A citation-based method for searching scientific literature

Dina Demner-Fushman, Willie J Rogers, Alan R Aronson. J Am Med Inform Assoc 2017
Times Cited: 57







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



Times Cited
  Times     Co-cited
Similarity



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
761
36

An overview of MetaMap: historical perspective and recent advances.
Alan R Aronson, François-Michel Lang. J Am Med Inform Assoc 2010
548
29

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
21

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
375
17

A simple algorithm for identifying negated findings and diseases in discharge summaries.
W W Chapman, W Bridewell, P Hanbury, G F Cooper, B G Buchanan. J Biomed Inform 2001
440
17


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
110
14

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
430
12

ConText: an algorithm for determining negation, experiencer, and temporal status from clinical reports.
Henk Harkema, John N Dowling, Tyler Thornblade, Wendy W Chapman. J Biomed Inform 2009
155
10

The Unified Medical Language System.
D A Lindberg, B L Humphreys, A T McCray. Methods Inf Med 1993
590
10

Clinical information extraction applications: A literature review.
Yanshan Wang, Liwei Wang, Majid Rastegar-Mojarad, Sungrim Moon, Feichen Shen, Naveed Afzal, Sijia Liu, Yuqun Zeng, Saeed Mehrabi, Sunghwan Sohn,[...]. J Biomed Inform 2018
192
10

Long short-term memory.
S Hochreiter, J Schmidhuber. Neural Comput 1997
10

DNorm: disease name normalization with pairwise learning to rank.
Robert Leaman, Rezarta Islamaj Dogan, Zhiyong Lu. Bioinformatics 2013
181
8

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

NCBI disease corpus: a resource for disease name recognition and concept normalization.
Rezarta Islamaj Doğan, Robert Leaman, Zhiyong Lu. J Biomed Inform 2014
133
8

A general natural-language text processor for clinical radiology.
C Friedman, P O Alderson, J H Austin, J J Cimino, S B Johnson. J Am Med Inform Assoc 1994
393
8

Negation's not solved: generalizability versus optimizability in clinical natural language processing.
Stephen Wu, Timothy Miller, James Masanz, Matt Coarr, Scott Halgrim, David Carrell, Cheryl Clark. PLoS One 2014
43
9

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
66
7

Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review.
Kory Kreimeyer, Matthew Foster, Abhishek Pandey, Nina Arya, Gwendolyn Halford, Sandra F Jones, Richard Forshee, Mark Walderhaug, Taxiarchis Botsis. J Biomed Inform 2017
153
7

ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis.
Cole A Deisseroth, Johannes Birgmeier, Ethan E Bodle, Jennefer N Kohler, Dena R Matalon, Yelena Nazarenko, Casie A Genetti, Catherine A Brownstein, Klaus Schmitz-Abe, Kelly Schoch,[...]. Genet Med 2019
29
13

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, Daniel Danis, Jean-Philippe Gourdine, Michael Gargano, Nomi L Harris, Nicolas Matentzoglu, Julie A McMurry,[...]. Nucleic Acids Res 2019
293
7

Comparing deep learning and concept extraction based methods for patient phenotyping from clinical narratives.
Sebastian Gehrmann, Franck Dernoncourt, Yeran Li, Eric T Carlson, Joy T Wu, Jonathan Welt, John Foote, Edward T Moseley, David W Grant, Patrick D Tyler,[...]. PLoS One 2018
55
7

A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature.
Benjamin Nye, Junyi Jessy Li, Roma Patel, Yinfei Yang, Iain J Marshall, Ani Nenkova, Byron C Wallace. Proc Conf Assoc Comput Linguist Meet 2018
24
16

Comparison of MetaMap and cTAKES for entity extraction in clinical notes.
Ruth Reátegui, Sylvie Ratté. BMC Med Inform Decis Mak 2018
20
20

What can natural language processing do for clinical decision support?
Dina Demner-Fushman, Wendy W Chapman, Clement J McDonald. J Biomed Inform 2009
229
5

De-identification of patient notes with recurrent neural networks.
Franck Dernoncourt, Ji Young Lee, Ozlem Uzuner, Peter Szolovits. J Am Med Inform Assoc 2017
83
5

The FAIR Guiding Principles for scientific data management and stewardship.
Mark D Wilkinson, Michel Dumontier, I Jsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E Bourne,[...]. Sci Data 2016
5

A survey of current work in biomedical text mining.
Aaron M Cohen, William R Hersh. Brief Bioinform 2005
254
5

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.
Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall,[...]. Nat Biotechnol 2007
5

Approximate subgraph matching-based literature mining for biomedical events and relations.
Haibin Liu, Lawrence Hunter, Vlado Kešelj, Karin Verspoor. PLoS One 2013
21
14

Document-level classification of CT pulmonary angiography reports based on an extension of the ConText algorithm.
Brian E Chapman, Sean Lee, Hyunseok Peter Kang, Wendy W Chapman. J Biomed Inform 2011
61
5

DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx.
Saeed Mehrabi, Anand Krishnan, Sunghwan Sohn, Alexandra M Roch, Heidi Schmidt, Joe Kesterson, Chris Beesley, Paul Dexter, C Max Schmidt, Hongfang Liu,[...]. J Biomed Inform 2015
29
10

Extending the NegEx lexicon for multiple languages.
Wendy W Chapman, Dieter Hillert, Sumithra Velupillai, Maria Kvist, Maria Skeppstedt, Brian E Chapman, Mike Conway, Melissa Tharp, Danielle L Mowery, Louise Deleger. Stud Health Technol Inform 2013
34
8

Sophia: A Expedient UMLS Concept Extraction Annotator.
Guy Divita, Qing T Zeng, Adi V Gundlapalli, Scott Duvall, Jonathan Nebeker, Matthew H Samore. AMIA Annu Symp Proc 2014
15
20

NOBLE - Flexible concept recognition for large-scale biomedical natural language processing.
Eugene Tseytlin, Kevin Mitchell, Elizabeth Legowski, Julia Corrigan, Girish Chavan, Rebecca S Jacobson. BMC Bioinformatics 2016
47
6

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
79
5


Deep learning with word embeddings improves biomedical named entity recognition.
Maryam Habibi, Leon Weber, Mariana Neves, David Luis Wiegandt, Ulf Leser. Bioinformatics 2017
122
5

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
70
5

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.
Ada Hamosh, Alan F Scott, Joanna S Amberger, Carol A Bocchini, Victor A McKusick. Nucleic Acids Res 2005
5

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Christopher J Mungall, Julie A McMurry, Sebastian Köhler, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad,[...]. Nucleic Acids Res 2017
145
5

Evaluating temporal relations in clinical text: 2012 i2b2 Challenge.
Weiyi Sun, Anna Rumshisky, Ozlem Uzuner. J Am Med Inform Assoc 2013
142
5


A study of deep learning approaches for medication and adverse drug event extraction from clinical text.
Qiang Wei, Zongcheng Ji, Zhiheng Li, Jingcheng Du, Jingqi Wang, Jun Xu, Yang Xiang, Firat Tiryaki, Stephen Wu, Yaoyun Zhang,[...]. J Am Med Inform Assoc 2020
27
11

Ensembles of natural language processing systems for portable phenotyping solutions.
Cong Liu, Casey N Ta, James R Rogers, Ziran Li, Junghwan Lee, Alex M Butler, Ning Shang, Fabricio Sampaio Peres Kury, Liwei Wang, Feichen Shen,[...]. J Biomed Inform 2019
8
37

A simple algorithm for identifying abbreviation definitions in biomedical text.
Ariel S Schwartz, Marti A Hearst. Pac Symp Biocomput 2003
119
5

SNOMED-CT: The advanced terminology and coding system for eHealth.
Kevin Donnelly. Stud Health Technol Inform 2006
158
5

SemMedDB: a PubMed-scale repository of biomedical semantic predications.
Halil Kilicoglu, Dongwook Shin, Marcelo Fiszman, Graciela Rosemblat, Thomas C Rindflesch. Bioinformatics 2012
111
5

deepBioWSD: effective deep neural word sense disambiguation of biomedical text data.
Ahmad Pesaranghader, Stan Matwin, Marina Sokolova, Ali Pesaranghader. J Am Med Inform Assoc 2019
8
37


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.