J Biomed Inform - A mutation-centric approach to identifying pharmacogenomic relations in text.

Tópicos

{ search(2224) databas(1162) retriev(909) }
{ extract(1171) text(1153) clinic(932) }
{ gene(2352) biolog(1181) express(1162) }
{ model(3404) distribut(989) bayesian(671) }
{ use(976) code(926) identifi(902) }
{ compound(1573) activ(1297) structur(1058) }
{ general(901) number(790) one(736) }
{ age(1611) year(1155) adult(843) }
{ assess(1506) score(1403) qualiti(1306) }
{ perform(999) metric(946) measur(919) }
{ medic(1828) order(1363) alert(1069) }
{ data(1737) use(1416) pattern(1282) }
{ studi(2440) review(1878) systemat(933) }
{ concept(1167) ontolog(924) domain(897) }
{ howev(809) still(633) remain(590) }
{ research(1085) discuss(1038) issu(1018) }
{ model(2656) set(1616) predict(1553) }
{ group(2977) signific(1463) compar(1072) }
{ method(2212) result(1239) propos(1039) }
{ imag(1947) propos(1133) code(1026) }
{ sequenc(1873) structur(1644) protein(1328) }
{ take(945) account(800) differ(722) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ studi(1410) differ(1259) use(1210) }
{ visual(1396) interact(850) tool(830) }
{ result(1111) use(1088) new(759) }
{ 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) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
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{ network(2748) neural(1063) input(814) }
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{ patient(2315) diseas(1263) diabet(1191) }
{ motion(1329) object(1292) video(1091) }
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{ framework(1458) process(801) describ(734) }
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{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ care(1570) inform(1187) nurs(1089) }
{ method(984) reconstruct(947) comput(926) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ data(3963) clinic(1234) research(1004) }
{ risk(3053) factor(974) diseas(938) }
{ system(1050) medic(1026) inform(1018) }
{ import(1318) role(1303) understand(862) }
{ model(2341) predict(2261) use(1141) }
{ 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) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ data(2317) use(1299) case(1017) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ data(3008) multipl(1320) sourc(1022) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ 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) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ implement(1333) system(1263) develop(1122) }
{ 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) }
{ method(1969) cluster(1462) data(1082) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

JECTIVES: To explore the notion of mutation-centric pharmacogenomic relation extraction and to evaluate our approach against reference pharmacogenomic relations.METHODS: From a corpus of MEDLINE abstracts relevant to genetic variation, we identify co-occurrences between drug mentions extracted using MetaMap and RxNorm, and genetic variants extracted by EMU. The recall of our approach is evaluated against reference relations curated manually in PharmGKB. We also reviewed a random sample of 180 relations in order to evaluate its precision.RESULTS: One crucial aspect of our strategy is the use of biological knowledge for identifying specific genetic variants in text, not simply gene mentions. On the 104 reference abstracts from PharmGKB, the recall of our mutation-centric approach is 33-46%. Applied to 282,000 abstracts from MEDLINE, our approach identifies pharmacogenomic relations in 4534 abstracts, with a precision of 65%.CONCLUSIONS: Compared to a relation-centric approach, our mutation-centric approach shows similar recall, but slightly lower precision. We show that both approaches have limited overlap in their results, but are complementary and can be used in combination. Rather than a solution for the automatic curation of pharmacogenomic knowledge, we see these high-throughput approaches as tools to assist biocurators in the identification of pharmacogenomic relations of interest from the published literature. This investigation also identified three challenging aspects of the extraction of pharmacogenomic relations, namely processing full-text articles, sequence validation of DNA variants and resolution of genetic variants to reference databases, such as dbSNP.

Resumo Limpo

jectiv explor notion mutationcentr pharmacogenom relat extract evalu approach refer pharmacogenom relationsmethod corpus medlin abstract relev genet variat identifi cooccurr drug mention extract use metamap rxnorm genet variant extract emu recal approach evalu refer relat curat manual pharmgkb also review random sampl relat order evalu precisionresult one crucial aspect strategi use biolog knowledg identifi specif genet variant text simpli gene mention refer abstract pharmgkb recal mutationcentr approach appli abstract medlin approach identifi pharmacogenom relat abstract precis conclus compar relationcentr approach mutationcentr approach show similar recal slight lower precis show approach limit overlap result complementari can use combin rather solut automat curat pharmacogenom knowledg see highthroughput approach tool assist biocur identif pharmacogenom relat interest publish literatur investig also identifi three challeng aspect extract pharmacogenom relat name process fulltext articl sequenc valid dna variant resolut genet variant refer databas dbsnp

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