J Biomed Inform - Acquisition and evaluation of verb subcategorization resources for biomedicine.

Tópicos

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

Resumo

CKGROUND: Biomedical natural language processing (NLP) applications that have access to detailed resources about the linguistic characteristics of biomedical language demonstrate improved performance on tasks such as relation extraction and syntactic or semantic parsing. Such applications are important for transforming the growing unstructured information buried in the biomedical literature into structured, actionable information. In this paper, we address the creation of linguistic resources that capture how individual biomedical verbs behave. We specifically consider verb subcategorization, or the tendency of verbs to "select" co-occurrence with particular phrase types, which influences the interpretation of verbs and identification of verbal arguments in context. There are currently a limited number of biomedical resources containing information about subcategorization frames (SCFs), and these are the result of either labor-intensive manual collation, or automatic methods that use tools adapted to a single biomedical subdomain. Either method may result in resources that lack coverage. Moreover, the quality of existing verb SCF resources for biomedicine is unknown, due to a lack of available gold standards for evaluation.RESULTS: This paper presents three new resources related to verb subcategorization frames in biomedicine, and four experiments making use of the new resources. We present the first biomedical SCF gold standards, capturing two different but widely-used definitions of subcategorization, and a new SCF lexicon, BioCat, covering a large number of biomedical sub-domains. We evaluate the SCF acquisition methodologies for BioCat with respect to the gold standards, and compare the results with the accuracy of the only previously existing automatically-acquired SCF lexicon for biomedicine, the BioLexicon. Our results show that the BioLexicon has greater precision while BioCat has better coverage of SCFs. Finally, we explore the definition of subcategorization using these resources and its implications for biomedical NLP. All resources are made publicly available.CONCLUSION: The SCF resources we have evaluated still show considerably lower accuracy than that reported with general English lexicons, demonstrating the need for domain- and subdomain-specific SCF acquisition tools for biomedicine. Our new gold standards reveal major differences when annotators use the different definitions. Moreover, evaluation of BioCat yields major differences in accuracy depending on the gold standard, demonstrating that the definition of subcategorization adopted will have a direct impact on perceived system accuracy for specific tasks.

Resumo Limpo

ckground biomed natur languag process nlp applic access detail resourc linguist characterist biomed languag demonstr improv perform task relat extract syntact semant pars applic import transform grow unstructur inform buri biomed literatur structur action inform paper address creation linguist resourc captur individu biomed verb behav specif consid verb subcategor tendenc verb select cooccurr particular phrase type influenc interpret verb identif verbal argument context current limit number biomed resourc contain inform subcategor frame scfs result either laborintens manual collat automat method use tool adapt singl biomed subdomain either method may result resourc lack coverag moreov qualiti exist verb scf resourc biomedicin unknown due lack avail gold standard evaluationresult paper present three new resourc relat verb subcategor frame biomedicin four experi make use new resourc present first biomed scf gold standard captur two differ widelyus definit subcategor new scf lexicon biocat cover larg number biomed subdomain evalu scf acquisit methodolog biocat respect gold standard compar result accuraci previous exist automaticallyacquir scf lexicon biomedicin biolexicon result show biolexicon greater precis biocat better coverag scfs final explor definit subcategor use resourc implic biomed nlp resourc made public availableconclus scf resourc evalu still show consider lower accuraci report general english lexicon demonstr need domain subdomainspecif scf acquisit tool biomedicin new gold standard reveal major differ annot use differ definit moreov evalu biocat yield major differ accuraci depend gold standard demonstr definit subcategor adopt will direct impact perceiv system accuraci specif task

Resumos Similares

J Biomed Inform - Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies. ( 0,874294442178633 )
J Biomed Inform - Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules. ( 0,834778405117075 )
J Biomed Inform - Natural Language Processing methods and systems for biomedical ontology learning. ( 0,827030353417444 )
BMC Med Inform Decis Mak - Translating the Foundational Model of Anatomy into French using knowledge-based and lexical methods. ( 0,824995813323096 )
J Biomed Inform - A methodology for extending domain coverage in SemRep. ( 0,824383414842871 )
J Biomed Inform - Terminology representation guidelines for biomedical ontologies in the semantic web notations. ( 0,819454224643657 )
J Am Med Inform Assoc - Approaching semantic interoperability in Health Level Seven. ( 0,818875491241683 )
J Biomed Inform - A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains. ( 0,818750884560267 )
Methods Inf Med - Biomedical ontologies: toward scientific debate. ( 0,811088599266997 )
J Biomed Inform - Enabling international adoption of LOINC through translation. ( 0,81063015930089 )
J Biomed Inform - An ontology-based measure to compute semantic similarity in biomedicine. ( 0,807453325675986 )
Int J Med Inform - Semantic similarity-based alignment between clinical archetypes and SNOMED CT: an application to observations. ( 0,805290231270803 )
AMIA Annu Symp Proc - Deriving an abstraction network to support quality assurance in OCRe. ( 0,802865484825931 )
J Biomed Inform - Translating standards into practice - one Semantic Web API for Gene Expression. ( 0,802796693333967 )
J Am Med Inform Assoc - A semantic-web oriented representation of the clinical element model for secondary use of electronic health records data. ( 0,802475892964828 )
Appl Clin Inform - Ontology content patterns as bridge for the semantic representation of clinical information. ( 0,801204551616993 )
Int J Med Inform - A modified Delphi translation strategy and challenges of International Classification for Nursing Practice (ICNP?). ( 0,797977180758216 )
Artif Intell Med - The Foundational Model of Anatomy in OWL 2 and its use. ( 0,797460934125366 )
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. ( 0,796673281617733 )
J Am Med Inform Assoc - Life sciences domain analysis model. ( 0,794213752580681 )
AMIA Annu Symp Proc - Fostering Multilinguality in the UMLS: A Computational Approach to Terminology Expansion for Multiple Languages. ( 0,793810842835581 )
BMC Med Inform Decis Mak - Querying phenotype-genotype relationships on patient datasets using semantic web technology: the example of Cerebrotendinous xanthomatosis. ( 0,78814754039287 )
Methods Inf Med - An evolutionary approach to realism-based adverse event representations. ( 0,786173998065875 )
AMIA Annu Symp Proc - Metonymies in medical terminologies. A SNOMED CT case study. ( 0,786157860916511 )
J Med Syst - An ontological case base engineering methodology for diabetes management. ( 0,784489127079131 )
J Biomed Inform - BOAT: automatic alignment of biomedical ontologies using term informativeness and candidate selection. ( 0,782608921879109 )
Methods Inf Med - Evaluation of the content coverage of SNOMED CT representing ICNP seven-axis version 1 concepts. ( 0,780171230561106 )
J Biomed Inform - Cross-domain targeted ontology subsets for annotation: the case of SNOMED CORE and RxNorm. ( 0,779128543013808 )
AMIA Annu Symp Proc - Modeling and executing electronic health records driven phenotyping algorithms using the NQF Quality Data Model and JBoss? Drools Engine. ( 0,775716635529313 )
AMIA Annu Symp Proc - Evaluation of RxNorm for Representing Ambulatory Prescriptions. ( 0,770976731102375 )
Methods Inf Med - Construction of an interface terminology on SNOMED CT. Generic approach and its application in intensive care. ( 0,770397544397278 )
J Am Med Inform Assoc - Scalable quality assurance for large SNOMED CT hierarchies using subject-based subtaxonomies. ( 0,769612535493478 )
J Biomed Inform - Reuse of termino-ontological resources and text corpora for building a multilingual domain ontology: an application to Alzheimer's disease. ( 0,767856437865633 )
J Chem Inf Model - Setting the record straight: the origin of the pharmacophore concept. ( 0,767074448812845 )
J Biomed Inform - Semantic mappings and locality of nursing diagnostic concepts in UMLS. ( 0,765558741195159 )
J Biomed Inform - Using LOINC to link 10 terminology standards to one unified standard in a specialized domain. ( 0,765010934745314 )
Inform Health Soc Care - Semantics-driven modelling of user preferences for information retrieval in the biomedical domain. ( 0,764195060259869 )
AMIA Annu Symp Proc - Auditing SNOMED Integration into the UMLS for Duplicate Concepts. ( 0,763911203812767 )
J. Med. Internet Res. - Development of an obesity management ontology based on the nursing process for the mobile-device domain. ( 0,762579391683458 )
J Biomed Inform - Validating the semantics of a medical iconic language using ontological reasoning. ( 0,762185619371994 )
J Biomed Inform - A query integrator and manager for the query web. ( 0,759106213528658 )
J Biomed Inform - Enabling semantic similarity estimation across multiple ontologies: an evaluation in the biomedical domain. ( 0,759058267651589 )
AMIA Annu Symp Proc - Towards the creation of a visual ontology of biomedical imaging entities. ( 0,757505336139036 )
AMIA Annu Symp Proc - Quality assurance in LOINC using Description Logic. ( 0,756788271471456 )
J Biomed Inform - A graph-based recovery and decomposition of Swanson's hypothesis using semantic predications. ( 0,756751601880715 )
J Am Med Inform Assoc - Applying knowledge-anchored hypothesis discovery methods to advance clinical and translational research: the OAMiner project. ( 0,75509023271526 )
IEEE J Biomed Health Inform - Exploiting Semantic Web Technologies to Develop OWL-Based Clinical Practice Guideline Execution Engines. ( 0,754324450860866 )
IEEE Trans Image Process - Structure-preserving sparse decomposition for facial expression analysis. ( 0,752417880230914 )
Methods Inf Med - An eligibility criteria query language for heterogeneous data warehouses. ( 0,75185775211154 )
AMIA Annu Symp Proc - An evaluation of the UMLS in representing corpus derived clinical concepts. ( 0,751768553304288 )
Appl Clin Inform - An empiric analysis of omaha system targets. ( 0,750643121599468 )
J Biomed Inform - Hematopoietic cell types: prototype for a revised cell ontology. ( 0,750047741467176 )
J Integr Bioinform - An ontology for description of drug discovery investigations. ( 0,749341741436926 )
J Biomed Inform - Formalizing MedDRA to support semantic reasoning on adverse drug reaction terms. ( 0,74631617932156 )
AMIA Annu Symp Proc - Standardized mapping of nursing assessments across 59 U.S. military treatment facilities. ( 0,743868162105515 )
J Am Med Inform Assoc - Evaluating standard terminologies for encoding allergy information. ( 0,738825329863549 )
J Biomed Inform - vSPARQL: a view definition language for the semantic web. ( 0,736777893679382 )
J Biomed Inform - Abstraction of complex concepts with a refined partial-area taxonomy of SNOMED. ( 0,736125301554839 )
AMIA Annu Symp Proc - An OWL meta-ontology for representing the Clinical Element Model. ( 0,735458912962198 )
Artif Intell Med - Terminological resources for text mining over biomedical scientific literature. ( 0,732441418125594 )
J Biomed Inform - OntoVIP: an ontology for the annotation of object models used for medical image simulation. ( 0,729200782343534 )
Int J Med Inform - Using ontologies for structuring organizational knowledge in Home Care assistance. ( 0,728855918248243 )
J Biomed Inform - Understanding semantic mapping evolution by observing changes in biomedical ontologies. ( 0,725727056044827 )
BMC Med Inform Decis Mak - Determining correspondences between high-frequency MedDRA concepts and SNOMED: a case study. ( 0,720527149993149 )
J Med Syst - Time-related patient data retrieval for the case studies from the pharmacogenomics research network. ( 0,720190291699698 )
AMIA Annu Symp Proc - Large-scale, Exhaustive Lattice-based Structural Auditing of SNOMED CT. ( 0,718905175371409 )
J Integr Bioinform - A semi-automated approach for anatomical ontology mapping. ( 0,717856317073466 )
J Biomed Inform - Semantic similarity estimation in the biomedical domain: an ontology-based information-theoretic perspective. ( 0,71729359628952 )
Artif Intell Med - A semantic graph-based approach to biomedical summarisation. ( 0,715728631600491 )
AMIA Annu Symp Proc - Looking for Anemia (and Other Disorders) in SNOMED CT: Comparison of Three Approaches and Practical Implications. ( 0,714954525440877 )
Artif Intell Med - A four stage approach for ontology-based health information system design. ( 0,714687793647119 )
Int J Med Inform - Ontology driven health information systems architectures enable pHealth for empowered patients. ( 0,714297638279577 )
Comput Methods Programs Biomed - Searching biosignal databases by content and context: Research Oriented Integration System for ECG Signals (ROISES). ( 0,714177767818887 )
Methods Inf Med - Putting biomedical ontologies to work. ( 0,71370033508281 )
Telemed J E Health - Construction of a clinical decision support system for undergoing surgery based on domain ontology and rules reasoning. ( 0,713059903913083 )
J Med Syst - Automated mapping of clinical terms into SNOMED-CT. An application to codify procedures in pathology. ( 0,712946004891127 )
J Am Med Inform Assoc - Application of statistical machine translation to public health information: a feasibility study. ( 0,71231674866353 )
IEEE Trans Pattern Anal Mach Intell - Domain Anomaly Detection in Machine Perception: A System Architecture and Taxonomy. ( 0,711612406816631 )
AMIA Annu Symp Proc - A family-based framework for supporting quality assurance of biomedical ontologies in BioPortal. ( 0,710367984908549 )
J Biomed Inform - Cross-product extensions of the Gene Ontology. ( 0,70967673926932 )
AMIA Annu Symp Proc - Representation of nursing terminologies in UMLS. ( 0,708801879535776 )
AMIA Annu Symp Proc - Using Medical Text Extraction, Reasoning and Mapping System (MTERMS) to process medication information in outpatient clinical notes. ( 0,707682164967107 )
J Med Syst - SeDeLo: using semantics and description logics to support aided clinical diagnosis. ( 0,707331652167327 )
AMIA Annu Symp Proc - Reasoning based quality assurance of medical ontologies: a case study. ( 0,706451034637391 )
J Biomed Inform - Comparing different knowledge sources for the automatic summarization of biomedical literature. ( 0,706053374461085 )
J Biomed Inform - Development and evaluation of an ontology for guiding appropriate antibiotic prescribing. ( 0,705402318538028 )
AMIA Annu Symp Proc - Modeling patient safety incidents knowledge with the Categorial Structure method. ( 0,704061429414735 )
Brief. Bioinformatics - Semantic Web meets Integrative Biology: a survey. ( 0,703539052843404 )
AMIA Annu Symp Proc - An empirically derived taxonomy of errors in SNOMED CT. ( 0,70305602544499 )
J Biomed Inform - OWL-based reasoning methods for validating archetypes. ( 0,702566056566635 )
Artif Intell Med - Visually defining and querying consistent multi-granular clinical temporal abstractions. ( 0,702362634020563 )
AMIA Annu Symp Proc - Adapting a Clinical Data Repository to ICD-10-CM through the use of a Terminology Repository. ( 0,701690613302756 )
J Biomed Inform - TRAK ontology: defining standard care for the rehabilitation of knee conditions. ( 0,701016338860371 )
Artif Intell Med - Modeling surgical processes: a four-level translational approach. ( 0,700948830677531 )
J Integr Bioinform - An evaluation of the performance of three semantic background knowledge sources in comparative anatomy. ( 0,699888352859974 )
J Am Med Inform Assoc - Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience. ( 0,699394411474272 )
J Am Med Inform Assoc - Using the wisdom of the crowds to find critical errors in biomedical ontologies: a study of SNOMED CT. ( 0,6984249382969 )
AMIA Annu Symp Proc - Integrating heterogeneous knowledge sources to acquire executable drug-related knowledge. ( 0,698301787489444 )
J Biomed Inform - COnto-Diff: generation of complex evolution mappings for life science ontologies. ( 0,697768461599522 )
AMIA Annu Symp Proc - Applying Evolutionary Terminology Auditing to SNOMED CT. ( 0,696924456604795 )