J Biomed Inform - Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text.

Tópicos

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

Resumo

TRODUCTION: In this article, we evaluate a knowledge-based word sense disambiguation method that determines the intended concept associated with an ambiguous word in biomedical text using semantic similarity and relatedness measures. These measures quantify the degree of similarity or relatedness between concepts in the Unified Medical Language System (UMLS). The objective of this work is to develop a method that can disambiguate terms in biomedical text by exploiting similarity and relatedness information extracted from biomedical resources and to evaluate the efficacy of these measure on WSD.METHOD: We evaluate our method on a biomedical dataset (MSH-WSD) that contains 203 ambiguous terms and acronyms.RESULTS: We show that information content-based measures derived from either a corpus or taxonomy obtain a higher disambiguation accuracy than path-based measures or relatedness measures on the MSH-WSD dataset.AVAILABILITY: The WSD system is open source and freely available from http://search.cpan.org/dist/UMLS-SenseRelate/. The MSH-WSD dataset is available from the National Library of Medicine http://wsd.nlm.nih.gov.

Resumo Limpo

troduct articl evalu knowledgebas word sens disambigu method determin intend concept associ ambigu word biomed text use semant similar related measur measur quantifi degre similar related concept unifi medic languag system uml object work develop method can disambigu term biomed text exploit similar related inform extract biomed resourc evalu efficaci measur wsdmethod evalu method biomed dataset mshwsd contain ambigu term acronymsresult show inform contentbas measur deriv either corpus taxonomi obtain higher disambigu accuraci pathbas measur related measur mshwsd datasetavail wsd system open sourc freeli avail httpsearchcpanorgdistumlssenserel mshwsd dataset avail nation librari medicin httpwsdnlmnihgov

Resumos Similares

J Am Med Inform Assoc - Towards comprehensive syntactic and semantic annotations of the clinical narrative. ( 0,858307144483787 )
J Am Med Inform Assoc - Knowledge-based biomedical word sense disambiguation: an evaluation and application to clinical document classification. ( 0,856025509569862 )
AMIA Annu Symp Proc - A cloud-based approach to medical NLP. ( 0,830879536070134 )
J Biomed Inform - Desiderata for ontologies to be used in semantic annotation of biomedical documents. ( 0,829111679696496 )
AMIA Annu Symp Proc - Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method. ( 0,827829518392133 )
Appl Clin Inform - Representation of information about family relatives as structured data in electronic health records. ( 0,827564596343886 )
Int J Med Inform - Detection of infectious symptoms from VA emergency department and primary care clinical documentation. ( 0,817818527690561 )
J Am Med Inform Assoc - Anaphoric relations in the clinical narrative: corpus creation. ( 0,814128783275269 )
AMIA Annu Symp Proc - Inter-annotator reliability of medical events, coreferences and temporal relations in clinical narratives by annotators with varying levels of clinical expertise. ( 0,812651214229922 )
J Biomed Inform - Common data model for natural language processing based on two existing standard information models: CDA+GrAF. ( 0,812003661595066 )
J Biomed Inform - Unsupervised biomedical named entity recognition: experiments with clinical and biological texts. ( 0,806556817031426 )
J Am Med Inform Assoc - Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. ( 0,80531582729826 )
J Biomed Inform - Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. ( 0,801408978378931 )
J Biomed Inform - UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. ( 0,799857688703596 )
J Am Med Inform Assoc - Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. ( 0,79761076310947 )
AMIA Annu Symp Proc - Throw the bath water out, keep the baby: keeping medically-relevant terms for text mining. ( 0,790345761419669 )
J Med Syst - Redactable signatures for signed CDA Documents. ( 0,786642028517844 )
J Biomed Inform - An ontology-based similarity measure for biomedical data-application to radiology reports. ( 0,786104283842944 )
J Am Med Inform Assoc - An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge. ( 0,784185586204135 )
AMIA Annu Symp Proc - Semantic processing to identify adverse drug event information from black box warnings. ( 0,783564571726681 )
AMIA Annu Symp Proc - Natural language processing to extract follow-up provider information from hospital discharge summaries. ( 0,783346230211597 )
J Biomed Inform - Enhancing clinical concept extraction with distributional semantics. ( 0,780827774564533 )
J Biomed Inform - Anaphoric reference in clinical reports: characteristics of an annotated corpus. ( 0,777529266725294 )
J Biomed Inform - A concept-driven biomedical knowledge extraction and visualization framework for conceptualization of text corpora. ( 0,774915358772898 )
J Am Med Inform Assoc - A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. ( 0,774506106380053 )
J Biomed Inform - Ontology modularization to improve semantic medical image annotation. ( 0,768658551324828 )
J Biomed Inform - MedTime: a temporal information extraction system for clinical narratives. ( 0,76632778820015 )
AMIA Annu Symp Proc - Knowledge-based method for determining the meaning of ambiguous biomedical terms using information content measures of similarity. ( 0,766026490592188 )
AMIA Annu Symp Proc - Using Medical Text Extraction, Reasoning and Mapping System (MTERMS) to process medication information in outpatient clinical notes. ( 0,764879294914417 )
AMIA Annu Symp Proc - Semantic characteristics of NLP-extracted concepts in clinical notes vs. biomedical literature. ( 0,762011871792672 )
J Biomed Inform - Development and evaluation of RapTAT: a machine learning system for concept mapping of phrases from medical narratives. ( 0,761789939505834 )
J Am Med Inform Assoc - A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources. ( 0,760951962530982 )
J Biomed Inform - Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text. ( 0,759200709637583 )
J Am Med Inform Assoc - Eventual situations for timeline extraction from clinical reports. ( 0,758990203497976 )
J. Med. Internet Res. - Web 2.0-based crowdsourcing for high-quality gold standard development in clinical natural language processing. ( 0,758987554773974 )
J Am Med Inform Assoc - A hybrid system for temporal information extraction from clinical text. ( 0,757615763251625 )
J Am Med Inform Assoc - Comparison of a semi-automatic annotation tool and a natural language processing application for the generation of clinical statement entries. ( 0,755411982920936 )
J Am Med Inform Assoc - Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. ( 0,754222051484985 )
AMIA Annu Symp Proc - Extracting Concepts Related to Homelessness from the Free Text of VA Electronic Medical Records. ( 0,754217837800207 )
Artif Intell Med - Biomedical events extraction using the hidden vector state model. ( 0,753729218594718 )
Comput Methods Programs Biomed - BioAnnote: a software platform for annotating biomedical documents with application in medical learning environments. ( 0,753397365731734 )
J Am Med Inform Assoc - Automatic discourse connective detection in biomedical text. ( 0,750723191111853 )
J Biomed Inform - Lessons learnt from the DDIExtraction-2013 Shared Task. ( 0,749531138602548 )
J Biomed Inform - Towards generating a patient's timeline: extracting temporal relationships from clinical notes. ( 0,746677803026095 )
J Biomed Inform - A new clustering method for detecting rare senses of abbreviations in clinical notes. ( 0,745169083050839 )
Int J Med Inform - Bootstrapping a de-identification system for narrative patient records: cost-performance tradeoffs. ( 0,742981883169818 )
AMIA Annu Symp Proc - Building gold standard corpora for medical natural language processing tasks. ( 0,742857421943761 )
J Am Med Inform Assoc - Assisted annotation of medical free text using RapTAT. ( 0,740978366859022 )
AMIA Annu Symp Proc - TagLine: Information Extraction for Semi-Structured Text in Medical Progress Notes. ( 0,739815465832414 )
J Am Med Inform Assoc - Using rule-based natural language processing to improve disease normalization in biomedical text. ( 0,739593652506322 )
J Am Med Inform Assoc - Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification. ( 0,739439828096626 )
AMIA Annu Symp Proc - Critical finding capture in the impression section of radiology reports. ( 0,739166498706961 )
J Biomed Inform - Lexical patterns, features and knowledge resources for coreference resolution in clinical notes. ( 0,738074723559868 )
AMIA Annu Symp Proc - Towards a semantic lexicon for clinical natural language processing. ( 0,73799464358074 )
Int J Med Inform - Detecting temporal expressions in medical narratives. ( 0,737585420869287 )
J Biomed Inform - Semantator: semantic annotator for converting biomedical text to linked data. ( 0,736616825517958 )
J Am Med Inform Assoc - Evaluating the impact of pre-annotation on annotation speed and potential bias: natural language processing gold standard development for clinical named entity recognition in clinical trial announcements. ( 0,736251784202355 )
J Biomed Inform - Identifying non-elliptical entity mentions in a coordinated NP with ellipses. ( 0,735989391523537 )
AMIA Annu Symp Proc - Detecting abbreviations in discharge summaries using machine learning methods. ( 0,731909504831864 )
J Biomed Inform - Extraction of events and temporal expressions from clinical narratives. ( 0,731850010651156 )
Brief. Bioinformatics - A survey on annotation tools for the biomedical literature. ( 0,731695603458891 )
AMIA Annu Symp Proc - Automatic acquisition of sublanguage semantic schema: towards the word sense disambiguation of clinical narratives. ( 0,730146890153704 )
J Am Med Inform Assoc - MITRE system for clinical assertion status classification. ( 0,729120477951634 )
J Biomed Inform - Ontology-guided feature engineering for clinical text classification. ( 0,727359738492132 )
J Biomed Inform - NCBI disease corpus: a resource for disease name recognition and concept normalization. ( 0,726302350170311 )
J Am Med Inform Assoc - A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text. ( 0,726211325227019 )
J Integr Bioinform - Automatic extraction of microorganisms and their habitats from free text using text mining workflows. ( 0,725917479895862 )
J Am Med Inform Assoc - 2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text. ( 0,723555176366709 )
AMIA Annu Symp Proc - An evaluation of the UMLS in representing corpus derived clinical concepts. ( 0,723173857319221 )
AMIA Annu Symp Proc - Pharmacovigilance on twitter? Mining tweets for adverse drug reactions. ( 0,72306734854369 )
Artif Intell Med - Terminological resources for text mining over biomedical scientific literature. ( 0,722827475241961 )
AMIA Annu Symp Proc - Automatically pairing measured findings across narrative abdomen CT reports. ( 0,718345273822821 )
AMIA Annu Symp Proc - Sophia: A Expedient UMLS Concept Extraction Annotator. ( 0,716762019924203 )
Comput Math Methods Med - Ranking biomedical annotations with annotator's semantic relevancy. ( 0,715418149945404 )
AMIA Annu Symp Proc - Mapping annotations with textual evidence using an scLDA model. ( 0,714343691760916 )
AMIA Annu Symp Proc - Natural language processing for lines and devices in portable chest x-rays. ( 0,711677913770104 )
Int J Med Inform - A methodology to enhance spatial understanding of disease outbreak events reported in news articles. ( 0,71079749300377 )
J Am Med Inform Assoc - MedXN: an open source medication extraction and normalization tool for clinical text. ( 0,71067087099503 )
AMIA Annu Symp Proc - Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics. ( 0,708168286334546 )
J Am Med Inform Assoc - Automated concept-level information extraction to reduce the need for custom software and rules development. ( 0,707625943607011 )
J Am Med Inform Assoc - Text mining for the Vaccine Adverse Event Reporting System: medical text classification using informative feature selection. ( 0,707093004313823 )
J Biomed Inform - Automatic recognition of disorders, findings, pharmaceuticals and body structures from clinical text: an annotation and machine learning study. ( 0,706453136773218 )
AMIA Annu Symp Proc - Semantic processing to identify adverse drug event information from black box warnings. ( 0,706333884944172 )
J Am Med Inform Assoc - Automated clinical trial eligibility prescreening: increasing the efficiency of patient identification for clinical trials in the emergency department. ( 0,705135761028958 )
AMIA Annu Symp Proc - Developing a section labeler for clinical documents. ( 0,704604344717901 )
BMC Med Inform Decis Mak - Text summarization as a decision support aid. ( 0,703658927492344 )
J Am Med Inform Assoc - Extracting drug indication information from structured product labels using natural language processing. ( 0,701532853945681 )
AMIA Annu Symp Proc - Automated illustration of patients instructions. ( 0,700813842712943 )
J Biomed Inform - Text de-identification for privacy protection: a study of its impact on clinical text information content. ( 0,700309160506823 )
J Biomed Inform - Using text to build semantic networks for pharmacogenomics. ( 0,70021007645248 )
J Biomed Inform - Using an ensemble system to improve concept extraction from clinical records. ( 0,70019150588889 )
J Am Med Inform Assoc - Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. ( 0,698275571360718 )
AMIA Annu Symp Proc - Mining Biomedical Literature for Terms related to Epidemiologic Exposures. ( 0,697048409924251 )
J Biomed Inform - The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions. ( 0,693816359173762 )
AMIA Annu Symp Proc - EpiDEA: extracting structured epilepsy and seizure information from patient discharge summaries for cohort identification. ( 0,693276279309844 )
AMIA Annu Symp Proc - Combining corpus-derived sense profiles with estimated frequency information to disambiguate clinical abbreviations. ( 0,689081102288043 )
J Am Med Inform Assoc - Automatic abstraction of imaging observations with their characteristics from mammography reports. ( 0,688931960657589 )
J Biomed Inform - Secondary use of electronic health records for building cohort studies through top-down information extraction. ( 0,688840206900618 )
Inform Health Soc Care - A model based on multi-features to enhance healthcare and medical document retrieval. ( 0,688707978598806 )
Sci Data - Building the graph of medicine from millions of clinical narratives. ( 0,68552164948738 )