J Biomed Inform - LabeledIn: cataloging labeled indications for human drugs.


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


Drug-disease treatment relationships, i.e., which drug(s) are indicated to treat which disease(s), are among the most frequently sought information in PubMed?. Such information is useful for feeding the Google Knowledge Graph, designing computational methods to predict novel drug indications, and validating clinical information in EMRs. Given the importance and utility of this information, there have been several efforts to create repositories of drugs and their indications. However, existing resources are incomplete. Furthermore, they neither label indications in a structured way nor differentiate them by drug-specific properties such as dosage form, and thus do not support computer processing or semantic interoperability. More recently, several studies have proposed automatic methods to extract structured indications from drug descriptions; however, their performance is limited by natural language challenges in disease named entity recognition and indication selection. In response, we report LabeledIn: a human-reviewed, machine-readable and source-linked catalog of labeled indications for human drugs. More specifically, we describe our semi-automatic approach to derive LabeledIn from drug descriptions through human annotations with aids from automatic methods. As the data source, we use the drug labels (or package inserts) submitted to the FDA by drug manufacturers and made available in DailyMed. Our machine-assisted human annotation workflow comprises: (i) a grouping method to remove redundancy and identify representative drug labels to be used for human annotation, (ii) an automatic method to recognize and normalize mentions of diseases in drug labels as candidate indications, and (iii) a two-round annotation workflow for human experts to judge the pre-computed candidates and deliver the final gold standard. In this study, we focused on 250 highly accessed drugs in PubMed Health, a newly developed public web resource for consumers and clinicians on prevention and treatment of diseases. These 250 drugs corresponded to more than 8000 drug labels (500 unique) in DailyMed in which 2950 candidate indications were pre-tagged by an automatic tool. After being reviewed independently by two experts, 1618 indications were selected, and additional 97 (missed by computer) were manually added, with an inter-annotator agreement of 88.35% as measured by the Kappa coefficient. Our final annotation results in LabeledIn consist of 7805 drug-disease treatment relationships where drugs are represented as a triplet of ingredient, dose form, and strength. A systematic comparison of LabeledIn with an existing computer-derived resource revealed significant discrepancies, confirming the need to involve humans in the creation of such a resource. In addition, LabeledIn is unique in that it contains detailed textual context of the selected indications in drug labels, making it suitable for the development of advanced computational methods for the automatic extraction of indications from free text. Finally, motivated by the studies on drug nomenclature and medication errors in EMRs, we adopted a fine-grained drug representation scheme, which enables the automatic identification of drugs with indications specific to certain dose forms or strengths. Future work includes expanding our coverage to more drugs and integration with other resources. The LabeledIn dataset and the annotation guidelines are available at http://ftp.ncbi.nlm.nih.gov/pub/lu/LabeledIn/.

Resumo Limpo

drugdiseas treatment relationship ie drug indic treat diseas among frequent sought inform pubm inform use feed googl knowledg graph design comput method predict novel drug indic valid clinic inform emr given import util inform sever effort creat repositori drug indic howev exist resourc incomplet furthermor neither label indic structur way differenti drugspecif properti dosag form thus support comput process semant interoper recent sever studi propos automat method extract structur indic drug descript howev perform limit natur languag challeng diseas name entiti recognit indic select respons report labeledin humanreview machineread sourcelink catalog label indic human drug specif describ semiautomat approach deriv labeledin drug descript human annot aid automat method data sourc use drug label packag insert submit fda drug manufactur made avail dailym machineassist human annot workflow compris group method remov redund identifi repres drug label use human annot ii automat method recogn normal mention diseas drug label candid indic iii tworound annot workflow human expert judg precomput candid deliv final gold standard studi focus high access drug pubm health newli develop public web resourc consum clinician prevent treatment diseas drug correspond drug label uniqu dailym candid indic pretag automat tool review independ two expert indic select addit miss comput manual ad interannot agreement measur kappa coeffici final annot result labeledin consist drugdiseas treatment relationship drug repres triplet ingredi dose form strength systemat comparison labeledin exist computerderiv resourc reveal signific discrep confirm need involv human creation resourc addit labeledin uniqu contain detail textual context select indic drug label make suitabl develop advanc comput method automat extract indic free text final motiv studi drug nomenclatur medic error emr adopt finegrain drug represent scheme enabl automat identif drug indic specif certain dose form strength futur work includ expand coverag drug integr resourc labeledin dataset annot guidelin avail httpftpncbinlmnihgovpublulabeledin

Resumos Similares

J Biomed Inform - Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. ( 0,784201942002659 )
J Biomed Inform - Automatic signal extraction, prioritizing and filtering approaches in detecting post-marketing cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS). ( 0,77186787832758 )
BMC Med Inform Decis Mak - Mining adverse drug reactions from online healthcare forums using hidden Markov model. ( 0,767002348064744 )
BMC Med Inform Decis Mak - A pipeline to extract drug-adverse event pairs from multiple data sources. ( 0,735948165968116 )
J Biomed Inform - A comparison of machine learning techniques for detection of drug target articles. ( 0,728372223691281 )
AMIA Annu Symp Proc - A drug-adverse event extraction algorithm to support pharmacovigilance knowledge mining from PubMed citations. ( 0,720996747736133 )
J Biomed Inform - A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions. ( 0,719808614426411 )
BMC Med Inform Decis Mak - Automatic identification and normalization of dosage forms in drug monographs. ( 0,710199450324792 )
J Am Med Inform Assoc - Drug side effect extraction from clinical narratives of psychiatry and psychology patients. ( 0,704001014978953 )
J Biomed Inform - Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles. ( 0,696535972391413 )
J. Med. Internet Res. - Postmarket drug surveillance without trial costs: discovery of adverse drug reactions through large-scale analysis of web search queries. ( 0,694811541947664 )
J Am Med Inform Assoc - Extracting drug indication information from structured product labels using natural language processing. ( 0,692374332853981 )
J Biomed Inform - Identifying plausible adverse drug reactions using knowledge extracted from the literature. ( 0,684083587596685 )
AMIA Annu Symp Proc - Towards drug repositioning: a unified computational framework for integrating multiple aspects of drug similarity and disease similarity. ( 0,680457206093015 )
J Biomed Inform - Exploring the associations between drug side-effects and therapeutic indications. ( 0,675944033468285 )
AMIA Annu Symp Proc - Semantic processing to identify adverse drug event information from black box warnings. ( 0,671903599366906 )
AMIA Annu Symp Proc - Predicting adverse drug events from personal health messages. ( 0,668800100217549 )
J Am Med Inform Assoc - Mining clinical text for signals of adverse drug-drug interactions. ( 0,665575742051376 )
Wiley Interdiscip Rev Syst Biol Med - Systems pharmacology, pharmacogenetics, and clinical trial design in network medicine. ( 0,661664809659466 )
Comput. Biol. Med. - Cladograms with Path to Event (ClaPTE): a novel algorithm to detect associations between genotypes or phenotypes using phylogenies. ( 0,656830730755885 )
Comput. Biol. Med. - Preclinical evaluation and molecular docking of 4-phenyl-1-Napthyl phenyl acetamide (4P1NPA) from Streptomyces sp. DPTB16 as a potent antifungal compound. ( 0,643126391955839 )
J Am Med Inform Assoc - Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. ( 0,642686574598484 )
Methods Inf Med - Exploiting online discussions to discover unrecognized drug side effects. ( 0,642684748304692 )
J Am Med Inform Assoc - A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. ( 0,642635615769778 )
J Am Med Inform Assoc - Drug-drug interaction through molecular structure similarity analysis. ( 0,642186250276353 )
Wiley Interdiscip Rev Syst Biol Med - Drug repurposing and adverse event prediction using high-throughput literature analysis. ( 0,641348428129194 )
AMIA Annu Symp Proc - Automatic extraction of drug indications from FDA drug labels. ( 0,640947990740152 )
Brief. Bioinformatics - Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases. ( 0,639749206389114 )
J. Med. Internet Res. - Packaging and labeling of pharmaceutical products obtained from the internet. ( 0,639116979764046 )
AMIA Annu Symp Proc - ADESSA: A Real-Time Decision Support Service for Delivery of Semantically Coded Adverse Drug Event Data. ( 0,636151512964403 )
J Am Med Inform Assoc - Toward creation of a cancer drug toxicity knowledge base: automatically extracting cancer drug-side effect relationships from the literature. ( 0,629718888969906 )
J Chem Inf Model - Prediction of polypharmacological profiles of drugs by the integration of chemical, side effect, and therapeutic space. ( 0,628633542208424 )
AMIA Annu Symp Proc - Harnessing a health information exchange to identify surgical device adverse events for urogynecologic mesh. ( 0,625026528563911 )
J. Med. Internet Res. - Natural supplements for H1N1 influenza: retrospective observational infodemiology study of information and search activity on the Internet. ( 0,620736767039956 )
Comput. Biol. Med. - Comparative structural modeling and docking studies of uricase: possible implication in enzyme supplementation therapy for hyperuricemic disorders. ( 0,617539492102836 )
J Am Med Inform Assoc - Validating a strategy for psychosocial phenotyping using a large corpus of clinical text. ( 0,617114650941533 )
J Integr Bioinform - Identifying interactions between chemical entities in biomedical text. ( 0,611337071896433 )
Appl Clin Inform - Lessons learned from developing a drug evidence base to support pharmacovigilance. ( 0,61034913595708 )
AMIA Annu Symp Proc - Pattern mining for extraction of mentions of Adverse Drug Reactions from user comments. ( 0,608919815358373 )
J Am Med Inform Assoc - Vaccine adverse event text mining system for extracting features from vaccine safety reports. ( 0,608637668176401 )
Comput Math Methods Med - Antibody Drug Conjugate bioinformatics: drug delivery through the letterbox. ( 0,60848825421519 )
J Integr Bioinform - An integrative clinical database and diagnostics platform for biomarker identification and analysis in ion mobility spectra of human exhaled air. ( 0,607753572470071 )
AMIA Annu Symp Proc - Modeling drug exposure data in electronic medical records: an application to warfarin. ( 0,607657503803885 )
J Am Med Inform Assoc - Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis. ( 0,605741239892077 )
Methods Inf Med - Design and evaluation of an ontology-based drug application database. ( 0,605303920218273 )
J Clin Monit Comput - Anesthetic agent vapor analyzers and propellants of pressurized meter-dose inhalers. ( 0,603768138277629 )
J Biomed Inform - Using text to build semantic networks for pharmacogenomics. ( 0,601759770116286 )
AMIA Annu Symp Proc - Large-scale, Exhaustive Lattice-based Structural Auditing of SNOMED CT. ( 0,599249132671622 )
J Chem Inf Model - ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning. ( 0,598717396327025 )
AMIA Annu Symp Proc - Exploring the relationship between drug side-effects and therapeutic indications. ( 0,598520533187699 )
J. Comput. Biol. - A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient. ( 0,59684549447558 )
J Chem Inf Model - Adverse drug events: database construction and in silico prediction. ( 0,593809529622424 )
Int J Health Geogr - Selection for resistance to oseltamivir in seasonal and pandemic H1N1 influenza and widespread co-circulation of the lineages. ( 0,593412756867255 )
J Chem Inf Model - Efficient a priori identification of drug resistant mutations using Dead-End Elimination and MM-PBSA. ( 0,593002502130273 )
Brief. Bioinformatics - The relationship between rational drug design and drug side effects. ( 0,592937709405207 )
BMC Med Inform Decis Mak - Rule-based multi-scale simulation for drug effect pathway analysis. ( 0,590778281741101 )
J Chem Inf Model - Network-based analysis and characterization of adverse drug-drug interactions. ( 0,590550534442834 )
J Med Syst - A high-speed drug interaction search system for ease of use in the clinical environment. ( 0,589400351641427 )
J Biomed Inform - Identifying potential adverse effects using the web: a new approach to medical hypothesis generation. ( 0,589089286837933 )
Comput. Biol. Med. - Time-series analysis in the medical domain: a study of Tacrolimus administration and influence on kidney graft function. ( 0,586828808561983 )
BMC Med Inform Decis Mak - Managing protected health information in distributed research network environments: automated review to facilitate collaboration. ( 0,585333441649427 )
AMIA Annu Symp Proc - Structured vs. unstructured: factors affecting adverse drug reaction documentation in an EMR repository. ( 0,58465271766124 )
J. Med. Internet Res. - Building a transnational biosurveillance network using semantic web technologies: requirements, design, and preliminary evaluation. ( 0,58149281999303 )
AMIA Annu Symp Proc - Pharmacovigilance on twitter? Mining tweets for adverse drug reactions. ( 0,581050172779255 )
J Clin Monit Comput - Perioperative metabolic alkalemia is more frequent than metabolic acidemia in major elective abdominal surgery. ( 0,580685007114271 )
J Chem Inf Model - Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and Ayurvedic medicines. ( 0,580546728067921 )
BMC Med Inform Decis Mak - Designing concept maps for a precise and objective description of pharmaceutical innovations. ( 0,57936759478692 )
J Biomed Inform - Uncovering influence links in molecular knowledge networks to streamline personalized medicine. ( 0,578781804167955 )
AMIA Annu Symp Proc - Application of a temporal reasoning framework tool in analysis of medical device adverse events. ( 0,576230358314318 )
J Biomed Inform - Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. ( 0,57459611868772 )
Comput. Biol. Med. - Systems pharmacology-based approach for dissecting the addition and subtraction theory of traditional Chinese medicine: An example using Xiao-Chaihu-Decoction and Da-Chaihu-Decoction. ( 0,573869546769951 )
BMC Med Inform Decis Mak - Identifying work related injuries: comparison of methods for interrogating text fields. ( 0,572115415701688 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology-embedded target validation: improving efficacy in drug discovery. ( 0,570703298087329 )
J Chem Inf Model - Curation and analysis of multitargeting agents for polypharmacological modeling. ( 0,570381291095946 )
J Am Med Inform Assoc - The pattern of name tokens in narrative clinical text and a comparison of five systems for redacting them. ( 0,568502864818251 )
J Chem Inf Model - Pathway analysis for drug repositioning based on public database mining. ( 0,568081831127632 )
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. ( 0,56788268211618 )
J Chem Inf Model - A mechanistic hypothesis for the cytochrome P450-catalyzed cis-trans isomerization of 4-hydroxytamoxifen: an unusual redox reaction. ( 0,565051702174881 )
J Am Med Inform Assoc - Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties. ( 0,564920872353861 )
AMIA Annu Symp Proc - Mining consumer health vocabulary from community-generated text. ( 0,562643157271438 )
AMIA Annu Symp Proc - An evaluation of a natural language processing tool for identifying and encoding allergy information in emergency department clinical notes. ( 0,560076829344957 )
J Biomed Inform - NCBI disease corpus: a resource for disease name recognition and concept normalization. ( 0,558990765390227 )
Comput Biol Chem - Pharmacoepidemiological characterization of drug-induced adverse reaction clusters towards understanding of their mechanisms. ( 0,558399784249467 )
J Am Med Inform Assoc - Text mining for the Vaccine Adverse Event Reporting System: medical text classification using informative feature selection. ( 0,558298653972741 )
Int J Med Inform - Computerized detection of adverse drug reactions in the medical intensive care unit. ( 0,558273869269853 )
Methods Inf Med - Bridging data models and terminologies to support adverse drug event reporting using EHR data. ( 0,557077708031579 )
J Biomed Inform - Automatic construction of a large-scale and accurate drug-side-effect association knowledge base from biomedical literature. ( 0,555299833491436 )
J Chem Inf Model - A collection of robust organic synthesis reactions for in silico molecule design. ( 0,551997722374023 )
Brief. Bioinformatics - Drug repositioning for orphan diseases. ( 0,550635438816873 )
Int J Neural Syst - Efficacy of a new charge-balanced biphasic electrical stimulus in the isolated sciatic nerve and the hippocampal slice. ( 0,549476824941354 )
AMIA Annu Symp Proc - Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics. ( 0,548240687356308 )
J Chem Inf Model - Characterizing binding of small molecules. II. Evaluating the potency of small molecules to combat resistance based on docking structures. ( 0,547527786514056 )
Comput Biol Chem - Identification and characterization of potential drug targets by subtractive genome analyses of methicillin resistant Staphylococcus aureus. ( 0,547523549274083 )
J Biomed Inform - PREDOSE: a semantic web platform for drug abuse epidemiology using social media. ( 0,547434234020693 )
J Integr Bioinform - An integrated dataset for in silico drug discovery. ( 0,540220259300966 )
Comput Methods Programs Biomed - stab: an R package for drug stability data analysis. ( 0,540133334779246 )
Comput. Biol. Med. - A P300-based brain computer interface system for words typing. ( 0,536574574858581 )
J Integr Bioinform - In silico strain optimization by adding reactions to metabolic models. ( 0,536440692650075 )
Artif Intell Med - Discovering human immunodeficiency virus mutational pathways using temporal Bayesian networks. ( 0,535469663709367 )
J Chem Inf Model - Drug-disease association and drug-repositioning predictions in complex diseases using causal inference-probabilistic matrix factorization. ( 0,534648626945986 )