J Am Med Inform Assoc - Toward creation of a cancer drug toxicity knowledge base: automatically extracting cancer drug-side effect relationships from the literature.

Tópicos

{ drug(1928) target(777) effect(648) }
{ extract(1171) text(1153) clinic(932) }
{ method(1219) similar(1157) match(930) }
{ cancer(2502) breast(956) screen(824) }
{ algorithm(1844) comput(1787) effici(935) }
{ imag(2830) propos(1344) filter(1198) }
{ research(1218) medic(880) student(794) }
{ use(976) code(926) identifi(902) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ search(2224) databas(1162) retriev(909) }
{ gene(2352) biolog(1181) express(1162) }
{ concept(1167) ontolog(924) domain(897) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ record(1888) medic(1808) patient(1693) }
{ monitor(1329) mobil(1314) devic(1160) }
{ result(1111) use(1088) new(759) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ model(2341) predict(2261) use(1141) }
{ visual(1396) interact(850) tool(830) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ data(3008) multipl(1320) sourc(1022) }
{ time(1939) patient(1703) rate(768) }
{ can(981) present(881) function(850) }
{ health(1844) social(1437) communiti(874) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ method(2212) result(1239) propos(1039) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ 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) }
{ sequenc(1873) structur(1644) protein(1328) }
{ featur(3375) classif(2383) classifi(1994) }
{ network(2748) neural(1063) input(814) }
{ motion(1329) object(1292) video(1091) }
{ assess(1506) score(1403) qualiti(1306) }
{ treatment(1704) effect(941) patient(846) }
{ 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) }
{ clinic(1479) use(1117) guidelin(835) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ general(901) number(790) one(736) }
{ method(984) reconstruct(947) comput(926) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ research(1085) discuss(1038) issu(1018) }
{ import(1318) role(1303) understand(862) }
{ 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) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ patient(2837) hospit(1953) medic(668) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ group(2977) signific(1463) compar(1072) }
{ sampl(1606) size(1419) use(1276) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ analysi(2126) use(1163) compon(1037) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ 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) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

JECTIVE: A comprehensive and machine-understandable cancer drug-side effect (drug-SE) relationship knowledge base is important for in silico cancer drug target discovery, drug repurposing, and toxicity predication, and for personalized risk-benefit decisions by cancer patients. While US Food and Drug Administration (FDA) drug labels capture well-known cancer drug SE information, much cancer drug SE knowledge remains buried the published biomedical literature. We present a relationship extraction approach to extract cancer drug-SE pairs from the literature.DATA AND METHODS: We used 21,354,075 MEDLINE records as the text corpus. We extracted drug-SE co-occurrence pairs using a cancer drug lexicon and a clean SE lexicon that we created. We then developed two filtering approaches to remove drug-disease treatment pairs and subsequently a ranking scheme to further prioritize filtered pairs. Finally, we analyzed relationships among SEs, gene targets, and indications.RESULTS: We extracted 56,602 cancer drug-SE pairs. The filtering algorithms improved the precision of extracted pairs from 0.252 at baseline to 0.426, representing a 69% improvement in precision with no decrease in recall. The ranking algorithm further prioritized filtered pairs and achieved a precision of 0.778 for top-ranked pairs. We showed that cancer drugs that share SEs tend to have overlapping gene targets and overlapping indications.CONCLUSIONS: The relationship extraction approach is effective in extracting many cancer drug-SE pairs from the literature. This unique knowledge base, when combined with existing cancer drug SE knowledge, can facilitate drug target discovery, drug repurposing, and toxicity prediction.

Resumo Limpo

jectiv comprehens machineunderstand cancer drugsid effect drugs relationship knowledg base import silico cancer drug target discoveri drug repurpos toxic predic person riskbenefit decis cancer patient us food drug administr fda drug label captur wellknown cancer drug se inform much cancer drug se knowledg remain buri publish biomed literatur present relationship extract approach extract cancer drugs pair literaturedata method use medlin record text corpus extract drugs cooccurr pair use cancer drug lexicon clean se lexicon creat develop two filter approach remov drugdiseas treatment pair subsequ rank scheme priorit filter pair final analyz relationship among ses gene target indicationsresult extract cancer drugs pair filter algorithm improv precis extract pair baselin repres improv precis decreas recal rank algorithm priorit filter pair achiev precis toprank pair show cancer drug share ses tend overlap gene target overlap indicationsconclus relationship extract approach effect extract mani cancer drugs pair literatur uniqu knowledg base combin exist cancer drug se knowledg can facilit drug target discoveri drug repurpos toxic predict

Resumos Similares

BMC Med Inform Decis Mak - Mining adverse drug reactions from online healthcare forums using hidden Markov model. ( 0,801009944573585 )
J Biomed Inform - A SNPshot of PubMed to associate genetic variants with drugs, diseases, and adverse reactions. ( 0,796473455501792 )
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). ( 0,772821718768404 )
J Biomed Inform - Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles. ( 0,767969105090864 )
Comput Math Methods Med - Antibody Drug Conjugate bioinformatics: drug delivery through the letterbox. ( 0,758820426477072 )
J Am Med Inform Assoc - Drug side effect extraction from clinical narratives of psychiatry and psychology patients. ( 0,756022064603187 )
BMC Med Inform Decis Mak - A pipeline to extract drug-adverse event pairs from multiple data sources. ( 0,749922666183768 )
Comput Biol Chem - Pharmacoepidemiological characterization of drug-induced adverse reaction clusters towards understanding of their mechanisms. ( 0,742641130812078 )
J Chem Inf Model - Prediction of polypharmacological profiles of drugs by the integration of chemical, side effect, and therapeutic space. ( 0,741548319051881 )
J Biomed Inform - Disambiguation of PharmGKB drug-disease relations with NDF-RT and SPL. ( 0,723706684362188 )
Wiley Interdiscip Rev Syst Biol Med - Drug repurposing and adverse event prediction using high-throughput literature analysis. ( 0,714432596495523 )
AMIA Annu Symp Proc - Towards drug repositioning: a unified computational framework for integrating multiple aspects of drug similarity and disease similarity. ( 0,709015787913121 )
J. Med. Internet Res. - Postmarket drug surveillance without trial costs: discovery of adverse drug reactions through large-scale analysis of web search queries. ( 0,708739049889085 )
AMIA Annu Symp Proc - Pattern mining for extraction of mentions of Adverse Drug Reactions from user comments. ( 0,694638849564956 )
J Biomed Inform - Identifying plausible adverse drug reactions using knowledge extracted from the literature. ( 0,692605810097751 )
J Biomed Inform - Exploring the associations between drug side-effects and therapeutic indications. ( 0,690839702079361 )
J Chem Inf Model - Virtual libraries of tetrapyrrole macrocycles. Combinatorics, isomers, product distributions, and data mining. ( 0,689984086342568 )
J Chem Inf Model - Efficient a priori identification of drug resistant mutations using Dead-End Elimination and MM-PBSA. ( 0,683777504781111 )
J Am Med Inform Assoc - Drug-drug interaction through molecular structure similarity analysis. ( 0,682998442775252 )
BMC Med Inform Decis Mak - Designing concept maps for a precise and objective description of pharmaceutical innovations. ( 0,679193316139469 )
AMIA Annu Symp Proc - Semantic processing to identify adverse drug event information from black box warnings. ( 0,67809675123607 )
J Chem Inf Model - Network-based analysis and characterization of adverse drug-drug interactions. ( 0,675348645415878 )
J Biomed Inform - A comparison of machine learning techniques for detection of drug target articles. ( 0,674089884879908 )
J. Med. Internet Res. - Packaging and labeling of pharmaceutical products obtained from the internet. ( 0,673008458083319 )
J. Comput. Biol. - A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient. ( 0,671658255933356 )
AMIA Annu Symp Proc - ADESSA: A Real-Time Decision Support Service for Delivery of Semantically Coded Adverse Drug Event Data. ( 0,670140011068033 )
Brief. Bioinformatics - The relationship between rational drug design and drug side effects. ( 0,668699640085529 )
J Am Med Inform Assoc - A novel signal detection algorithm for identifying hidden drug-drug interactions in adverse event reports. ( 0,668412134492386 )
J Chem Inf Model - Pathway analysis for drug repositioning based on public database mining. ( 0,661759775725008 )
IEEE J Biomed Health Inform - Using Boolean Logic Modeling of Gene Regulatory Networks to Exploit the Links between Cancer and Metabolism for Therapeutic Purposes. ( 0,657913241440873 )
Methods Inf Med - Exploiting online discussions to discover unrecognized drug side effects. ( 0,653242770926547 )
Wiley Interdiscip Rev Syst Biol Med - Systems pharmacology, pharmacogenetics, and clinical trial design in network medicine. ( 0,653179691772186 )
J Biomed Inform - Uncovering influence links in molecular knowledge networks to streamline personalized medicine. ( 0,650921741015427 )
Comput Biol Chem - Identification and characterization of potential drug targets by subtractive genome analyses of methicillin resistant Staphylococcus aureus. ( 0,649363012303749 )
AMIA Annu Symp Proc - Exploring the relationship between drug side-effects and therapeutic indications. ( 0,649321786097847 )
Methods Inf Med - Design and evaluation of an ontology-based drug application database. ( 0,646839020162538 )
J Am Med Inform Assoc - Extracting drug indication information from structured product labels using natural language processing. ( 0,643258615814076 )
J Chem Inf Model - ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning. ( 0,643258414198441 )
J Biomed Inform - Kinase inhibition-related adverse events predicted from in vitro kinome and clinical trial data. ( 0,636175772356686 )
AMIA Annu Symp Proc - Predicting adverse drug events from personal health messages. ( 0,631123984285655 )
Comput Biol Chem - Detecting breakdown points in metabolic networks. ( 0,631119273942343 )
J Chem Inf Model - Characterizing binding of small molecules. II. Evaluating the potency of small molecules to combat resistance based on docking structures. ( 0,630097184605889 )
J Biomed Inform - LabeledIn: cataloging labeled indications for human drugs. ( 0,629718888969906 )
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. ( 0,627374929643237 )
Brief. Bioinformatics - Drug repositioning for orphan diseases. ( 0,624492101608827 )
J Biomed Inform - Identifying potential adverse effects using the web: a new approach to medical hypothesis generation. ( 0,622650701600154 )
J Chem Inf Model - Adverse drug events: database construction and in silico prediction. ( 0,620422610205082 )
Wiley Interdiscip Rev Syst Biol Med - Systems biology-embedded target validation: improving efficacy in drug discovery. ( 0,61753410670031 )
J Biomed Inform - Network-based target ranking for polypharmacological therapies. ( 0,613987290813825 )
J Chem Inf Model - Chemogenomics approaches to rationalizing the mode-of-action of traditional Chinese and Ayurvedic medicines. ( 0,612955263525917 )
BMC Med Inform Decis Mak - Rule-based multi-scale simulation for drug effect pathway analysis. ( 0,612055910967876 )
Wiley Interdiscip Rev Syst Biol Med - Role of systems pharmacology in understanding drug adverse events. ( 0,611403141285472 )
J Med Syst - A high-speed drug interaction search system for ease of use in the clinical environment. ( 0,607804318509089 )
J Chem Inf Model - Modular architecture of metabolic pathways revealed by conserved sequences of reactions. ( 0,606135949015549 )
J Integr Bioinform - Re-annotation of the genome sequence of Helicobacter pylori 26695. ( 0,604694417289524 )
J Chem Inf Model - Virtual affinity fingerprints for target fishing: a new application of Drug Profile Matching. ( 0,604517266317902 )
Artif Intell Med - Discovering human immunodeficiency virus mutational pathways using temporal Bayesian networks. ( 0,603624115063865 )
Comput Methods Programs Biomed - The application of support vector regression for prediction of the antiallodynic effect of drug combinations in the mouse model of streptozocin-induced diabetic neuropathy. ( 0,599696282631878 )
Comput Methods Programs Biomed - stab: an R package for drug stability data analysis. ( 0,593517250432066 )
J Integr Bioinform - An integrated dataset for in silico drug discovery. ( 0,591193543298066 )
Comput Math Methods Med - Microdosimetry for targeted alpha therapy of cancer. ( 0,589817361992954 )
BMC Med Inform Decis Mak - Automatic identification and normalization of dosage forms in drug monographs. ( 0,587827589117772 )
J Am Med Inform Assoc - Machine learning-based prediction of drug-drug interactions by integrating drug phenotypic, therapeutic, chemical, and genomic properties. ( 0,5855900763898 )
AMIA Annu Symp Proc - Modeling drug exposure data in electronic medical records: an application to warfarin. ( 0,583007363550963 )
Brief. Bioinformatics - Data mining the human gut microbiota for therapeutic targets. ( 0,581399064311634 )
AMIA Annu Symp Proc - Automated plan-recognition of chemotherapy protocols. ( 0,577391817182748 )
AMIA Annu Symp Proc - Automatic extraction of drug indications from FDA drug labels. ( 0,57718532031991 )
Wiley Interdiscip Rev Syst Biol Med - Developing melanoma therapeutics: overview and update. ( 0,576454746170374 )
J. Comput. Biol. - Analysis of metabolic evolution in bacteria using whole-genome metabolic models. ( 0,575851121479019 )
AMIA Annu Symp Proc - Application of a temporal reasoning framework tool in analysis of medical device adverse events. ( 0,568342296707654 )
J Chem Inf Model - A mechanistic hypothesis for the cytochrome P450-catalyzed cis-trans isomerization of 4-hydroxytamoxifen: an unusual redox reaction. ( 0,567361295828487 )
J Integr Bioinform - In silico strain optimization by adding reactions to metabolic models. ( 0,567018853928769 )
J Am Med Inform Assoc - The pattern of name tokens in narrative clinical text and a comparison of five systems for redacting them. ( 0,563198022713334 )
Brief. Bioinformatics - Exploiting drug-disease relationships for computational drug repositioning. ( 0,562715215434686 )
AMIA Annu Symp Proc - Structured vs. unstructured: factors affecting adverse drug reaction documentation in an EMR repository. ( 0,561578459345108 )
J Chem Inf Model - Exploring the desumoylation process of SENP1: a study combined MD simulations with QM/MM calculations on SENP1-SUMO1-RanGAP1. ( 0,559819767047846 )
Comput. Biol. Med. - An algorithm for rapid computational construction of metabolic networks: a cholesterol biosynthesis example. ( 0,559289493156617 )
J Chem Inf Model - 2D SMARTCyp reactivity-based site of metabolism prediction for major drug-metabolizing cytochrome P450 enzymes. ( 0,557274366664768 )
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. ( 0,556365474661929 )
Wiley Interdiscip Rev Syst Biol Med - Lipid-sensing nuclear receptors in the pathophysiology and treatment of the metabolic syndrome. ( 0,555796858637703 )
Int J Neural Syst - Efficacy of a new charge-balanced biphasic electrical stimulus in the isolated sciatic nerve and the hippocampal slice. ( 0,553965077487403 )
J Am Med Inform Assoc - Mining clinical text for signals of adverse drug-drug interactions. ( 0,552898992976162 )
J Biomed Inform - Using semantic predications to uncover drug-drug interactions in clinical data. ( 0,548762184583128 )
J Chem Inf Model - CLCA: maximum common molecular substructure queries within the MetRxn database. ( 0,547248194368801 )
Brief. Bioinformatics - Network-based drug discovery by integrating systems biology and computational technologies. ( 0,547015400580049 )
Comput. Biol. Med. - Comparative structural modeling and docking studies of uricase: possible implication in enzyme supplementation therapy for hyperuricemic disorders. ( 0,544485184906444 )
AMIA Annu Symp Proc - Development of an Alert System to Detect Drug Interactions with Herbal Supplements using Medical Record Data. ( 0,544127508572542 )
J Am Med Inform Assoc - Comparison and validation of genomic predictors for anticancer drug sensitivity. ( 0,542396703283971 )
AMIA Annu Symp Proc - Pharmacovigilance on twitter? Mining tweets for adverse drug reactions. ( 0,541854324221232 )
J Chem Inf Model - Drug side-effect prediction based on the integration of chemical and biological spaces. ( 0,541287332780465 )
AMIA Annu Symp Proc - A drug-adverse event extraction algorithm to support pharmacovigilance knowledge mining from PubMed citations. ( 0,539335229572804 )
J Am Med Inform Assoc - Leveraging biodiversity knowledge for potential phyto-therapeutic applications. ( 0,539261010565342 )
J Chem Inf Model - Curation and analysis of multitargeting agents for polypharmacological modeling. ( 0,537922755628353 )
Brief. Bioinformatics - Modern bioinformatics meets traditional Chinese medicine. ( 0,537393788542437 )
AMIA Annu Symp Proc - Exploring schizophrenia drug-gene interactions through molecular network and pathway modeling. ( 0,532548707253979 )
J Chem Inf Model - Drug effect prediction by polypharmacology-based interaction profiling. ( 0,530117100699032 )
J Am Med Inform Assoc - Dictionary construction and identification of possible adverse drug events in Danish clinical narrative text. ( 0,527657709194467 )
J Integr Bioinform - Identifying interactions between chemical entities in biomedical text. ( 0,525364210297154 )
J Chem Inf Model - Automated extraction of information on chemical-P-glycoprotein interactions from the literature. ( 0,522428182325157 )
Int J Med Robot - A respiratory correlated image guided surgery method: quantitative accuracy results in swine and human cadaver environments. ( 0,521245984795291 )