random walks. ( 0,715334295967093 )
J Biomed Inform - Reflective random indexing for semi-automatic indexing of the biomedical literature. ( 0,715206885820434 )
Int J Med Inform - FindZebra: a search engine for rare diseases. ( 0,714865242625453 )
Res Synth Methods - Comprehensive computer searches and reporting in systematic reviews. ( 0,713751855956071 )
J Am Med Inform Assoc - A practical approach to achieve private medical record linkage in light of public resources. ( 0,707085307833434 )
AMIA Annu Symp Proc - A bottom-up approach to MEDLINE indexing recommendations. ( 0,705256458592669 )
J Chem Inf Model - Efficient substructure searching of large chemical libraries: the ABCD chemical cartridge. ( 0,705044792611192 )
AMIA Annu Symp Proc - Development and evaluation of a prototype search engine to meet public health information needs. ( 0,70496984118647 )
J. Med. Internet Res. - The impact of search engine selection and sorting criteria on vaccination beliefs and attitudes: two experiments manipulating Google output. ( 0,704633404416072 )
J Biomed Inform - Knowledge-based personalized search engine for the Web-based Human Musculoskeletal System Resources (HMSR) in biomechanics. ( 0,704218657216499 )
J. Med. Internet Res. - Comparative analysis of online health queries originating from personal computers and smart devices on a consumer health information portal. ( 0,702444743112938 )
J Chem Inf Model - Speeding up chemical searches using the inverted index: the convergence of chemoinformatics and text search methods. ( 0,700082997336517 )
Perspect Health Inf Manag - Risk factors for bladder cancer: challenges of conducting a literature search using PubMed. ( 0,69973814322611 )
J Biomed Inform - A comparison of evaluation metrics for biomedical journals, articles, and websites in terms of sensitivity to topic. ( 0,698294494757266 )
IEEE Trans Vis Comput Graph - WORDGRAPH: Keyword-in-Context Visualization for NETSPEAK's Wildcard Search. ( 0,696181182033768 )
AMIA Annu Symp Proc - A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE Citations. ( 0,692459448865865 )
Health Info Libr J - Searching MEDLINE for Aboriginal and Torres Strait Islander health literature: questionable sensitivity. ( 0,688354024972709 )
AMIA Annu Symp Proc - Finding and accessing diagrams in biomedical publications. ( 0,687776267465537 )
BMC Med Inform Decis Mak - Dynamic summarization of bibliographic-based data. ( 0,679867496887382 )
J Biomed Inform - Improving MeSH classification of biomedical articles using citation contexts. ( 0,679189738805513 )
J Am Med Inform Assoc - Automatically extracting sentences from Medline citations to support clinicians' information needs. ( 0,678362634328758 )
J Am Med Inform Assoc - Federated queries of clinical data repositories: the sum of the parts does not equal the whole. ( 0,676039574707569 )
J Integr Bioinform - GMB: an efficient query processor for biological data. ( 0,675697247924309 )
AMIA Annu Symp Proc - Synonym, topic model and predicate-based query expansion for retrieving clinical documents. ( 0,671926160392492 )
J Biomed Inform - Automatic generation of investigator bibliographies for institutional research networking systems. ( 0,670388580914718 )
Health Info Libr J - Can we prioritise which databases to search? A case study using a systematic review of frozen shoulder management. ( 0,666874810477576 )
Methods Inf Med - A survey on visual information search behavior and requirements of radiologists. ( 0,666752533688896 )
AMIA Annu Symp Proc - Optimizing the txt2MEDLINE search portal for low-resource clinical decision support. ( 0,664295676919165 )
Methods Inf Med - Technology-induced errors. The current use of frameworks and models from the biomedical and life sciences literatures. ( 0,663914009753295 )
J Am Med Inform Assoc - Clinical research data warehouse governance for distributed research networks in the USA: a systematic review of the literature. ( 0,663487952704345 )
BMC Med Inform Decis Mak - Information discovery on electronic health records using authority flow techniques. ( 0,662180651931766 )
Brief. Bioinformatics - Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. ( 0,659256524138491 )
Sci Data - Erratum: Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. ( 0,657938357965914 )
J Am Med Inform Assoc - Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project. ( 0,657875058080845 )
J Am Med Inform Assoc - Design and usability study of an iconic user interface to ease information retrieval of medical guidelines. ( 0,655048309888888 )
J. Med. Internet Res. - A study of innovative features in scholarly open access journals. ( 0,653840868800268 )
J. Med. Internet Res. - Net improvement of correct answers to therapy questions after pubmed searches: pre/post comparison. ( 0,650481340831165 )
Methods Inf Med - Chi-square-based scoring function for categorization of MEDLINE citations. ( 0,649885845408425 )
Int J Med Inform - The publication echo: effects of retrieving literature in PubMed by year of publication. ( 0,649049868176733 )
AMIA Annu Symp Proc - Deterministic binary vectors for efficient automated indexing of MEDLINE/PubMed abstracts. ( 0,648753167078597 )
J. Med. Internet Res. - Accessing suicide-related information on the internet: a retrospective observational study of search behavior. ( 0,648212423897549 )
AMIA Annu Symp Proc - Web to world: predicting transitions from self-diagnosis to the pursuit of local medical assistance in web search. ( 0,64488531847545 )
J Chem Inf Model - Critical analysis of CCSD data quality. ( 0,642263577125858 )
AMIA Annu Symp Proc - MeSH term explosion and author rank improve expert recommendations. ( 0,642052118220395 )