A citation-based method for searching scientific literature

Rezarta Islamaj Doğan, Robert Leaman, Zhiyong Lu. J Biomed Inform 2014
Times Cited: 135







List of co-cited articles
454 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


BioCreative V CDR task corpus: a resource for chemical disease relation extraction.
Jiao Li, Yueping Sun, Robin J Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J Mattingly, Thomas C Wiegers, Zhiyong Lu. Database (Oxford) 2016
83
49

DNorm: disease name normalization with pairwise learning to rank.
Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu. Bioinformatics 2013
184
35

BioBERT: a pre-trained biomedical language representation model for biomedical text mining.
Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, Jaewoo Kang. Bioinformatics 2020
474
33


2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text.
Özlem Uzuner, Brett R South, Shuying Shen, Scott L DuVall. J Am Med Inform Assoc 2011
379
27


LINNAEUS: a species name identification system for biomedical literature.
Martin Gerner, Goran Nenadic, Casey M Bergman. BMC Bioinformatics 2010
126
23

Deep learning with word embeddings improves biomedical named entity recognition.
Maryam Habibi, Leon Weber, Mariana Neves, David Luis Wiegandt, Ulf Leser. Bioinformatics 2017
130
23

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.
Guergana K Savova, James J Masanz, Philip V Ogren, Jiaping Zheng, Sunghwan Sohn, Karin C Kipper-Schuler, Christopher G Chute. J Am Med Inform Assoc 2010
773
22

The CHEMDNER corpus of chemicals and drugs and its annotation principles.
Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe,[...]. J Cheminform 2015
69
30

Overview of BioCreative II gene mention recognition.
Larry Smith, Lorraine K Tanabe, Rie Johnson nee Ando, Cheng-Ju Kuo, I-Fang Chung, Chun-Nan Hsu, Yu-Shi Lin, Roman Klinger, Christoph M Friedrich, Kuzman Ganchev,[...]. Genome Biol 2008
164
20

Long short-term memory.
S Hochreiter, J Schmidhuber. Neural Comput 1997
20



An overview of MetaMap: historical perspective and recent advances.
Alan R Aronson, François-Michel Lang. J Am Med Inform Assoc 2010
555
16

PubTator: a web-based text mining tool for assisting biocuration.
Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu. Nucleic Acids Res 2013
259
16

The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text.
Evangelos Pafilis, Sune P Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, Lars Juhl Jensen. PLoS One 2013
62
25

CHEMDNER: The drugs and chemical names extraction challenge.
Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, Alfonso Valencia. J Cheminform 2015
74
20

MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database.
Allan Peter Davis, Thomas C Wiegers, Michael C Rosenstein, Carolyn J Mattingly. Database (Oxford) 2012
89
15

Cross-type biomedical named entity recognition with deep multi-task learning.
Xuan Wang, Yu Zhang, Xiang Ren, Yuhao Zhang, Marinka Zitnik, Jingbo Shang, Curtis Langlotz, Jiawei Han. Bioinformatics 2019
40
35

Evaluating the state of the art in disorder recognition and normalization of the clinical narrative.
Sameer Pradhan, Noémie Elhadad, Brett R South, David Martinez, Lee Christensen, Amy Vogel, Hanna Suominen, Wendy W Chapman, Guergana Savova. J Am Med Inform Assoc 2015
67
19

Concept annotation in the CRAFT corpus.
Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, K Bretonnel Cohen, Karin Verspoor, Judith A Blake,[...]. BMC Bioinformatics 2012
89
14

The DDI corpus: an annotated corpus with pharmacological substances and drug-drug interactions.
María Herrero-Zazo, Isabel Segura-Bedmar, Paloma Martínez, Thierry Declerck. J Biomed Inform 2013
110
13

CollaboNet: collaboration of deep neural networks for biomedical named entity recognition.
Wonjin Yoon, Chan Ho So, Jinhyuk Lee, Jaewoo Kang. BMC Bioinformatics 2019
23
56

BANNER: an executable survey of advances in biomedical named entity recognition.
Robert Leaman, Graciela Gonzalez. Pac Symp Biocomput 2008
192
12

MIMIC-III, a freely accessible critical care database.
Alistair E W Johnson, Tom J Pollard, Lu Shen, Li-Wei H Lehman, Mengling Feng, Mohammad Ghassemi, Benjamin Moody, Peter Szolovits, Leo Anthony Celi, Roger G Mark. Sci Data 2016
12

Challenges in clinical natural language processing for automated disorder normalization.
Robert Leaman, Ritu Khare, Zhiyong Lu. J Biomed Inform 2015
45
24

GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains.
Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu. Biomed Res Int 2015
85
12

BioInfer: a corpus for information extraction in the biomedical domain.
Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski. BMC Bioinformatics 2007
137
11

CLAMP - a toolkit for efficiently building customized clinical natural language processing pipelines.
Ergin Soysal, Jingqi Wang, Min Jiang, Yonghui Wu, Serguei Pakhomov, Hongfang Liu, Hua Xu. J Am Med Inform Assoc 2018
118
11

The EU-ADR corpus: annotated drugs, diseases, targets, and their relationships.
Erik M van Mulligen, Annie Fourrier-Reglat, David Gurwitz, Mariam Molokhia, Ainhoa Nieto, Gianluca Trifiro, Jan A Kors, Laura I Furlong. J Biomed Inform 2012
47
21

Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task.
Chih-Hsuan Wei, Yifan Peng, Robert Leaman, Allan Peter Davis, Carolyn J Mattingly, Jiao Li, Thomas C Wiegers, Zhiyong Lu. Database (Oxford) 2016
76
13

An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition.
Ling Luo, Zhihao Yang, Pei Yang, Yin Zhang, Lei Wang, Hongfei Lin, Jian Wang. Bioinformatics 2018
45
22

Overview of BioCreative II gene normalization.
Alexander A Morgan, Zhiyong Lu, Xinglong Wang, Aaron M Cohen, Juliane Fluck, Patrick Ruch, Anna Divoli, Katrin Fundel, Robert Leaman, Jörg Hakenberg,[...]. Genome Biol 2008
169
9

SR4GN: a species recognition software tool for gene normalization.
Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu. PLoS One 2012
47
19

GENIA corpus--semantically annotated corpus for bio-textmining.
J-D Kim, T Ohta, Y Tateisi, J Tsujii. Bioinformatics 2003
236
9

Gimli: open source and high-performance biomedical name recognition.
David Campos, Sérgio Matos, José Luís Oliveira. BMC Bioinformatics 2013
41
21

A transition-based joint model for disease named entity recognition and normalization.
Yinxia Lou, Yue Zhang, Tao Qian, Fei Li, Shufeng Xiong, Donghong Ji. Bioinformatics 2017
18
50

Medical Subject Headings (MeSH).
C E Lipscomb. Bull Med Libr Assoc 2000
319
9


ChemSpot: a hybrid system for chemical named entity recognition.
Tim Rocktäschel, Michael Weidlich, Ulf Leser. Bioinformatics 2012
91
8


tmVar: a text mining approach for extracting sequence variants in biomedical literature.
Chih-Hsuan Wei, Bethany R Harris, Hung-Yu Kao, Zhiyong Lu. Bioinformatics 2013
86
9

Abbreviation definition identification based on automatic precision estimates.
Sunghwan Sohn, Donald C Comeau, Won Kim, W John Wilbur. BMC Bioinformatics 2008
42
19

A neural network multi-task learning approach to biomedical named entity recognition.
Gamal Crichton, Sampo Pyysalo, Billy Chiu, Anna Korhonen. BMC Bioinformatics 2017
33
24

Semantic annotation in biomedicine: the current landscape.
Jelena Jovanović, Ebrahim Bagheri. J Biomed Semantics 2017
22
36

AuDis: an automatic CRF-enhanced disease normalization in biomedical text.
Hsin-Chun Lee, Yi-Yu Hsu, Hung-Yu Kao. Database (Oxford) 2016
12
58

EDGAR: extraction of drugs, genes and relations from the biomedical literature.
T C Rindflesch, L Tanabe, J N Weinstein, L Hunter. Pac Symp Biocomput 2000
115
7


Extracting information from textual documents in the electronic health record: a review of recent research.
S M Meystre, G K Savova, K C Kipper-Schuler, J F Hurdle. Yearb Med Inform 2008
344
7


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.