J Biomed Inform - Automated curation of gene name normalization results using the Konstanz information miner.

Tópicos

{ extract(1171) text(1153) clinic(932) }
{ state(1844) use(1261) util(961) }
{ gene(2352) biolog(1181) express(1162) }
{ high(1669) rate(1365) level(1280) }
{ detect(2391) sensit(1101) algorithm(908) }
{ activ(1138) subject(705) human(624) }
{ data(1737) use(1416) pattern(1282) }
{ process(1125) use(805) approach(778) }
{ featur(3375) classif(2383) classifi(1994) }
{ data(1714) softwar(1251) tool(1186) }
{ first(2504) two(1366) second(1323) }
{ can(981) present(881) function(850) }
{ use(976) code(926) identifi(902) }
{ use(1733) differ(960) four(931) }
{ inform(2794) health(2639) internet(1427) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ ehr(2073) health(1662) electron(1139) }
{ research(1218) medic(880) student(794) }
{ data(2317) use(1299) case(1017) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ implement(1333) system(1263) develop(1122) }
{ measur(2081) correl(1212) valu(896) }
{ studi(2440) review(1878) systemat(933) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ algorithm(1844) comput(1787) effici(935) }
{ studi(1410) differ(1259) use(1210) }
{ import(1318) role(1303) understand(862) }
{ visual(1396) interact(850) tool(830) }
{ result(1111) use(1088) new(759) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ system(1976) rule(880) can(841) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1219) similar(1157) match(930) }
{ 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) }
{ 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) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ method(1557) propos(1049) approach(1037) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ search(2224) databas(1162) retriev(909) }
{ 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) }
{ 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) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ 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) }
{ sampl(1606) size(1419) use(1276) }
{ 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) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ structur(1116) can(940) graph(676) }
{ cancer(2502) breast(956) screen(824) }
{ drug(1928) target(777) effect(648) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }

Resumo

CKGROUND: Gene name recognition and normalization is, together with detection of other named entities, a crucial step in biomedical text mining and the underlying basis for development of more advanced techniques like extraction of complex events. While the current state of the art solutions achieve highly promising results on average, performance can drop significantly for specific genes with highly ambiguous synonyms. Depending on the topic of interest, this can cause the need for extensive manual curation of such text mining results. Our goal was to enhance this curation step based on tools widely used in pharmaceutical industry utilizing the text processing and classification capabilities of the Konstanz Information Miner (KNIME) along with publicly available sources.RESULTS: F-score achieved on gene specific test corpora for highly ambiguous genes could be improved from values close to zero, due to very low precision, to values >0.9 for several cases. Interestingly the presented approach even resulted in an increased F-score for genes showing already good results in initial gene name normalization. For most test cases, we could significantly improve precision, while retaining a high recall.CONCLUSIONS: We could show that KNIME can be used to assist in manual curation of text mining results containing high numbers of false positive hits. Our results also indicate that it could be beneficial for future development in the field of gene name normalization to create gene specific training corpora based on incorrectly identified genes common to current state of the art algorithms.

Resumo Limpo

ckground gene name recognit normal togeth detect name entiti crucial step biomed text mine under basi develop advanc techniqu like extract complex event current state art solut achiev high promis result averag perform can drop signific specif gene high ambigu synonym depend topic interest can caus need extens manual curat text mine result goal enhanc curat step base tool wide use pharmaceut industri util text process classif capabl konstanz inform miner knime along public avail sourcesresult fscore achiev gene specif test corpora high ambigu gene improv valu close zero due low precis valu sever case interest present approach even result increas fscore gene show alreadi good result initi gene name normal test case signific improv precis retain high recallconclus show knime can use assist manual curat text mine result contain high number fals posit hit result also indic benefici futur develop field gene name normal creat gene specif train corpora base incorrect identifi gene common current state art algorithm

Resumos Similares

AMIA Annu Symp Proc - It's about this and that: a description of anaphoric expressions in clinical text. ( 0,636824609257276 )
J Biomed Inform - Lessons learnt from the DDIExtraction-2013 Shared Task. ( 0,62403072475207 )
J Am Med Inform Assoc - Evaluating temporal relations in clinical text: 2012 i2b2 Challenge. ( 0,618760844333891 )
Artif Intell Med - Biomedical events extraction using the hidden vector state model. ( 0,615587802027463 )
J Am Med Inform Assoc - Anaphoric relations in the clinical narrative: corpus creation. ( 0,615116306186958 )
J Biomed Inform - MedTime: a temporal information extraction system for clinical narratives. ( 0,613769907914989 )
Comput. Biol. Med. - A P300-based brain computer interface system for words typing. ( 0,596668946156799 )
J Am Med Inform Assoc - Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. ( 0,584594143593584 )
J Am Med Inform Assoc - Eventual situations for timeline extraction from clinical reports. ( 0,582408441383512 )
J Am Med Inform Assoc - MedXN: an open source medication extraction and normalization tool for clinical text. ( 0,58061479551898 )
Neural Comput - A neurocomputational approach to prepositional phrase attachment ambiguity resolution. ( 0,580219450185057 )
J Biomed Inform - Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. ( 0,577896270374365 )
J Biomed Inform - Complex epilepsy phenotype extraction from narrative clinical discharge summaries. ( 0,577586516727441 )
AMIA Annu Symp Proc - A machine learning approach for identifying anatomical locations of actionable findings in radiology reports. ( 0,576930175580781 )
Comput Math Methods Med - Ranking biomedical annotations with annotator's semantic relevancy. ( 0,574048438955601 )
AMIA Annu Symp Proc - Developing a section labeler for clinical documents. ( 0,573705166327245 )
J Biomed Inform - Detecting hedge cues and their scope in biomedical text with conditional random fields. ( 0,570238678065373 )
J Am Med Inform Assoc - Assisted annotation of medical free text using RapTAT. ( 0,567537900611909 )
J Am Med Inform Assoc - Text mining for the Vaccine Adverse Event Reporting System: medical text classification using informative feature selection. ( 0,566812279229258 )
Med Decis Making - Automatically annotating topics in transcripts of patient-provider interactions via machine learning. ( 0,566552351709572 )
Int J Med Inform - Detection of infectious symptoms from VA emergency department and primary care clinical documentation. ( 0,564577780444783 )
J Biomed Inform - Relation mining experiments in the pharmacogenomics domain. ( 0,562920032087101 )
Int J Med Inform - A methodology to enhance spatial understanding of disease outbreak events reported in news articles. ( 0,561780209236149 )
J Am Med Inform Assoc - MITRE system for clinical assertion status classification. ( 0,560987764482157 )
Methods Inf Med - Adaptive semantic tag mining from heterogeneous clinical research texts. ( 0,559400883007713 )
J Biomed Inform - A concept-driven biomedical knowledge extraction and visualization framework for conceptualization of text corpora. ( 0,557522155302328 )
J Biomed Inform - Anaphoric reference in clinical reports: characteristics of an annotated corpus. ( 0,556648680223165 )
AMIA Annu Symp Proc - Mapping annotations with textual evidence using an scLDA model. ( 0,555453336587388 )
Comput Math Methods Med - Objectifying facial expressivity assessment of Parkinson's patients: preliminary study. ( 0,555219742712938 )
AMIA Annu Symp Proc - Using UMLS lexical resources to disambiguate abbreviations in clinical text. ( 0,555181717870055 )
J Am Med Inform Assoc - An end-to-end system to identify temporal relation in discharge summaries: 2012 i2b2 challenge. ( 0,554392013120442 )
Int J Med Inform - Detecting temporal expressions in medical narratives. ( 0,554312041490024 )
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. ( 0,552942851075167 )
J Am Med Inform Assoc - Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. ( 0,552188315804792 )
Curr Protoc Bioinformatics - Genome Annotation and Curation Using MAKER and MAKER-P. ( 0,552083361034097 )
J Biomed Inform - A new clustering method for detecting rare senses of abbreviations in clinical notes. ( 0,55148514531196 )
J Am Med Inform Assoc - Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text. ( 0,550796269152879 )
Neural Comput - Detection of hidden structures in nonstationary spike trains. ( 0,546270262151804 )
J Biomed Inform - ProNormz--an integrated approach for human proteins and protein kinases normalization. ( 0,54538766523362 )
J Biomed Inform - The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions. ( 0,54510376556963 )
J Biomed Inform - Development and evaluation of RapTAT: a machine learning system for concept mapping of phrases from medical narratives. ( 0,544665405889244 )
J Biomed Inform - Towards generating a patient's timeline: extracting temporal relationships from clinical notes. ( 0,54439456915665 )
J Biomed Inform - Biomedical text mining and its applications in cancer research. ( 0,544121492170281 )
J Am Med Inform Assoc - Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. ( 0,543808740793966 )
BMC Med Inform Decis Mak - Detecting causality from online psychiatric texts using inter-sentential language patterns. ( 0,542343146915731 )
J Am Med Inform Assoc - A la Recherche du Temps Perdu: extracting temporal relations from medical text in the 2012 i2b2 NLP challenge. ( 0,54190802744113 )
J Biomed Inform - NCBI disease corpus: a resource for disease name recognition and concept normalization. ( 0,541834092670675 )
J. Med. Internet Res. - Web 2.0-based crowdsourcing for high-quality gold standard development in clinical natural language processing. ( 0,539277201096161 )
AMIA Annu Symp Proc - Qualitative analysis of workflow modifications used to generate the reference standard for the 2010 i2b2/VA challenge. ( 0,538613558278984 )
J Am Med Inform Assoc - Syntactic parsing of clinical text: guideline and corpus development with handling ill-formed sentences. ( 0,537900375315833 )
AMIA Annu Symp Proc - TagLine: Information Extraction for Semi-Structured Text in Medical Progress Notes. ( 0,537362491096015 )
J Am Med Inform Assoc - A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources. ( 0,536447883095818 )
J Am Med Inform Assoc - A hybrid system for temporal information extraction from clinical text. ( 0,53445466227206 )
J Integr Bioinform - PathJam: a new service for integrating biological pathway information. ( 0,534252756927978 )
Wiley Interdiscip Rev Syst Biol Med - Branched-chain amino acid supplementation: impact on signaling and relevance to critical illness. ( 0,533242784919846 )
J Biomed Inform - Lexical patterns, features and knowledge resources for coreference resolution in clinical notes. ( 0,532957880513261 )
AMIA Annu Symp Proc - Semantic processing to identify adverse drug event information from black box warnings. ( 0,532043578598507 )
BMC Med Inform Decis Mak - A framework for enhancing spatial and temporal granularity in report-based health surveillance systems. ( 0,530758333733529 )
J Am Med Inform Assoc - Automatic discourse connective detection in biomedical text. ( 0,530231338797963 )
AMIA Annu Symp Proc - Towards a semantic lexicon for clinical natural language processing. ( 0,529237212369344 )
J Am Med Inform Assoc - A flexible framework for recognizing events, temporal expressions, and temporal relations in clinical text. ( 0,526649326881488 )
Appl Clin Inform - Representation of information about family relatives as structured data in electronic health records. ( 0,524322318007487 )
J Biomed Inform - Approaches to verb subcategorization for biomedicine. ( 0,523201792551387 )
J Integr Bioinform - Automatic extraction of microorganisms and their habitats from free text using text mining workflows. ( 0,522338106272432 )
Sci Data - Building the graph of medicine from millions of clinical narratives. ( 0,522023594805902 )
J Am Med Inform Assoc - Temporal reasoning over clinical text: the state of the art. ( 0,521249287014312 )
AMIA Annu Symp Proc - Sophia: A Expedient UMLS Concept Extraction Annotator. ( 0,520636091491949 )
J Biomed Inform - UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. ( 0,520086248971763 )
J Biomed Inform - Enhancing clinical concept extraction with distributional semantics. ( 0,519648881153937 )
Comput Methods Programs Biomed - BioAnnote: a software platform for annotating biomedical documents with application in medical learning environments. ( 0,518826913478886 )
J Am Med Inform Assoc - Automatic abstraction of imaging observations with their characteristics from mammography reports. ( 0,518680548265925 )
AMIA Annu Symp Proc - Extracting semantic lexicons from discharge summaries using machine learning and the C-Value method. ( 0,518321969845535 )
AMIA Annu Symp Proc - Natural language processing for lines and devices in portable chest x-rays. ( 0,517491959354787 )
J Am Med Inform Assoc - A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries. ( 0,51705875176417 )
J Med Syst - Redactable signatures for signed CDA Documents. ( 0,516998708903968 )
AMIA Annu Symp Proc - Throw the bath water out, keep the baby: keeping medically-relevant terms for text mining. ( 0,51634609109793 )
J Biomed Inform - Extraction of events and temporal expressions from clinical narratives. ( 0,515459747743894 )
Int J Med Inform - Text mining of cancer-related information: review of current status and future directions. ( 0,515215166443034 )
AMIA Annu Symp Proc - Automatically pairing measured findings across narrative abdomen CT reports. ( 0,515072420712641 )
AMIA Annu Symp Proc - Parenthetically speaking: classifying the contents of parentheses for text mining. ( 0,514299778542563 )
Comput Biol Chem - Revealing weak differential gene expressions and their reproducible functions associated with breast cancer metastasis. ( 0,513318571682708 )
J Am Med Inform Assoc - Vaccine adverse event text mining system for extracting features from vaccine safety reports. ( 0,512757195535417 )
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. ( 0,512473121899584 )
AMIA Annu Symp Proc - Voice-dictated versus typed-in clinician notes: linguistic properties and the potential implications on natural language processing. ( 0,512263389748632 )
Int J Med Inform - Bootstrapping a de-identification system for narrative patient records: cost-performance tradeoffs. ( 0,511097863068926 )
AMIA Annu Symp Proc - Pharmacovigilance on twitter? Mining tweets for adverse drug reactions. ( 0,510171802438892 )
J Biomed Inform - Ontology-guided feature engineering for clinical text classification. ( 0,510024060806151 )
Med Biol Eng Comput - Comparison of displacement and acceleration transducers for the characterization of mechanics of muscle and subcutaneous tissues by system identification of a mechanomyogram. ( 0,509259860103603 )
AMIA Annu Symp Proc - Generalizability and comparison of automatic clinical text de-identification methods and resources. ( 0,508508716691585 )
AMIA Annu Symp Proc - Syntactic dependency parsers for biomedical-NLP. ( 0,508202377889416 )
AMIA Annu Symp Proc - Semantic annotation of clinical events for generating a problem list. ( 0,507977733462121 )
J Biomed Inform - Desiderata for ontologies to be used in semantic annotation of biomedical documents. ( 0,507336803535755 )
J. Med. Internet Res. - Development of a national agreement on human papillomavirus vaccination in Japan: an infodemiology study. ( 0,507093848464679 )
J. Med. Internet Res. - Evaluating a web-based clinical decision support system for language disorders screening in a nursery school. ( 0,506125816230807 )
J Biomed Inform - A natural language processing pipeline for pairing measurements uniquely across free-text CT reports. ( 0,505809804369324 )
Med Decis Making - Comparison of general population, patient, and carer utility values for dementia health states. ( 0,505319611015939 )
J Biomed Inform - Text de-identification for privacy protection: a study of its impact on clinical text information content. ( 0,505281230746099 )
IEEE Trans Pattern Anal Mach Intell - Discriminative Video Pattern Search for Efficient Action Detection. ( 0,503557309719594 )
J Biomed Inform - Using an ensemble system to improve concept extraction from clinical records. ( 0,502779376377459 )
J Am Med Inform Assoc - Knowledge-based biomedical word sense disambiguation: an evaluation and application to clinical document classification. ( 0,502628074839048 )