PubTator: a web-based text mining tool for assisting biocuration
Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with the rapid growth of the literature. There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we descr...
Saved in:
| Published in | Nucleic acids research Vol. 41; no. W1; pp. W518 - W522 |
|---|---|
| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
01.07.2013
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 0305-1048 1362-4962 1362-4954 1362-4962 |
| DOI | 10.1093/nar/gkt441 |
Cover
| Abstract | Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with the rapid growth of the literature. There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we describe PubTator, a web-based system for assisting biocuration. PubTator is different from the few existing tools by featuring a PubMed-like interface, which many biocurators find familiar, and being equipped with multiple challenge-winning text mining algorithms to ensure the quality of its automatic results. Through a formal evaluation with two external user groups, PubTator was shown to be capable of improving both the efficiency and accuracy of manual curation. PubTator is publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/. |
|---|---|
| AbstractList | Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with the rapid growth of the literature. There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we describe PubTator, a web-based system for assisting biocuration. PubTator is different from the few existing tools by featuring a PubMed-like interface, which many biocurators find familiar, and being equipped with multiple challenge-winning text mining algorithms to ensure the quality of its automatic results. Through a formal evaluation with two external user groups, PubTator was shown to be capable of improving both the efficiency and accuracy of manual curation. PubTator is publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/. Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with the rapid growth of the literature. There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we describe PubTator, a web-based system for assisting biocuration. PubTator is different from the few existing tools by featuring a PubMed-like interface, which many biocurators find familiar, and being equipped with multiple challenge-winning text mining algorithms to ensure the quality of its automatic results. Through a formal evaluation with two external user groups, PubTator was shown to be capable of improving both the efficiency and accuracy of manual curation. PubTator is publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/.Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with the rapid growth of the literature. There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we describe PubTator, a web-based system for assisting biocuration. PubTator is different from the few existing tools by featuring a PubMed-like interface, which many biocurators find familiar, and being equipped with multiple challenge-winning text mining algorithms to ensure the quality of its automatic results. Through a formal evaluation with two external user groups, PubTator was shown to be capable of improving both the efficiency and accuracy of manual curation. PubTator is publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/. |
| Author | Wei, Chih-Hsuan Lu, Zhiyong Kao, Hung-Yu |
| AuthorAffiliation | 1 National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA and 2 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, 701, Taiwan, R.O.C |
| AuthorAffiliation_xml | – name: 1 National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA and 2 Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, 701, Taiwan, R.O.C |
| Author_xml | – sequence: 1 givenname: Chih-Hsuan surname: Wei fullname: Wei, Chih-Hsuan – sequence: 2 givenname: Hung-Yu surname: Kao fullname: Kao, Hung-Yu – sequence: 3 givenname: Zhiyong surname: Lu fullname: Lu, Zhiyong |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23703206$$D View this record in MEDLINE/PubMed |
| BookMark | eNp9kMlOwzAQhi1UREvhwgOgHBEo1FuzcEAgxCYhwQHOlu1MiiG1i-2wvD0pZRfi4pHsb-b3fKuoZ50FhDYI3iW4ZCMr_WhyHzknS2hAWEZTXma0hwaY4XFKMC_6aDWEO4wJJ2O-gvqU5ZhRnA3QwVWrrmV0fi-RyROoVMkAVRLhOSZTY42dJNG5JqmdT2QIJsT5lTJOt15G4-waWq5lE2D9vQ7Rzcnx9dFZenF5en50eJFqlvOYVpKpnGPOiM5LPla0lBwYBqgyUIUiNeWsqGCsWVEroIQWvCJUV4yUNeSQsSHaWcxt7Uy-PMmmETNvptK_CILF3IPoPIiFh47eX9CzVk2h0mCjl18dThrx88WaWzFxj4JlZedlHrf1PsC7hxZCFFMTNDSNtODaIAjLCc1Jd3To5vesz5APyR2AF4D2LgQPtdAmvsnrok3z9_-3f7X8s-wrEpKgfQ |
| CitedBy_id | crossref_primary_10_1016_j_jmst_2020_01_067 crossref_primary_10_1093_bioinformatics_bty845 crossref_primary_10_1093_bib_bbac465 crossref_primary_10_1093_database_baw064 crossref_primary_10_1093_database_baw066 crossref_primary_10_1093_database_bay122 crossref_primary_10_1093_database_baw068 crossref_primary_10_1038_s41597_022_01350_1 crossref_primary_10_1093_database_bay129 crossref_primary_10_1093_database_bay128 crossref_primary_10_1038_s41525_019_0100_0 crossref_primary_10_5808_GI_2019_17_2_e18 crossref_primary_10_15388_23_INFOR517 crossref_primary_10_1016_j_cpb_2014_12_002 crossref_primary_10_1016_j_jtbi_2019_110112 crossref_primary_10_1093_humupd_dmz034 crossref_primary_10_1093_nar_gkt926 crossref_primary_10_1038_s41596_020_00455_4 crossref_primary_10_2196_19612 crossref_primary_10_1093_database_bay011 crossref_primary_10_1371_journal_pcbi_1007239 crossref_primary_10_1016_j_gpb_2018_11_006 crossref_primary_10_1186_s12918_018_0612_8 crossref_primary_10_1093_database_baw076 crossref_primary_10_1016_j_celrep_2020_107884 crossref_primary_10_1007_s00799_023_00356_3 crossref_primary_10_1093_database_bay137 crossref_primary_10_1007_s12539_021_00425_8 crossref_primary_10_1093_bioinformatics_btaa095 crossref_primary_10_1093_database_baae104 crossref_primary_10_1186_s40708_022_00174_4 crossref_primary_10_1186_s12859_024_05730_9 crossref_primary_10_2196_medinform_6918 crossref_primary_10_1186_s12859_020_03542_1 crossref_primary_10_1371_journal_pcbi_1006390 crossref_primary_10_1021_acs_jproteome_8b00393 crossref_primary_10_1093_bioinformatics_bty869 crossref_primary_10_3389_frma_2024_1368534 crossref_primary_10_1088_1742_6596_1069_1_012037 crossref_primary_10_1093_database_baw161 crossref_primary_10_1093_bioinformatics_btab067 crossref_primary_10_1093_database_baw042 crossref_primary_10_1093_database_baw043 crossref_primary_10_15252_embr_202052141 crossref_primary_10_1016_j_lssr_2024_01_004 crossref_primary_10_1093_jamiaopen_ooy001 crossref_primary_10_1016_j_jbi_2019_103143 crossref_primary_10_1186_s12859_021_04358_3 crossref_primary_10_1186_1758_2946_7_S1_S3 crossref_primary_10_1016_j_cmpb_2014_11_005 crossref_primary_10_1038_s41592_021_01076_9 crossref_primary_10_1186_s13326_018_0181_1 crossref_primary_10_3390_biom12040520 crossref_primary_10_1093_nar_gky1151 crossref_primary_10_1371_journal_pone_0292356 crossref_primary_10_1007_s12539_024_00605_2 crossref_primary_10_1093_bib_bbaa054 crossref_primary_10_1186_s12859_019_2873_7 crossref_primary_10_3390_proteomes9020029 crossref_primary_10_1186_s12859_018_2163_9 crossref_primary_10_3389_fgene_2022_820361 crossref_primary_10_1371_journal_pone_0152725 crossref_primary_10_1093_nar_gky355 crossref_primary_10_1371_journal_pcbi_1007022 crossref_primary_10_1371_journal_pdig_0000086 crossref_primary_10_1186_s12864_020_07185_7 crossref_primary_10_1155_2015_674296 crossref_primary_10_1016_j_cpb_2017_11_001 crossref_primary_10_1093_nar_gkab779 crossref_primary_10_1016_j_jbi_2024_104716 crossref_primary_10_1093_nar_gkz1007 crossref_primary_10_1002_cpe_5005 crossref_primary_10_1093_bioinformatics_btx439 crossref_primary_10_1177_1049731515624966 crossref_primary_10_1093_bib_bbac543 crossref_primary_10_1093_bioinformatics_btac057 crossref_primary_10_3390_diagnostics14020174 crossref_primary_10_1016_j_jbi_2018_07_007 crossref_primary_10_1093_database_bay045 crossref_primary_10_1016_j_techfore_2020_120513 crossref_primary_10_1093_bioinformatics_btaa674 crossref_primary_10_1186_s12879_022_07219_3 crossref_primary_10_3389_fgene_2021_771435 crossref_primary_10_1038_s41593_023_01259_x crossref_primary_10_1016_j_ygeno_2016_10_003 crossref_primary_10_1248_bpb_b24_00319 crossref_primary_10_1515_mr_2023_0011 crossref_primary_10_5808_gi_19_3_e1 crossref_primary_10_1007_s13721_020_00248_5 crossref_primary_10_12688_f1000research_18214_1 crossref_primary_10_12688_f1000research_18214_2 crossref_primary_10_1093_bib_bbv021 crossref_primary_10_1093_bib_bbv024 crossref_primary_10_1038_s41598_021_93809_1 crossref_primary_10_1109_TCBB_2022_3157630 crossref_primary_10_1093_bib_bbv020 crossref_primary_10_1186_s13321_018_0317_4 crossref_primary_10_1007_s00203_023_03776_6 crossref_primary_10_1016_j_engappai_2020_104130 crossref_primary_10_1093_nar_gkaa333 crossref_primary_10_1093_database_bax081 crossref_primary_10_1093_database_bax082 crossref_primary_10_3390_genes12070998 crossref_primary_10_1093_bioinformatics_btx541 crossref_primary_10_1093_bioinformatics_bty871 crossref_primary_10_3389_fphar_2019_00839 crossref_primary_10_1093_database_baab031 crossref_primary_10_1097_MD_0000000000020338 crossref_primary_10_1093_nar_gkz389 crossref_primary_10_1186_s12911_018_0645_3 crossref_primary_10_1108_IDD_06_2022_0054 crossref_primary_10_1155_2015_318064 crossref_primary_10_1093_nar_gkx1104 crossref_primary_10_2196_28247 crossref_primary_10_1126_scitranslmed_aau9113 crossref_primary_10_1038_s41598_022_12093_9 crossref_primary_10_1007_s10549_023_06996_y crossref_primary_10_1016_j_jbi_2015_03_010 crossref_primary_10_1038_s42256_024_00899_3 crossref_primary_10_1093_bib_bbaa142 crossref_primary_10_1186_s12859_018_2316_x crossref_primary_10_1093_database_bay146 crossref_primary_10_1021_acs_jproteome_7b00772 crossref_primary_10_3389_fgene_2018_00527 crossref_primary_10_1186_s13059_019_1708_1 crossref_primary_10_2196_jmir_6676 crossref_primary_10_1007_s00799_023_00368_z crossref_primary_10_1186_s13321_016_0165_z crossref_primary_10_1109_TCBB_2018_2838661 crossref_primary_10_1093_database_baw090 crossref_primary_10_18699_VJ19_501 crossref_primary_10_1007_s11192_021_03933_y crossref_primary_10_1093_database_bau129 crossref_primary_10_1093_database_bay031 crossref_primary_10_7717_peerj_13061 crossref_primary_10_1093_database_baw096 crossref_primary_10_3389_fpsyt_2025_1452557 crossref_primary_10_1093_database_baw098 crossref_primary_10_1093_database_baz124 crossref_primary_10_1016_j_jbi_2019_103353 crossref_primary_10_3390_ijms17020191 crossref_primary_10_1007_s12559_021_09903_z crossref_primary_10_1109_JBHI_2015_2422651 crossref_primary_10_1186_s40168_019_0742_2 crossref_primary_10_1093_jamia_ocaa117 crossref_primary_10_1371_journal_pone_0246901 crossref_primary_10_1016_j_artmed_2019_101767 crossref_primary_10_1093_database_baz051 crossref_primary_10_1186_s12859_018_2567_6 crossref_primary_10_1016_j_envint_2022_107323 crossref_primary_10_1093_database_baae079 crossref_primary_10_3389_fmicb_2018_02183 crossref_primary_10_1016_j_compbiomed_2022_105788 crossref_primary_10_1186_s12859_017_1857_8 crossref_primary_10_3897_BDJ_7_e29626 crossref_primary_10_1093_database_baae073 crossref_primary_10_1016_j_ebiom_2024_104988 crossref_primary_10_1038_s41597_023_02617_x crossref_primary_10_1093_bioinformatics_btz528 crossref_primary_10_1093_nar_gkae977 crossref_primary_10_1186_s12859_022_04768_x crossref_primary_10_12688_f1000research_19427_1 crossref_primary_10_1093_database_bay092 crossref_primary_10_1093_database_baz060 crossref_primary_10_1093_nar_gkab347 crossref_primary_10_3389_fnins_2021_680762 crossref_primary_10_1093_database_bay097 crossref_primary_10_1093_database_baz064 crossref_primary_10_3390_genes13020365 crossref_primary_10_1093_database_bav116 crossref_primary_10_7717_peerj_524 crossref_primary_10_1186_s12859_020_3457_2 crossref_primary_10_1016_j_jbi_2023_104362 crossref_primary_10_1038_s41598_018_24457_1 crossref_primary_10_1093_bib_bbz130 crossref_primary_10_1093_database_baw113 crossref_primary_10_2174_1574893614666190204153531 crossref_primary_10_2196_48115 crossref_primary_10_1016_j_jbi_2019_103094 crossref_primary_10_1080_0952813X_2022_2058619 crossref_primary_10_1093_database_baaa024 crossref_primary_10_1016_j_jbi_2013_12_006 crossref_primary_10_1371_journal_pone_0135305 crossref_primary_10_1371_journal_pone_0164680 crossref_primary_10_1080_21592799_2017_1392400 crossref_primary_10_1093_database_bax091 crossref_primary_10_1093_bioinformatics_btz678 crossref_primary_10_1111_nyas_13134 crossref_primary_10_1093_database_bau056 crossref_primary_10_1109_TKDE_2021_3087532 crossref_primary_10_1093_bioinformatics_btae183 crossref_primary_10_1093_database_bau053 crossref_primary_10_7717_peerj_17470 crossref_primary_10_1093_database_bau050 crossref_primary_10_1186_s40168_018_0545_x crossref_primary_10_1002_2211_5463_13309 crossref_primary_10_1155_2018_6217812 crossref_primary_10_1093_bib_bbz122 crossref_primary_10_5515_KJKIEES_2020_31_10_839 crossref_primary_10_1186_s12859_021_04200_w crossref_primary_10_1016_j_fgb_2016_01_012 crossref_primary_10_1016_j_biochi_2021_10_016 crossref_primary_10_3390_diagnostics12040887 crossref_primary_10_1186_s12935_023_03106_2 crossref_primary_10_1093_database_baz045 crossref_primary_10_1093_database_bay076 crossref_primary_10_1093_database_bau048 crossref_primary_10_1093_database_bav016 crossref_primary_10_1093_bioinformatics_btae194 crossref_primary_10_1093_database_baac100 crossref_primary_10_1016_j_patter_2020_100153 crossref_primary_10_1093_nargab_lqab090 crossref_primary_10_1093_nar_gkz289 crossref_primary_10_1038_s41597_019_0342_9 crossref_primary_10_3390_biochem1020007 crossref_primary_10_1093_gigascience_giad036 crossref_primary_10_17660_ActaHortic_2024_1404_2 crossref_primary_10_3389_frai_2022_932665 crossref_primary_10_1016_j_jbi_2023_104317 crossref_primary_10_1093_nar_gky1042 crossref_primary_10_1093_bioinformatics_btt474 crossref_primary_10_1021_acs_chemrev_6b00851 crossref_primary_10_1186_s12859_016_1249_5 crossref_primary_10_1186_s12859_019_2693_9 crossref_primary_10_3390_healthcare11091268 crossref_primary_10_2196_38584 crossref_primary_10_1016_j_jbi_2018_05_001 crossref_primary_10_1038_s41598_018_31439_w crossref_primary_10_1093_jamia_ocw009 crossref_primary_10_1093_nar_gkaa969 crossref_primary_10_1093_bioinformatics_btz571 crossref_primary_10_1093_database_baw145 crossref_primary_10_1038_srep10021 crossref_primary_10_1155_2015_918710 crossref_primary_10_1093_database_bau074 crossref_primary_10_1093_database_bau073 crossref_primary_10_18632_oncotarget_13544 crossref_primary_10_1093_bib_bbac138 crossref_primary_10_1093_nar_gkaa1074 crossref_primary_10_1016_j_ajhg_2023_08_018 crossref_primary_10_3390_app122312012 crossref_primary_10_1016_j_cmet_2023_03_001 crossref_primary_10_1093_database_baad061 crossref_primary_10_3389_fcell_2023_1260507 crossref_primary_10_1093_bioinformatics_btv760 crossref_primary_10_1093_bioinformatics_bty114 crossref_primary_10_1186_s12859_024_05710_z crossref_primary_10_1186_s12859_019_3026_8 crossref_primary_10_1093_database_baw150 crossref_primary_10_1016_j_nbt_2023_09_001 crossref_primary_10_1093_nar_gkz428 crossref_primary_10_12688_f1000research_21463_1 crossref_primary_10_1109_TCBB_2016_2542802 crossref_primary_10_2196_37701 crossref_primary_10_3390_app11167318 crossref_primary_10_1093_database_baae025 crossref_primary_10_1109_ACCESS_2019_2920708 crossref_primary_10_1016_j_compbiomed_2019_04_008 crossref_primary_10_1371_journal_pone_0163794 crossref_primary_10_1021_acs_jproteome_8b00378 crossref_primary_10_1186_s12896_020_00667_2 crossref_primary_10_1002_ajhb_23867 crossref_primary_10_1186_s40001_024_01983_5 crossref_primary_10_1093_bioinformatics_btac230 crossref_primary_10_1016_j_compbiolchem_2022_107772 crossref_primary_10_1093_nar_gky428 crossref_primary_10_7717_peerj_13351 crossref_primary_10_1080_0144929X_2015_1128975 crossref_primary_10_1186_s12881_017_0440_5 crossref_primary_10_1088_1757_899X_1022_1_012055 crossref_primary_10_1093_database_baae057 crossref_primary_10_1021_acs_jcim_7b00589 crossref_primary_10_12688_wellcomeopenres_10210_2 crossref_primary_10_3390_diagnostics12081914 crossref_primary_10_1002_asi_24411 crossref_primary_10_12688_wellcomeopenres_10210_1 crossref_primary_10_1145_3490238 crossref_primary_10_1186_s12859_015_0609_x crossref_primary_10_1097_SCS_0000000000004583 crossref_primary_10_1109_TCBB_2019_2933825 crossref_primary_10_1186_s12859_018_2029_1 crossref_primary_10_1186_s13321_018_0314_7 crossref_primary_10_1093_bioinformatics_btw511 crossref_primary_10_1093_bioinformatics_btz227 crossref_primary_10_1186_s12859_019_2958_3 crossref_primary_10_1038_s41597_023_02781_0 crossref_primary_10_1007_s00894_022_05310_9 crossref_primary_10_1093_jamia_ocab176 crossref_primary_10_1093_nar_gkaa952 crossref_primary_10_1007_s11192_022_04314_9 crossref_primary_10_3389_fmicb_2022_872671 crossref_primary_10_1016_j_jbi_2023_104464 crossref_primary_10_1186_s12859_022_04642_w crossref_primary_10_3389_frma_2025_1509502 crossref_primary_10_1093_bioinformatics_btab157 crossref_primary_10_1186_s12918_017_0402_8 crossref_primary_10_1371_journal_pcbi_1007617 crossref_primary_10_3389_frai_2021_732381 crossref_primary_10_1016_j_compbiomed_2023_106988 crossref_primary_10_1186_s12859_023_05406_w crossref_primary_10_1534_g3_120_401775 crossref_primary_10_1093_database_bau086 crossref_primary_10_1186_s12859_021_04292_4 crossref_primary_10_1038_s41467_019_13208_z crossref_primary_10_1186_s12911_019_0936_3 crossref_primary_10_1016_j_preghy_2020_03_011 crossref_primary_10_1093_database_baaf011 crossref_primary_10_2174_1386207323666200606211342 crossref_primary_10_1097_MD_0000000000020999 |
| Cites_doi | 10.1371/journal.pbio.0020309 10.1093/database/bas021 10.1093/database/bas016 10.1093/database/bap019 10.1093/bioinformatics/btr042 10.1093/database/bas050 10.1186/1471-2105-9-205 10.1093/database/bas026 10.1093/bioinformatics/btt156 10.1093/database/bar059 10.1093/database/bas017 10.1093/database/bas043 10.1371/journal.pcbi.0020142 10.1093/bioinformatics/bts435 10.1371/journal.pone.0038460 10.1093/database/bas056 10.1186/1471-2105-10-228 10.1038/455047a 10.1093/database/bas041 10.1093/database/bas037 10.1186/1471-2105-12-S8-S5 |
| ContentType | Journal Article |
| Copyright | Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US. |
| Copyright_xml | – notice: Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US. |
| DBID | AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 5PM ADTOC UNPAY |
| DOI | 10.1093/nar/gkt441 |
| DatabaseName | CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic PubMed Central (Full Participant titles) Unpaywall for CDI: Periodical Content Unpaywall |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database – sequence: 3 dbid: UNPAY name: Unpaywall url: https://proxy.k.utb.cz/login?url=https://unpaywall.org/ sourceTypes: Open Access Repository |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Anatomy & Physiology Chemistry |
| EISSN | 1362-4962 |
| EndPage | W522 |
| ExternalDocumentID | 10.1093/nar/gkt441 PMC3692066 23703206 10_1093_nar_gkt441 |
| Genre | Journal Article Research Support, N.I.H., Intramural |
| GrantInformation_xml | – fundername: Intramural NIH HHS |
| GroupedDBID | --- -DZ -~X .I3 0R~ 123 18M 1TH 29N 2WC 4.4 482 53G 5VS 5WA 70E 85S A8Z AAFWJ AAHBH AAMVS AAOGV AAPXW AAUQX AAVAP AAYXX ABEJV ABGNP ABPTD ABQLI ABXVV ACGFO ACGFS ACIWK ACNCT ACPRK ACUTJ ADBBV ADHZD AEGXH AENEX AENZO AFFNX AFPKN AFRAH AFYAG AHMBA AIAGR ALMA_UNASSIGNED_HOLDINGS ALUQC AMNDL AOIJS BAWUL BAYMD BCNDV CAG CIDKT CITATION CS3 CZ4 DIK DU5 D~K E3Z EBD EBS EJD EMOBN ESTFP F5P GROUPED_DOAJ GX1 H13 HH5 HYE HZ~ IH2 KAQDR KQ8 KSI OAWHX OBC OBS OEB OES OJQWA OVD OVT P2P PEELM PQQKQ R44 RD5 RNS ROL ROZ RPM RXO SV3 TEORI TN5 TOX TR2 WG7 WOQ X7H XSB YSK ZKX ~91 ~D7 ~KM .55 .GJ 3O- AAWDT AAYJJ ABIME ABNGD ABPIB ABSMQ ABZEO ACFRR ACIPB ACPQN ACUKT ACVCV ACZBC AEHUL AEKPW AFSHK AGKRT AGMDO AGQPQ ANFBD APJGH AQDSO ASAOO ASPBG ATDFG ATTQO AVWKF AZFZN BEYMZ C1A CGR COF CUY CVF CXTWN D0S DFGAJ ECM EIF ELUNK FEDTE HVGLF H~9 MBTAY MVM NPM NTWIH O~Y PB- QBD RNI RZF RZO SJN TCN UHB X7M XSW ZXP 7X8 5PM ADTOC UNPAY |
| ID | FETCH-LOGICAL-c374t-da3b740431c7945b29a4e30eed6eb8b1f2438de5c38fbe21284d12cd319fe7e63 |
| IEDL.DBID | UNPAY |
| ISSN | 0305-1048 1362-4962 1362-4954 |
| IngestDate | Sun Oct 26 04:00:33 EDT 2025 Tue Sep 30 16:53:10 EDT 2025 Thu Oct 02 07:36:55 EDT 2025 Mon Jul 21 05:55:33 EDT 2025 Wed Oct 01 02:24:59 EDT 2025 Thu Apr 24 23:05:39 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | W1 |
| Language | English |
| License | public-domain |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c374t-da3b740431c7945b29a4e30eed6eb8b1f2438de5c38fbe21284d12cd319fe7e63 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| OpenAccessLink | https://proxy.k.utb.cz/login?url=https://academic.oup.com/nar/article-pdf/41/W1/W518/3859973/gkt441.pdf |
| PMID | 23703206 |
| PQID | 1371271712 |
| PQPubID | 23479 |
| ParticipantIDs | unpaywall_primary_10_1093_nar_gkt441 pubmedcentral_primary_oai_pubmedcentral_nih_gov_3692066 proquest_miscellaneous_1371271712 pubmed_primary_23703206 crossref_citationtrail_10_1093_nar_gkt441 crossref_primary_10_1093_nar_gkt441 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2013-07-01 |
| PublicationDateYYYYMMDD | 2013-07-01 |
| PublicationDate_xml | – month: 07 year: 2013 text: 2013-07-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England |
| PublicationTitle | Nucleic acids research |
| PublicationTitleAlternate | Nucleic Acids Res |
| PublicationYear | 2013 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| References | Neves ( key 20171013114415_gkt441-B15) 2012 Auken ( key 20171013114415_gkt441-B9) 2009; 10 Bourne ( key 20171013114415_gkt441-B3) 2006; 2 Salgado ( key 20171013114415_gkt441-B17) 2012; 28 Wei ( key 20171013114415_gkt441-B20) 2012; 7 Wei ( key 20171013114415_gkt441-B18) 2011; 12 Névéol ( key 20171013114415_gkt441-B5) 2012; 2012 Howe ( key 20171013114415_gkt441-B2) 2008; 455 Lu ( key 20171013114415_gkt441-B6) 2012; 2012 Wei ( key 20171013114415_gkt441-B14) 2012 Vishnyakova ( key 20171013114415_gkt441-B4) 2012; 2012 Yu ( key 20171013114415_gkt441-B10) 2008; 9 Wiegers ( key 20171013114415_gkt441-B8) 2012; 2012 Dowell ( key 20171013114415_gkt441-B11) 2009; 2009 Wei ( key 20171013114415_gkt441-B23) 2012; 2012 Arighi ( key 20171013114415_gkt441-B13) 2013; 2013 Müller ( key 20171013114415_gkt441-B16) 2004; 2 Rinaldi ( key 20171013114415_gkt441-B7) 2012; 2012 Krallinger ( key 20171013114415_gkt441-B12) 2012; 2012 Wei ( key 20171013114415_gkt441-B21) 2013; 29 Laulederkind ( key 20171013114415_gkt441-B24) 2012; 2012 Huang ( key 20171013114415_gkt441-B19) 2011; 27 Divoli ( key 20171013114415_gkt441-B22) 2008 Burge ( key 20171013114415_gkt441-B1) 2012; 2012 23255168 - Brief Bioinform. 2014 Mar;15(2):327-40 22529178 - Database (Oxford). 2012;2012:bas021 23564842 - Bioinformatics. 2013 Jun 1;29(11):1433-9 18769432 - Nature. 2008 Sep 4;455(7209):47-50 21303863 - Bioinformatics. 2011 Apr 1;27(7):1032-3 23160416 - Database (Oxford). 2012;2012:bas043 22789588 - Bioinformatics. 2012 Sep 1;28(17):2285-7 18229716 - Pac Symp Biocomput. 2008;:568-79 18430222 - BMC Bioinformatics. 2008;9:205 23180769 - Database (Oxford). 2012;2012:bas037 15383839 - PLoS Biol. 2004 Nov;2(11):e309 22679507 - PLoS One. 2012;7(6):e38460 22685160 - Database (Oxford). 2012;2012:bas026 19622167 - BMC Bioinformatics. 2009;10:228 22434847 - Database (Oxford). 2012;2012:bas016 17411327 - PLoS Comput Biol. 2006 Oct 27;2(10):e142 23221176 - Database (Oxford). 2012;2012:bas050 20157492 - Database (Oxford). 2009;2009:bap019 23160414 - Database (Oxford). 2012;2012:bas041 22151999 - BMC Bioinformatics. 2011;12 Suppl 8:S5 23327936 - Database (Oxford). 2013;2013:bas056 22434828 - Database (Oxford). 2012;2012:bar059 22438567 - Database (Oxford). 2012;2012:bas017 |
| References_xml | – volume: 2 start-page: e309 year: 2004 ident: key 20171013114415_gkt441-B16 article-title: Textpresso: an ontology-based information retrieval and extraction system for biological literature publication-title: PLoS Biol. doi: 10.1371/journal.pbio.0020309 – volume: 2012 start-page: bas021 year: 2012 ident: key 20171013114415_gkt441-B7 article-title: Using ODIN for a PharmGKB revalidation experiment publication-title: Database (Oxford) doi: 10.1093/database/bas021 – year: 2012 ident: key 20171013114415_gkt441-B15 article-title: A survey on annotation tools for the biomedical literature publication-title: Brief. Bioinformatics – volume: 2012 start-page: bas016 year: 2012 ident: key 20171013114415_gkt441-B24 article-title: Ontology searching and browsing at the Rat Genome Database publication-title: Database (Oxford) doi: 10.1093/database/bas016 – start-page: 568 year: 2008 ident: key 20171013114415_gkt441-B22 article-title: Evidence for showing gene/protein name suggestions in bioscience literature search interfaces publication-title: Pac. Symp. Biocomput. – volume: 2009 start-page: bap019 year: 2009 ident: key 20171013114415_gkt441-B11 article-title: Integrating text mining into the MGI biocuration workflow publication-title: Database doi: 10.1093/database/bap019 – volume: 27 start-page: 1032 year: 2011 ident: key 20171013114415_gkt441-B19 article-title: GeneTUKit: a software for document-level gene normalization publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr042 – start-page: 145 volume-title: Proceedings of the BioCreative 2012 Workshop year: 2012 ident: key 20171013114415_gkt441-B14 article-title: PubTator: A PubMed-Like interactive curation system for document triage and literature curation – volume: 2012 start-page: bas050 year: 2012 ident: key 20171013114415_gkt441-B4 article-title: Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database publication-title: Database (Oxford) doi: 10.1093/database/bas050 – volume: 9 start-page: 205 year: 2008 ident: key 20171013114415_gkt441-B10 article-title: GAPscreener: an automatic tool for screening human genetic association literature in PubMed using the support vector machine technique publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-9-205 – volume: 2012 start-page: bas026 year: 2012 ident: key 20171013114415_gkt441-B5 article-title: Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE publication-title: Database (Oxford) doi: 10.1093/database/bas026 – volume: 29 start-page: 1433 year: 2013 ident: key 20171013114415_gkt441-B21 article-title: tmVar: a text mining approach for extracting sequence variants in biomedical literature publication-title: Bioinformatics doi: 10.1093/bioinformatics/btt156 – volume: 2012 start-page: bar059 year: 2012 ident: key 20171013114415_gkt441-B1 article-title: Biocurators and biocuration: surveying the 21st century challenges publication-title: Database (Oxford) doi: 10.1093/database/bar059 – volume: 2012 start-page: bas017 year: 2012 ident: key 20171013114415_gkt441-B12 article-title: How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience publication-title: Database (Oxford) doi: 10.1093/database/bas017 – volume: 2012 start-page: bas043 year: 2012 ident: key 20171013114415_gkt441-B6 article-title: Biocuration workflows and text mining: overview of the BioCreative Workshop Track II publication-title: Database (Oxford) doi: 10.1093/database/bas043 – volume: 2 start-page: e142 year: 2006 ident: key 20171013114415_gkt441-B3 article-title: Biocurators: contributors to the world of science publication-title: PLoS Comput. Biol. doi: 10.1371/journal.pcbi.0020142 – volume: 28 start-page: 2285 year: 2012 ident: key 20171013114415_gkt441-B17 article-title: MyMiner: a web application for computer-assisted biocuration and text annotation publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts435 – volume: 7 start-page: e38460 year: 2012 ident: key 20171013114415_gkt441-B20 article-title: SR4GN: a species recognition software tool for gene normalization publication-title: PLoS One doi: 10.1371/journal.pone.0038460 – volume: 2013 start-page: bas056 year: 2013 ident: key 20171013114415_gkt441-B13 article-title: An overview of the BioCreative 2012 Workshop Track III: interactive text mining task publication-title: Database doi: 10.1093/database/bas056 – volume: 10 start-page: 228 year: 2009 ident: key 20171013114415_gkt441-B9 article-title: Semi-automated curation of protein subcellular localization: a text mining-based approach to gene ontology (GO) cellular component curation publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-10-228 – volume: 455 start-page: 47 year: 2008 ident: key 20171013114415_gkt441-B2 article-title: Big data: the future of biocuration publication-title: Nature doi: 10.1038/455047a – volume: 2012 start-page: bas041 year: 2012 ident: key 20171013114415_gkt441-B23 article-title: Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts publication-title: Database (Oxford) doi: 10.1093/database/bas041 – volume: 2012 start-page: bas037 year: 2012 ident: key 20171013114415_gkt441-B8 article-title: Collaborative biocuration–text-mining development task for document prioritization for curation publication-title: Database (Oxford) doi: 10.1093/database/bas037 – volume: 12 start-page: S6 year: 2011 ident: key 20171013114415_gkt441-B18 article-title: Cross-species gene normalization by species inference publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-S8-S5 – reference: 22685160 - Database (Oxford). 2012;2012:bas026 – reference: 23160416 - Database (Oxford). 2012;2012:bas043 – reference: 23564842 - Bioinformatics. 2013 Jun 1;29(11):1433-9 – reference: 22151999 - BMC Bioinformatics. 2011;12 Suppl 8:S5 – reference: 15383839 - PLoS Biol. 2004 Nov;2(11):e309 – reference: 17411327 - PLoS Comput Biol. 2006 Oct 27;2(10):e142 – reference: 22438567 - Database (Oxford). 2012;2012:bas017 – reference: 23327936 - Database (Oxford). 2013;2013:bas056 – reference: 23221176 - Database (Oxford). 2012;2012:bas050 – reference: 23255168 - Brief Bioinform. 2014 Mar;15(2):327-40 – reference: 22529178 - Database (Oxford). 2012;2012:bas021 – reference: 22434828 - Database (Oxford). 2012;2012:bar059 – reference: 23160414 - Database (Oxford). 2012;2012:bas041 – reference: 19622167 - BMC Bioinformatics. 2009;10:228 – reference: 20157492 - Database (Oxford). 2009;2009:bap019 – reference: 22434847 - Database (Oxford). 2012;2012:bas016 – reference: 22679507 - PLoS One. 2012;7(6):e38460 – reference: 22789588 - Bioinformatics. 2012 Sep 1;28(17):2285-7 – reference: 18769432 - Nature. 2008 Sep 4;455(7209):47-50 – reference: 23180769 - Database (Oxford). 2012;2012:bas037 – reference: 18229716 - Pac Symp Biocomput. 2008;:568-79 – reference: 18430222 - BMC Bioinformatics. 2008;9:205 – reference: 21303863 - Bioinformatics. 2011 Apr 1;27(7):1032-3 |
| SSID | ssj0014154 |
| Score | 2.582971 |
| Snippet | Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with... |
| SourceID | unpaywall pubmedcentral proquest pubmed crossref |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source |
| StartPage | W518 |
| SubjectTerms | Data Mining - methods Databases, Factual Internet PubMed Software |
| Title | PubTator: a web-based text mining tool for assisting biocuration |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/23703206 https://www.proquest.com/docview/1371271712 https://pubmed.ncbi.nlm.nih.gov/PMC3692066 https://academic.oup.com/nar/article-pdf/41/W1/W518/3859973/gkt441.pdf |
| UnpaywallVersion | publishedVersion |
| Volume | 41 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVFSB databaseName: Free Full-Text Journals in Chemistry customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: HH5 dateStart: 19960101 isFulltext: true titleUrlDefault: http://abc-chemistry.org/ providerName: ABC ChemistRy – providerCode: PRVAFT databaseName: Open Access Digital Library customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: KQ8 dateStart: 19960101 isFulltext: true titleUrlDefault: http://grweb.coalliance.org/oadl/oadl.html providerName: Colorado Alliance of Research Libraries – providerCode: PRVAFT databaseName: Open Access Digital Library customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: KQ8 dateStart: 19740101 isFulltext: true titleUrlDefault: http://grweb.coalliance.org/oadl/oadl.html providerName: Colorado Alliance of Research Libraries – providerCode: PRVAFT databaseName: Open Access Digital Library customDbUrl: eissn: 1362-4962 dateEnd: 20301231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: KQ8 dateStart: 19960101 isFulltext: true titleUrlDefault: http://grweb.coalliance.org/oadl/oadl.html providerName: Colorado Alliance of Research Libraries – providerCode: PRVAON databaseName: DOAJ Directory of Open Access Journals customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: DOA dateStart: 20050101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVEBS databaseName: Food Science Source (Ebsco) customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: A8Z dateStart: 19960101 isFulltext: true titleUrlDefault: https://search.ebscohost.com/login.aspx?authtype=ip,uid&profile=ehost&defaultdb=fsr providerName: EBSCOhost – providerCode: PRVBFR databaseName: Free Medical Journals customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: DIK dateStart: 19960101 isFulltext: true titleUrlDefault: http://www.freemedicaljournals.com providerName: Flying Publisher – providerCode: PRVFQY databaseName: GFMER Free Medical Journals customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: GX1 dateStart: 19960101 isFulltext: true titleUrlDefault: http://www.gfmer.ch/Medical_journals/Free_medical.php providerName: Geneva Foundation for Medical Education and Research – providerCode: PRVAQN databaseName: PubMed Central customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: RPM dateStart: 19740101 isFulltext: true titleUrlDefault: https://www.ncbi.nlm.nih.gov/pmc/ providerName: National Library of Medicine – providerCode: PRVASL databaseName: Oxford Journals Free Titles 2012-2013 - NESLI2 customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: 70E dateStart: 0 isFulltext: true titleUrlDefault: https://academic.oup.com/journals providerName: Oxford University Press – providerCode: PRVASL databaseName: Oxford Journals Open Access Collection customDbUrl: eissn: 1362-4962 dateEnd: 99991231 omitProxy: true ssIdentifier: ssj0014154 issn: 1362-4962 databaseCode: TOX dateStart: 19960101 isFulltext: true titleUrlDefault: https://academic.oup.com/journals/ providerName: Oxford University Press |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Lb9QwEB6120O58Gh5LI-VERUSh2ziV5xwYlV1VXGoeuiKcor8Sqm6TVYlESq_HttJFpYihISUQxRPnHg89szY428ADhJlqHRqN8Im4REjKokU4yLSKpfWZLTUNqB9nqTHC_bxnJ9vwXw4CyP7qPDpcKShkjdxz8RoZcqY4fiTuzjOYprxPBc0vrhqnFKfutJt2Em5s8lHsLM4OZ197rYQPNRmSKOFwxGhnLOf9ykZMEtzGr7VVbappe6YnncjKHfbaiVvv8nl8hf1NH8AF0PDuqiUq2nbqKn-_hvm4_-3_CHc7y1YNOveeQRbttqD_VnlvPfrW_QWhZjSsFi_B7uHQz65ffhw2qoz7-K_RxK5yTvyCtQgH3mCrkOaCtTU9RI5Kxo5i97PPe6Ruqx120npY1jMj84Oj6M-f0OkqWBNZCRVIqD3aDfquSK5ZJYmTiunVmUKl4TRzFiuaVYqS7ymNJho42aF0gqb0icwqurKPgMkVKmocb4sk5hZH3RodGZzxzOujdF4DO-G_ip0D27uc2wsi26TnRaOm0XHrjG8WdOuOkiPP1K9Hrq9cIzy2yiysnX7tcBUYOK8YEzG8LQTg3U9hAqfkT4dg9gQkDWBR_PeLKkuvwRUb5rmHlp_DAdrUfrL7z3_N7IXcI-E_B0-vvgljJqb1r5yVlSjJrAtkqNJWIOY9MPlB-qkHng |
| linkProvider | Unpaywall |
| linkToUnpaywall | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1Lb9QwEB6V7aFceLQ8lpeMqJA4ZLN-5cGJVcWq4lD10BXlFPmVtuo2WZVEqPx6xk6ysBQhJKQconhix-OxZyYefwOwP9WWK1S7EbVTGQmmp5EWMo2MzpWzGS-NC2ifR8nhQnw6ladbMB_Owqg-KnwyHGmo1HXcMzFa2TIWNP6Ml6RZzDOZ5ymPzy4bVOoTLL0D24lEm3wE24uj49mXbgvBQ22GNFo0HBHKpfh5n7ABszTnoa2usk0tdcv0vB1BudNWK3XzTS2Xv6in-X04GzrWRaVcTtpGT8z33zAf_7_nD-Beb8GSWffOQ9hy1S7szSr03q9uyFsSYkrDz_pd2DkY8sntwYfjVp94F_89UQQX78grUEt85Am5CmkqSFPXS4JWNEGL3q89-Ehf1KbtpPQRLOYfTw4Ooz5_Q2R4KprIKq7TgN5jcNZLzXIlHJ-iVk6czjQtmeCZddLwrNSOeU1pKTMWV4XSpS7hj2FU1ZV7CiTVpeYWfVmhqHA-6NCazOXIM2msNXQM74bxKkwPbu5zbCyLbpOdF8jNomPXGN6saVcdpMcfqV4Pw14go_w2iqpc3X4tKE8pQy-YsjE86cRgXQ_jqc9In4wh3RCQNYFH894sqS7OA6o3T3IPrT-G_bUo_eXznv0b2XO4y0L-Dh9f_AJGzXXrXqIV1ehX_RT5AY76HLY |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=PubTator%3A+a+web-based+text+mining+tool+for+assisting+biocuration&rft.jtitle=Nucleic+acids+research&rft.au=Wei%2C+Chih-Hsuan&rft.au=Kao%2C+Hung-Yu&rft.au=Lu%2C+Zhiyong&rft.date=2013-07-01&rft.eissn=1362-4962&rft.volume=41&rft.issue=Web+Server+issue&rft.spage=W518&rft_id=info:doi/10.1093%2Fnar%2Fgkt441&rft_id=info%3Apmid%2F23703206&rft.externalDocID=23703206 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0305-1048&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0305-1048&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0305-1048&client=summon |