J Biomed Inform - Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets.

Tópicos

{ extract(1171) text(1153) clinic(932) }
{ data(2317) use(1299) case(1017) }
{ method(1969) cluster(1462) data(1082) }
{ method(984) reconstruct(947) comput(926) }
{ data(3963) clinic(1234) research(1004) }
{ health(1844) social(1437) communiti(874) }
{ howev(809) still(633) remain(590) }
{ compound(1573) activ(1297) structur(1058) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ research(1218) medic(880) student(794) }
{ use(1733) differ(960) four(931) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ studi(1119) effect(1106) posit(819) }
{ activ(1138) subject(705) human(624) }
{ take(945) account(800) differ(722) }
{ studi(2440) review(1878) systemat(933) }
{ chang(1828) time(1643) increas(1301) }
{ search(2224) databas(1162) retriev(909) }
{ import(1318) role(1303) understand(862) }
{ health(3367) inform(1360) care(1135) }
{ gene(2352) biolog(1181) express(1162) }
{ intervent(3218) particip(2042) group(1664) }
{ drug(1928) target(777) effect(648) }
{ estim(2440) model(1874) function(577) }
{ inform(2794) health(2639) internet(1427) }
{ system(1976) rule(880) can(841) }
{ bind(1733) structur(1185) ligand(1036) }
{ network(2748) neural(1063) input(814) }
{ research(1085) discuss(1038) issu(1018) }
{ model(2341) predict(2261) use(1141) }
{ perform(1367) use(1326) method(1137) }
{ record(1888) medic(1808) patient(1693) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ group(2977) signific(1463) compar(1072) }
{ data(3008) multipl(1320) sourc(1022) }
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{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ sequenc(1873) structur(1644) protein(1328) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
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{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ 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) }
{ algorithm(1844) comput(1787) effici(935) }
{ 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) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ perform(999) metric(946) measur(919) }
{ system(1050) medic(1026) inform(1018) }
{ visual(1396) interact(850) tool(830) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ age(1611) year(1155) adult(843) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ 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) }
{ structur(1116) can(940) graph(676) }
{ high(1669) rate(1365) level(1280) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ survey(1388) particip(1329) question(1065) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

Publicly available molecular datasets can be used for independent verification or investigative repurposing, but depends on the presence, consistency and quality of descriptive annotations. Annotation and indexing of molecular datasets using well-defined controlled vocabularies or ontologies enables accurate and systematic data discovery, yet the majority of molecular datasets available through public data repositories lack such annotations. A number of automated annotation methods have been developed; however few systematic evaluations of the quality of annotations supplied by application of these methods have been performed using annotations from standing public data repositories. Here, we compared manually-assigned Medical Subject Heading (MeSH) annotations associated with experiments by data submitters in the PRoteomics IDEntification (PRIDE) proteomics data repository to automated MeSH annotations derived through the National Center for Biomedical Ontology Annotator and National Library of Medicine MetaMap programs. These programs were applied to free-text annotations for experiments in PRIDE. As many submitted datasets were referenced in publications, we used the manually curated MeSH annotations of those linked publications in MEDLINE as "gold standard". Annotator and MetaMap exhibited recall performance 3-fold greater than that of the manual annotations. We connected PRIDE experiments in a network topology according to shared MeSH annotations and found 373 distinct clusters, many of which were found to be biologically coherent by network analysis. The results of this study suggest that both Annotator and MetaMap are capable of annotating public molecular datasets with a quality comparable, and often exceeding, that of the actual data submitters, highlighting a continuous need to improve and apply automated methods to molecular datasets in public data repositories to maximize their value and utility.

Resumo Limpo

public avail molecular dataset can use independ verif investig repurpos depend presenc consist qualiti descript annot annot index molecular dataset use welldefin control vocabulari ontolog enabl accur systemat data discoveri yet major molecular dataset avail public data repositori lack annot number autom annot method develop howev systemat evalu qualiti annot suppli applic method perform use annot stand public data repositori compar manuallyassign medic subject head mesh annot associ experi data submitt proteom identif pride proteom data repositori autom mesh annot deriv nation center biomed ontolog annot nation librari medicin metamap program program appli freetext annot experi pride mani submit dataset referenc public use manual curat mesh annot link public medlin gold standard annot metamap exhibit recal perform fold greater manual annot connect pride experi network topolog accord share mesh annot found distinct cluster mani found biolog coher network analysi result studi suggest annot metamap capabl annot public molecular dataset qualiti compar often exceed actual data submitt highlight continu need improv appli autom method molecular dataset public data repositori maxim valu util

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