-
2
-
-
79952765434
-
Semi-automatic semantic annotation of PubMed queries: A study on quality, efficiency, satisfaction
-
Neveol A, Islamaj Dogan R, Lu Z: Semi-automatic semantic annotation of PubMed queries: a study on quality, efficiency, satisfaction. J Biomed Inform 2011, 44(2):310-318.
-
(2011)
J Biomed Inform
, vol.44
, Issue.2
, pp. 310-318
-
-
Neveol, A.1
Islamaj Dogan, R.2
Lu, Z.3
-
3
-
-
84908087913
-
Understanding PubMed user search behavior through log analysis
-
Islamaj Dogan R, Murray GC, Neveol A, Lu Z: Understanding PubMed user search behavior through log analysis. Database (Oxford) 2009, 2009: bap018.
-
(2009)
Database (Oxford)
, vol.2009
, pp. bap018
-
-
Islamaj Dogan, R.1
Murray, G.C.2
Neveol, A.3
Lu, Z.4
-
4
-
-
84863506694
-
ChemSpot: A hybrid system for chemical named entity recognition
-
Rocktaschel T, Weidlich M, Leser U: ChemSpot: A Hybrid System for Chemical Named Entity Recognition. Bioinformatics 2012, 28(12):1633-1640.
-
(2012)
Bioinformatics
, vol.28
, Issue.12
, pp. 1633-1640
-
-
Rocktaschel, T.1
Weidlich, M.2
Leser, U.3
-
5
-
-
51049088874
-
Overview of BioCreative II gene mention recognition
-
Smith L, Tanabe LK, Ando RJ, Kuo CJ, Chung IF, Hsu CN, Lin YS, Klinger R, Friedrich CM, Ganchev K, Torii M, Liu H, Haddow B, Struble CA, Povinelli RJ, Vlachos A, Baumgartner WA, Hunter L, Carpenter B, Tsai RT, Dai HJ, Liu F, Chen Y, Sun C, Katrenko S, Adriaans P, Blaschke C, Torres R, Neves M, Nakov P, et al: Overview of BioCreative II gene mention recognition. Genome Biol 2008, 9(Suppl 2):S2.
-
(2008)
Genome Biol
, vol.9
, pp. S2
-
-
Smith, L.1
Tanabe, L.K.2
Ando, R.J.3
Kuo, C.J.4
Chung, I.F.5
Hsu, C.N.6
Lin, Y.S.7
Klinger, R.8
Friedrich, C.M.9
Ganchev, K.10
Torii, M.11
Liu, H.12
Haddow, B.13
Struble, C.A.14
Povinelli, R.J.15
Vlachos, A.16
Baumgartner, W.A.17
Hunter, L.18
Carpenter, B.19
Tsai, R.T.20
Dai, H.J.21
Liu, F.22
Chen, Y.23
Sun, C.24
Katrenko, S.25
Adriaans, P.26
Blaschke, C.27
Torres, R.28
Neves, M.29
Nakov, P.30
more..
-
6
-
-
84883572716
-
PubTator: A web-based text mining tool for assisting biocuration
-
Wei CH, Kao HY, Lu Z: PubTator: a web-based text mining tool for assisting biocuration. Nucleic Acids Res 2013, 41(W1):W518-W522.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.W1
, pp. W518-W522
-
-
Wei, C.H.1
Kao, H.Y.2
Lu, Z.3
-
8
-
-
84861856856
-
SR4GN: A species recognition software tool for gene normalization
-
Wei CH, Kao HY, Lu Z: SR4GN: a species recognition software tool for gene normalization. PloS one 2012, 7(6):e38460.
-
(2012)
PloS One
, vol.7
, Issue.6
, pp. e38460
-
-
Wei, C.H.1
Kao, H.Y.2
Lu, Z.3
-
9
-
-
84890064920
-
DNorm: Disease name normalization with pairwise learning-to-rank
-
Leaman R, Doʇan RI, Lu Z: DNorm: Disease name normalization with pairwise learning-to-rank. Bioinformatics 2013, 29(22):2909-2917.
-
(2013)
Bioinformatics
, vol.29
, Issue.22
, pp. 2909-2917
-
-
Leaman, R.1
Doʇan, R.I.2
Lu, Z.3
-
10
-
-
79960604459
-
Text mining for drugs and chemical compounds: Methods, tools and applications
-
Vazquez M, Krallinger M, Leitner F, Valencia A: Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications. Molecular Informatics 2011, 30(6-7):506-519.
-
(2011)
Molecular Informatics
, vol.30
, Issue.6-7
, pp. 506-519
-
-
Vazquez, M.1
Krallinger, M.2
Leitner, F.3
Valencia, A.4
-
11
-
-
84901001907
-
Chemical named entities recognition: A review on approaches and applications
-
Eltyeb S, Salim N: Chemical named entities recognition: a review on approaches and applications. Journal of cheminformatics 2014, 6:17.
-
(2014)
Journal of Cheminformatics
, vol.6
, pp. 17
-
-
Eltyeb, S.1
Salim, N.2
-
12
-
-
70449387056
-
A dictionary to identify small molecules and drugs in free text
-
Hettne KM, Stierum RH, Schuemie MJ, Hendriksen PJ, Schijvenaars BJ, Mulligen EM, Kleinjans J, Kors JA: A dictionary to identify small molecules and drugs in free text. Bioinformatics 2009, 25(22):2983-2991.
-
(2009)
Bioinformatics
, vol.25
, Issue.22
, pp. 2983-2991
-
-
Hettne, K.M.1
Stierum, R.H.2
Schuemie, M.J.3
Hendriksen, P.J.4
Schijvenaars, B.J.5
Mulligen, E.M.6
Kleinjans, J.7
Kors, J.A.8
-
13
-
-
46249113462
-
Detection of IUPAC and IUPAC-like chemical names
-
Klinger R, Kolarik C, Fluck J, Hofmann-Apitius M, Friedrich CM: Detection of IUPAC and IUPAC-like chemical names. Bioinformatics 2008, 24(13): i268-276.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
, pp. i268-276
-
-
Klinger, R.1
Kolarik, C.2
Fluck, J.3
Hofmann-Apitius, M.4
Friedrich, C.M.5
-
14
-
-
80053974142
-
OSCAR4: A flexible architecture for chemical text-mining
-
Jessop DM, Adams SE, Willighagen EL, Hawizy L, Murray-Rust P: OSCAR4: a flexible architecture for chemical text-mining. Journal of cheminformatics 2011, 3(1):41.
-
(2011)
Journal of Cheminformatics
, vol.3
, Issue.1
, pp. 41
-
-
Jessop, D.M.1
Adams, S.E.2
Willighagen, E.L.3
Hawizy, L.4
Murray-Rust, P.5
-
16
-
-
84949749640
-
Assessment of NER solutions against the first and second CALBC silver standard corpus
-
Rebholz-Schuhmann D, Jimeno Yepes A, Li C, Kafkas S, Lewin I, Kang N, Corbett P, Milward D, Buyko E, Beisswanger E, Hornbostel K, Kouznetsov A, Witte R, Laurila JB, Baker CJ, Kuo CJ, Clematide S, Rinaldi F, Farkas R, Mora G, Hara K, Furlong LI, Rautschka M, Neves ML, Pascual-Montano A, Wei Q, Collier N, Chowdhury MF, Lavelli A, Berlanga R, et al: Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. Journal of biomedical semantics 2011, 2(Suppl 5):S11.
-
(2011)
Journal of Biomedical Semantics
, vol.2
, pp. S11
-
-
Rebholz-Schuhmann, D.1
Jimeno Yepes, A.2
Li, C.3
Kafkas, S.4
Lewin, I.5
Kang, N.6
Corbett, P.7
Milward, D.8
Buyko, E.9
Beisswanger, E.10
Hornbostel, K.11
Kouznetsov, A.12
Witte, R.13
Laurila, J.B.14
Baker, C.J.15
Kuo, C.J.16
Clematide, S.17
Rinaldi, F.18
Farkas, R.19
Mora, G.20
Hara, K.21
Furlong, L.I.22
Rautschka, M.23
Neves, M.L.24
Pascual-Montano, A.25
Wei, Q.26
Collier, N.27
Chowdhury, M.F.28
Lavelli, A.29
Berlanga, R.30
more..
-
17
-
-
77951575659
-
CALBC silver standard corpus
-
Rebholz-Schuhmann D, Jimeno Yepes AJ, Van Mulligen EM, Kang N, Kors J, Milward D, Corbett P, Buyko E, Beisswanger E, Hahn U: CALBC silver standard corpus. Journal of bioinformatics and computational biology 2010, 8(1):163-179.
-
(2010)
Journal of Bioinformatics and Computational Biology
, vol.8
, Issue.1
, pp. 163-179
-
-
Rebholz-Schuhmann, D.1
Jimeno Yepes, A.J.2
Van Mulligen, E.M.3
Kang, N.4
Kors, J.5
Milward, D.6
Corbett, P.7
Buyko, E.8
Beisswanger, E.9
Hahn, U.10
-
18
-
-
84925683427
-
CHEMDNER: The drugs and chemical names extraction challenge
-
Krallinger M, Leitner F, Rabal O, Vazquez M, Oyarzabal J, Valencia A: CHEMDNER: The drugs and chemical names extraction challenge. J Cheminform 2015, 7(Suppl 1):S1.
-
(2015)
J Cheminform
, vol.7
, pp. S1
-
-
Krallinger, M.1
Leitner, F.2
Rabal, O.3
Vazquez, M.4
Oyarzabal, J.5
Valencia, A.6
-
19
-
-
84901066451
-
-
Fourth BioCreative Challenge Evaluation; Bethesda, Maryland, USA
-
Leaman R, Wei CH, Lu Z: NCBI at the BioCreative IV CHEMDNER Task: Recognizing chemical names in PubMed articles with tmChem. Fourth BioCreative Challenge Evaluation; Bethesda, Maryland, USA 2013, 34-41.
-
(2013)
NCBI at the BioCreative IV CHEMDNER Task: Recognizing Chemical Names in PubMed Articles with TmChem
, pp. 34-41
-
-
Leaman, R.1
Wei, C.H.2
Lu, Z.3
-
20
-
-
84925647188
-
The CHEMDNER corpus of chemicals and drugs and its annotation principles
-
Krallinger M, Rabal O, Leitner F, Vazquez M, Salgado D, Lu Z, Leaman R, Lu Y, Ji D, Lowe DM, Sayle RA, Batista-Navarro RT, Rak R, Huber T, Rocktaschel T, Matos S, Campos D, Tang B, Xu H, Munkhdalai T, Ryu KH, Ramanan SV, Nathan S, Zitnik S, Bajec M, Weber L, Irmer M, Akhondi SA, Kors JA, Xu S, An X, Sikdar UK, Ekbal A, Yoshioka M, Dieb TM, Choi M, Verspoor K, Khabsa M, Giles CL, Liu H, Ravikumar KE, Lamurias A, Couto FM, Dai H, Tsai RT, Ata C, Can T, Usie A, Alves R, Segura-Bedmar I, Martinez P, Oryzabal J, Valencia A: The CHEMDNER corpus of chemicals and drugs and its annotation principles. J Cheminform 2015, 7(Suppl 1):S2.
-
(2015)
J Cheminform
, vol.7
, pp. S2
-
-
Krallinger, M.1
Rabal, O.2
Leitner, F.3
Vazquez, M.4
Salgado, D.5
Lu, Z.6
Leaman, R.7
Lu, Y.8
Ji, D.9
Lowe, D.M.10
Sayle, R.A.11
Batista-Navarro, R.T.12
Rak, R.13
Huber, T.14
Rocktaschel, T.15
Matos, S.16
Campos, D.17
Tang, B.18
Xu, H.19
Munkhdalai, T.20
Ryu, K.H.21
Ramanan, S.V.22
Nathan, S.23
Zitnik, S.24
Bajec, M.25
Weber, L.26
Irmer, M.27
Akhondi, S.A.28
Kors, J.A.29
Xu, S.30
An, X.31
Sikdar, U.K.32
Ekbal, A.33
Yoshioka, M.34
Dieb, T.M.35
Choi, M.36
Verspoor, K.37
Khabsa, M.38
Giles, C.L.39
Liu, H.40
Ravikumar, K.E.41
Lamurias, A.42
Couto, F.M.43
Dai, H.44
Tsai, R.T.45
Ata, C.46
Can, T.47
Usie, A.48
Alves, R.49
Segura-Bedmar, I.50
Martinez, P.51
Oryzabal, J.52
Valencia, A.53
more..
-
22
-
-
40549140499
-
BANNER: An executable survey of advances in biomedical named entity recognition
-
Leaman R, Gonzalez G: BANNER: an executable survey of advances in biomedical named entity recognition. Pac Symp Biocomput 2008, 652-663.
-
(2008)
Pac Symp Biocomput
, pp. 652-663
-
-
Leaman, R.1
Gonzalez, G.2
-
24
-
-
84878281265
-
TmVar: A text mining approach for extracting sequence variants in biomedical literature
-
Wei C-H, Harris BR, Kao H-Y, Lu Z: tmVar: A text mining approach for extracting sequence variants in biomedical literature. Bioinformatics 2013, 29:1433-1439.
-
(2013)
Bioinformatics
, vol.29
, pp. 1433-1439
-
-
Wei, C.-H.1
Harris, B.R.2
Kao, H.-Y.3
Lu, Z.4
-
27
-
-
84948481845
-
An algorithm for suffix stripping
-
Porter MF: An algorithm for suffix stripping. Program 1980, 14:130-137.
-
(1980)
Program
, vol.14
, pp. 130-137
-
-
Porter, M.F.1
-
28
-
-
79953194522
-
Chemical name to structure: OPSIN, an open source solution
-
Lowe DM, Corbett PT, Murray-Rust P, Glen RC: Chemical name to structure: OPSIN, an open source solution. Journal of chemical information and modeling 2011, 51(3):739-753.
-
(2011)
Journal of Chemical Information and Modeling
, vol.51
, Issue.3
, pp. 739-753
-
-
Lowe, D.M.1
Corbett, P.T.2
Murray-Rust, P.3
Glen, R.C.4
-
29
-
-
55249111767
-
Abbreviation definition identification based on automatic precision estimates
-
Sohn S, Comeau DC, Kim W, Wilbur WJ: Abbreviation definition identification based on automatic precision estimates. BMC Bioinformatics 2008, 9:402.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 402
-
-
Sohn, S.1
Comeau, D.C.2
Kim, W.3
Wilbur, W.J.4
-
30
-
-
46249123634
-
Integrating high dimensional bi-directional parsing models for gene mention tagging
-
Hsu CN, Chang YM, Kuo CJ, Lin YS, Huang HS, Chung IF: Integrating high dimensional bi-directional parsing models for gene mention tagging. Bioinformatics 2008, 24(13):i286-294.
-
(2008)
Bioinformatics
, vol.24
, Issue.13
, pp. i286-294
-
-
Hsu, C.N.1
Chang, Y.M.2
Kuo, C.J.3
Lin, Y.S.4
Huang, H.S.5
Chung, I.F.6
-
32
-
-
0034953725
-
Medical subject headings used to search the biomedical literature
-
Coletti MH, Bleich HL: Medical subject headings used to search the biomedical literature. J Am Med Inform Assoc 2001, 8(4):317-323.
-
(2001)
J Am Med Inform Assoc
, vol.8
, Issue.4
, pp. 317-323
-
-
Coletti, M.H.1
Bleich, H.L.2
-
33
-
-
84856582104
-
ChEBI: A chemistry ontology and database
-
de Matos P, Dekker A, Ennis M, Hastings J, Haug K, Turner S, Steinbeck C: ChEBI: a chemistry ontology and database. Journal of cheminformatics 2010, 2(Suppl 1):P6-P6.
-
(2010)
Journal of Cheminformatics
, vol.2
, pp. P6-P6
-
-
De Matos, P.1
Dekker, A.2
Ennis, M.3
Hastings, J.4
Haug, K.5
Turner, S.6
Steinbeck, C.7
-
34
-
-
84895484578
-
Identifying nonelliptical entity mentions in a coordinated NP with ellipses
-
Chae J, Jung Y, Lee T, Jung S, Huh C, Kim G, Kim H, Oh H: Identifying nonelliptical entity mentions in a coordinated NP with ellipses. J Biomed Inform 2014, 47:139-152.
-
(2014)
J Biomed Inform
, vol.47
, pp. 139-152
-
-
Chae, J.1
Jung, Y.2
Lee, T.3
Jung, S.4
Huh, C.5
Kim, G.6
Kim, H.7
Oh, H.8
-
36
-
-
84888192341
-
Unsupervised biomedical named entity recognition: Experiments with clinical and biological texts
-
Zhang S, Elhadad N: Unsupervised biomedical named entity recognition: experiments with clinical and biological texts. J Biomed Inform 2013, 46(6):1088-1098.
-
(2013)
J Biomed Inform
, vol.46
, Issue.6
, pp. 1088-1098
-
-
Zhang, S.1
Elhadad, N.2
-
38
-
-
84876499465
-
Accelerating literature curation with text-mining tools: A case study of using PubTator to curate genes in PubMed abstracts
-
Wei CH, Harris BR, Li D, Berardini TZ, Huala E, Kao HY, Lu Z: Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database (Oxford) 2012, 2012: bas041.
-
(2012)
Database (Oxford)
, vol.2012
, pp. bas041
-
-
Wei, C.H.1
Harris, B.R.2
Li, D.3
Berardini, T.Z.4
Huala, E.5
Kao, H.Y.6
Lu, Z.7
-
39
-
-
80052774027
-
The gene normalization task in BioCreative III
-
Lu Z, Kao HY, Wei CH, Huang M, Liu J, Kuo CJ, Hsu CN, Tsai RT, Dai HJ, Okazaki N, Cho HC, Gerner M, Solt I, Agarwal S, Liu F, Vishnyakova D, Ruch P, Romacker M, Rinaldi F, Bhattacharya S, Srinivasan P, Liu H, Torii M, Matos S, Campos D, Verspoor K, Livingston KM, Wilbur WJ: The gene normalization task in BioCreative III. BMC Bioinformatics 2011, 12(Suppl 8):S2.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. S2
-
-
Lu, Z.1
Kao, H.Y.2
Wei, C.H.3
Huang, M.4
Liu, J.5
Kuo, C.J.6
Hsu, C.N.7
Tsai, R.T.8
Dai, H.J.9
Okazaki, N.10
Cho, H.C.11
Gerner, M.12
Solt, I.13
Agarwal, S.14
Liu, F.15
Vishnyakova, D.16
Ruch, P.17
Romacker, M.18
Rinaldi, F.19
Bhattacharya, S.20
Srinivasan, P.21
Liu, H.22
Torii, M.23
Matos, S.24
Campos, D.25
Verspoor, K.26
Livingston, K.M.27
Wilbur, W.J.28
more..
|