Appl Clin Inform - Automating case definitions using literature-based reasoning.

Tópicos

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

Resumo

CKGROUND: Establishing a Case Definition (CDef) is a first step in many epidemiological, clinical, surveillance, and research activities. The application of CDefs still relies on manual steps and this is a major source of inefficiency in surveillance and research.OBJECTIVE: Describe the need and propose an approach for automating the useful representation of CDefs for medical conditions.METHODS: We translated the existing Brighton Collaboration CDef for anaphylaxis by mostly relying on the identification of synonyms for the criteria of the CDef using the NLM MetaMap tool. We also generated a CDef for the same condition using all the related PubMed abstracts, processing them with a text mining tool, and further treating the synonyms with the above strategy. The co-occurrence of the anaphylaxis and any other medical term within the same sentence of the abstracts supported the construction of a large semantic network. The 'islands' algorithm reduced the network and revealed its densest region including the nodes that were used to represent the key criteria of the CDef. We evaluated the ability of the "translated" and the "generated" CDef to classify a set of 6034 H1N1 reports for anaphylaxis using two similarity approaches and comparing them with our previous semi-automated classification approach.RESULTS: Overall classification performance across approaches to producing CDefs was similar, with the generated CDef and vector space model with cosine similarity having the highest accuracy (0.825 ? 0.003) and the semi-automated approach and vector space model with cosine similarity having the highest recall (0.809 ? 0.042). Precision was low for all approaches.CONCLUSION: The useful representation of CDefs is a complicated task but potentially offers substantial gains in efficiency to support safety and clinical surveillance.

Resumo Limpo

ckground establish case definit cdef first step mani epidemiolog clinic surveil research activ applic cdef still reli manual step major sourc ineffici surveil researchobject describ need propos approach autom use represent cdef medic conditionsmethod translat exist brighton collabor cdef anaphylaxi most reli identif synonym criteria cdef use nlm metamap tool also generat cdef condit use relat pubm abstract process text mine tool treat synonym strategi cooccurr anaphylaxi medic term within sentenc abstract support construct larg semant network island algorithm reduc network reveal densest region includ node use repres key criteria cdef evalu abil translat generat cdef classifi set hn report anaphylaxi use two similar approach compar previous semiautom classif approachresult overal classif perform across approach produc cdef similar generat cdef vector space model cosin similar highest accuraci semiautom approach vector space model cosin similar highest recal precis low approachesconclus use represent cdef complic task potenti offer substanti gain effici support safeti clinic surveil

Resumos Similares

Artif Intell Med - Terminological resources for text mining over biomedical scientific literature. ( 0,66247236993083 )
Artif Intell Med - A semantic graph-based approach to biomedical summarisation. ( 0,651985095051475 )
AMIA Annu Symp Proc - Using ontology network structure in text mining. ( 0,651465586688183 )
J Biomed Inform - An ontology-based similarity measure for biomedical data-application to radiology reports. ( 0,643076514899707 )
AMIA Annu Symp Proc - Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method. ( 0,6424759161401 )
AMIA Annu Symp Proc - Knowledge-based method for determining the meaning of ambiguous biomedical terms using information content measures of similarity. ( 0,639429765050835 )
AMIA Annu Symp Proc - An evaluation of the UMLS in representing corpus derived clinical concepts. ( 0,636459179109956 )
Methods Inf Med - Bridging data models and terminologies to support adverse drug event reporting using EHR data. ( 0,632078226437473 )
J Biomed Inform - Comparing and combining chunkers of biomedical text. ( 0,630019891630056 )
AMIA Annu Symp Proc - Syndromic surveillance in an ICD-10 world. ( 0,625035456646924 )
J Biomed Inform - Evaluating measures of semantic similarity and relatedness to disambiguate terms in biomedical text. ( 0,623086662448018 )
J Biomed Inform - Ontology-guided feature engineering for clinical text classification. ( 0,621728354063506 )
J Biomed Inform - Desiderata for ontologies to be used in semantic annotation of biomedical documents. ( 0,620748666838922 )
J Biomed Inform - Comparing different knowledge sources for the automatic summarization of biomedical literature. ( 0,615057834692994 )
J Biomed Inform - Mapping Partners Master Drug Dictionary to RxNorm using an NLP-based approach. ( 0,60937570802357 )
IEEE J Biomed Health Inform - Identifying Similar Cases in Document Networks using Cross-reference Structures. ( 0,609236019351603 )
Int J Med Inform - Semantic similarity-based alignment between clinical archetypes and SNOMED CT: an application to observations. ( 0,609065231943307 )
J Am Med Inform Assoc - A system for coreference resolution for the clinical narrative. ( 0,606642639033976 )
AMIA Annu Symp Proc - Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics. ( 0,605289222742279 )
AMIA Annu Symp Proc - Word Sense Disambiguation of clinical abbreviations with hyperdimensional computing. ( 0,604654414782896 )
J Biomed Inform - Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. ( 0,602764916882685 )
AMIA Annu Symp Proc - Using Medical Text Extraction, Reasoning and Mapping System (MTERMS) to process medication information in outpatient clinical notes. ( 0,600207050693414 )
AMIA Annu Symp Proc - The use of semantic distance metrics to support ontology audit. ( 0,599256315561228 )
J Am Med Inform Assoc - Vaccine adverse event text mining system for extracting features from vaccine safety reports. ( 0,596799068092417 )
J Biomed Inform - Evaluating the effects of machine pre-annotation and an interactive annotation interface on manual de-identification of clinical text. ( 0,593428668530503 )
J Biomed Inform - Lessons learnt from the DDIExtraction-2013 Shared Task. ( 0,593171519366079 )
J Biomed Inform - A hybrid knowledge-based and data-driven approach to identifying semantically similar concepts. ( 0,591818440066285 )
J Biomed Inform - Coreference resolution: a review of general methodologies and applications in the clinical domain. ( 0,590159943088096 )
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. ( 0,589360884926033 )
J Biomed Inform - Ontology modularization to improve semantic medical image annotation. ( 0,588799717332059 )
J Biomed Inform - Unsupervised biomedical named entity recognition: experiments with clinical and biological texts. ( 0,585498558483831 )
AMIA Annu Symp Proc - A cloud-based approach to medical NLP. ( 0,584653394436176 )
J Biomed Inform - A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. ( 0,583800309687147 )
BMC Med Inform Decis Mak - Evaluation of natural language processing from emergency department computerized medical records for intra-hospital syndromic surveillance. ( 0,581357248100159 )
J Biomed Inform - A new clustering method for detecting rare senses of abbreviations in clinical notes. ( 0,581084998012082 )
J Biomed Inform - Enhancing clinical concept extraction with distributional semantics. ( 0,579760133532948 )
Artif Intell Med - A system for the extraction and representation of summary of product characteristics content. ( 0,577768986338921 )
J Am Med Inform Assoc - ccML, a new mark-up language to improve ISO/EN 13606-based electronic health record extracts practical edition. ( 0,576715015961981 )
J Am Med Inform Assoc - A comprehensive study of named entity recognition in Chinese clinical text. ( 0,575085278090044 )
Appl Clin Inform - Representation of information about family relatives as structured data in electronic health records. ( 0,574167129534411 )
J Am Med Inform Assoc - Towards comprehensive syntactic and semantic annotations of the clinical narrative. ( 0,573990446300393 )
AMIA Annu Symp Proc - Automatic acquisition of sublanguage semantic schema: towards the word sense disambiguation of clinical narratives. ( 0,571809111153734 )
J Am Med Inform Assoc - Feature engineering combined with machine learning and rule-based methods for structured information extraction from narrative clinical discharge summaries. ( 0,569185912281502 )
J Biomed Inform - UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. ( 0,568058390460581 )
J Biomed Inform - Tree kernel-based protein-protein interaction extraction from biomedical literature. ( 0,567800624581031 )
Artif Intell Med - Recognizing lexical and semantic change patterns in evolving life science ontologies to inform mapping adaptation. ( 0,56717233023212 )
J Biomed Inform - NCBI disease corpus: a resource for disease name recognition and concept normalization. ( 0,56368735215647 )
AMIA Annu Symp Proc - De-identification of Address, Date, and Alphanumeric Identifiers in Narrative Clinical Reports. ( 0,562924483614967 )
J Biomed Inform - Semantator: semantic annotator for converting biomedical text to linked data. ( 0,562576326811123 )
J Am Med Inform Assoc - A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. ( 0,562559027936305 )
J Am Med Inform Assoc - Text mining for the Vaccine Adverse Event Reporting System: medical text classification using informative feature selection. ( 0,560237568101335 )
J Biomed Inform - Using text to build semantic networks for pharmacogenomics. ( 0,557654787820084 )
Inform Health Soc Care - A model based on multi-features to enhance healthcare and medical document retrieval. ( 0,555508388980334 )
Comput Math Methods Med - A semantic medical multimedia retrieval approach using ontology information hiding. ( 0,553957538699125 )
J Am Med Inform Assoc - Learning regular expressions for clinical text classification. ( 0,553385625561637 )
AMIA Annu Symp Proc - A high throughput semantic concept frequency based approach for patient identification: a case study using type 2 diabetes mellitus clinical notes. ( 0,552399873182274 )
J Am Med Inform Assoc - Anaphoric relations in the clinical narrative: corpus creation. ( 0,552092247945978 )
AMIA Annu Symp Proc - Towards a semantic lexicon for clinical natural language processing. ( 0,551987794893897 )
J Biomed Inform - Towards generating a patient's timeline: extracting temporal relationships from clinical notes. ( 0,55130392869521 )
IEEE J Biomed Health Inform - Providing semantic interoperability between clinical care and clinical research domains. ( 0,548442728478449 )
J Am Med Inform Assoc - Pneumonia identification using statistical feature selection. ( 0,547438519859239 )
J Am Med Inform Assoc - Machine learning-based coreference resolution of concepts in clinical documents. ( 0,547297219594018 )
AMIA Annu Symp Proc - EpiDEA: extracting structured epilepsy and seizure information from patient discharge summaries for cohort identification. ( 0,546830471814999 )
J Biomed Inform - Leveraging concept-based approaches to identify potential phyto-therapies. ( 0,545922893836484 )
J Biomed Inform - Degree centrality for semantic abstraction summarization of therapeutic studies. ( 0,545652385143581 )
Artif Intell Med - Creating personalised clinical pathways by semantic interoperability with electronic health records. ( 0,543328150800283 )
Perspect Health Inf Manag - A comparison between a SNOMED CT problem list and the ICD-10-CM/PCS HIPAA code sets. ( 0,541978669551324 )
J Am Med Inform Assoc - Knowledge-based biomedical word sense disambiguation: an evaluation and application to clinical document classification. ( 0,541140840879851 )
Int J Med Inform - Detecting temporal expressions in medical narratives. ( 0,540714735858932 )
AMIA Annu Symp Proc - Voice-dictated versus typed-in clinician notes: linguistic properties and the potential implications on natural language processing. ( 0,540550540009739 )
AMIA Annu Symp Proc - Shortest Path Edit Distance for Enhancing UMLS Integration and Audit. ( 0,540370243444252 )
J Med Syst - SeDeLo: using semantics and description logics to support aided clinical diagnosis. ( 0,53975758520868 )
J Biomed Inform - An enhanced CRFs-based system for information extraction from radiology reports. ( 0,539529274054528 )
J Am Med Inform Assoc - A classification approach to coreference in discharge summaries: 2011 i2b2 challenge. ( 0,53808402015413 )
J Am Med Inform Assoc - Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. ( 0,536254007220951 )
Appl Clin Inform - The contribution of the vaccine adverse event text mining system to the classification of possible Guillain-Barr? syndrome reports. ( 0,535720397552524 )
AMIA Annu Symp Proc - Identifying discourse connectives in biomedical text. ( 0,534807241120465 )
AMIA Annu Symp Proc - Automated identification of medical concepts and assertions in medical text. ( 0,533797728840465 )
J Am Med Inform Assoc - Automated clinical trial eligibility prescreening: increasing the efficiency of patient identification for clinical trials in the emergency department. ( 0,533417951971474 )
Brief. Bioinformatics - A survey on annotation tools for the biomedical literature. ( 0,531137853816274 )
AMIA Annu Symp Proc - Identifying synonymy between SNOMED clinical terms of varying length using distributional analysis of electronic health records. ( 0,530752043675913 )
J Biomed Inform - Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies. ( 0,529482620478434 )
Int J Med Inform - Bootstrapping a de-identification system for narrative patient records: cost-performance tradeoffs. ( 0,52925526906155 )
J Biomed Inform - An ontology-based measure to compute semantic similarity in biomedicine. ( 0,52850994726001 )
BMC Med Inform Decis Mak - Retrospective checking of compliance with practice guidelines for acute stroke care: a novel experiment using openEHR's Guideline Definition Language. ( 0,528027563758261 )
AMIA Annu Symp Proc - Semantic characteristics of NLP-extracted concepts in clinical notes vs. biomedical literature. ( 0,527716867900964 )
J Biomed Inform - Lexical patterns, features and knowledge resources for coreference resolution in clinical notes. ( 0,526007705789302 )
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. ( 0,526002773257049 )
J Biomed Inform - Semantic similarity estimation in the biomedical domain: an ontology-based information-theoretic perspective. ( 0,525522647640344 )
AMIA Annu Symp Proc - Automatically pairing measured findings across narrative abdomen CT reports. ( 0,525322819371526 )
AMIA Annu Symp Proc - TagLine: Information Extraction for Semi-Structured Text in Medical Progress Notes. ( 0,524534294848716 )
J Am Med Inform Assoc - Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. ( 0,523425220763015 )
IEEE Trans Pattern Anal Mach Intell - Spatial and Anatomical Regularization of SVM: A General Framework for Neuroimaging Data. ( 0,520444240910453 )
J Biomed Inform - The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions. ( 0,52031658828027 )
J Am Med Inform Assoc - Hybrid methods for improving information access in clinical documents: concept, assertion, and relation identification. ( 0,520133514844978 )
J Biomed Inform - Common data model for natural language processing based on two existing standard information models: CDA+GrAF. ( 0,518947476451505 )
Artif Intell Med - Conceptual-driven classification for coding advise in health insurance reimbursement. ( 0,518420412892971 )
J. Med. Internet Res. - Developing a disease outbreak event corpus. ( 0,518311118938996 )
J Am Med Inform Assoc - Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts. ( 0,517795160951099 )
J Am Med Inform Assoc - Are Meaningful Use Stage 2 certified EHRs ready for interoperability? Findings from the SMART C-CDA Collaborative. ( 0,516935748825652 )