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An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology

CITE Title : An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology Personal Author(s) : Yu, Wei;Yesupriya, Ajay;Wulf, Anja;Qu, Junfeng;Khoury, Muin J;Gwinn, Marta; Published Date : Nov 09 2007 Source : BMC Bioinformatics. 2007; 8:436. URL : https://stacks.cdc.gov/view/cdc/3358 Yu, Wei et al. (2007). An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology. 8 Yu, Wei et al. "An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology" 8 (2007) Yu, Wei et al. "An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology" vol. 8, 2007 Export RIS Citation Information.

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Yu, Wei ;

Yesupriya, Ajay

Nov 09 2007 | BMC Bioinformatics. 2007; 8:436.

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BackgroundIdentifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specif...
Identification of methicillin-resistant Staphylococcus aureus within the Nation’s Veterans Affairs Medical Centers using natural language processing

CITE Title : Identification of methicillin-resistant Staphylococcus aureus within the Nation’s Veterans Affairs Medical Centers using natural language processing Personal Author(s) : Jones, Makoto;DuVall, Scott L;Spuhl, Joshua;Samore, Matthew H;Nielson, Christopher;Rubin, Michael; Published Date : Jul 11 2012 Source : BMC Med Inform Decis Mak. 2012; 12:34. URL : https://stacks.cdc.gov/view/cdc/22699 Jones, Makoto et al. (2012). Identification of methicillin-resistant Staphylococcus aureus within the Nation’s Veterans Affairs Medical Centers using natural language processing. 12 Jones, Makoto et al. "Identification of methicillin-resistant Staphylococcus aureus within the Nation’s Veterans Affairs Medical Centers using natural language processing" 12 (2012) Jones, Makoto et al. "Identification of methicillin-resistant Staphylococcus aureus within the Nation’s Veterans Affairs Medical Centers using natural language processing" vol. 12, 2012 Export RIS Citation Information.

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Jones, Makoto ;

DuVall, Scott L

Jul 11 2012 | BMC Med Inform Decis Mak. 2012; 12:34.

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BackgroundAccurate information is needed to direct healthcare systems’ efforts to control methicillin-resistant Staphylococcus aureus (MRSA). Assemb...
GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique

CITE Title : GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique Personal Author(s) : Yu, Wei;Clyne, Melinda;Dolan, Siobhan M;Yesupriya, Ajay;Wulf, Anja;Liu, Tiebin;Khoury, Muin J;Gwinn, Marta; Published Date : Apr 22 2008 Source : BMC Bioinformatics. 2008; 9:205. URL : https://stacks.cdc.gov/view/cdc/3359 Yu, Wei et al. (2008). GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique. 9 Yu, Wei et al. "GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique" 9 (2008) Yu, Wei et al. "GAPscreener: An automatic tool for screening human genetic association literature in PubMed using the support vector machine technique" vol. 9, 2008 Export RIS Citation Information.

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Yu, Wei ;

Clyne, Melinda

Apr 22 2008 | BMC Bioinformatics. 2008; 9:205.

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BackgroundSynthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into he...
The use of natural language processing to identify vaccine-related anaphylaxis at five health care systems in the Vaccine Safety Datalink

CITE Title : The use of natural language processing to identify vaccine-related anaphylaxis at five health care systems in the Vaccine Safety Datalink Personal Author(s) : Yu, Wei;Zheng, Chengyi;Xie, Fagen;Chen, Wansu;Mercado, Cheryl;Sy, Lina S.;Qian, Lei;Glenn, Sungching;Tseng, Hung F.;Lee, Gina;Duffy, Jonathan;McNeil, Michael M.;Daley, Matthew F.;Crane, Brad;McLean, Huong Q.;Jackson, Lisa A.;Jacobsen, Steven J.; Published Date : December 03 2019;2-2020; Source : Pharmacoepidemiol Drug Saf. 29(2):182-188 URL : https://stacks.cdc.gov/view/cdc/94616 Yu, Wei et al. (2019). The use of natural language processing to identify vaccine-related anaphylaxis at five health care systems in the Vaccine Safety Datalink. 29(2). Yu, Wei et al. "The use of natural language processing to identify vaccine-related anaphylaxis at five health care systems in the Vaccine Safety Datalink" 29, no. 2 (2019) Yu, Wei et al. "The use of natural language processing to identify vaccine-related anaphylaxis at five health care systems in the Vaccine Safety Datalink" vol. 29, no. 2, 2019 Export RIS Citation Information.

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Yu, Wei ;

Zheng, Chengyi

December 03 2019 | Pharmacoepidemiol Drug Saf. 29(2):182-188

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Purpose:The objective was to develop a natural language processing (NLP) algorithm to identify vaccine-related anaphylaxis from plain-text clinical no...
Large-scale automatic extraction of side effects associated with targeted anticancer drugs from full-text oncological articles

CITE Title : Large-scale automatic extraction of side effects associated with targeted anticancer drugs from full-text oncological articles Personal Author(s) : Xu, Rong;Wang, QuanQiu; Published Date : Mar 27 2015 Source : J Biomed Inform. 55:64-72. URL : https://stacks.cdc.gov/view/cdc/34602 Xu, Rong and Wang, QuanQiu (2015). Large-scale automatic extraction of side effects associated with targeted anticancer drugs from full-text oncological articles. 55 Xu, Rong and Wang, QuanQiu "Large-scale automatic extraction of side effects associated with targeted anticancer drugs from full-text oncological articles" 55 (2015) Xu, Rong and Wang, QuanQiu "Large-scale automatic extraction of side effects associated with targeted anticancer drugs from full-text oncological articles" vol. 55, 2015 Export RIS Citation Information.

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Xu, Rong ;

Wang, QuanQiu

Mar 27 2015 | J Biomed Inform. 55:64-72.

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Targeted anticancer drugs such as imatinib, trastuzumab and erlotinib dramatically improved treatment outcomes in cancer patients, however, these inno...
Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations

CITE Title : Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations Personal Author(s) : Yu, W.;Clyne, M.;Khoury, M. J.;Gwinn, M.; Published Date : Oct 27 2009 Source : Bioinformatics. 2009; 26(1):145-146. URL : https://stacks.cdc.gov/view/cdc/3783 Yu, W. et al. (2009). Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations. 26(1). Yu, W. et al. "Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations" 26, no. 1 (2009) Yu, W. et al. "Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations" vol. 26, no. 1, 2009 Export RIS Citation Information.

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Yu, W. ;

Clyne, M.

Oct 27 2009 | Bioinformatics. 2009; 26(1):145-146.

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We developed web-based applications that encourage the exploration of the literature on human genetic associations by using a database that is continu...
Natural language processing of electronic health records is superior to billing codes to identify symptom burden in hemodialysis patients.

CITE Title : Natural language processing of electronic health records is superior to billing codes to identify symptom burden in hemodialysis patients. Personal Author(s) : Chan, Lili;Beers, Kelly;Yau, Amy;Chauhan, Kinsuk;Duffy, Aine;Chaudhary, Kumardeep;Debnath, Neha;Saha, Aparna;Pattharanitima, Pattharawin;Cho, Judy;Kotanko, Peter;Federman, Alex;Coca, Steven;Van Vleck, Tielman;Nadkarni, Girish N.; Published Date : 2 2020;2-2020; Source : Kidney Int. 97(2):383-392 URL : https://stacks.cdc.gov/view/cdc/84937 Chan, Lili et al. (2020). Natural language processing of electronic health records is superior to billing codes to identify symptom burden in hemodialysis patients.. 97(2). Chan, Lili et al. "Natural language processing of electronic health records is superior to billing codes to identify symptom burden in hemodialysis patients." 97, no. 2 (2020) Chan, Lili et al. "Natural language processing of electronic health records is superior to billing codes to identify symptom burden in hemodialysis patients." vol. 97, no. 2, 2020 Export RIS Citation Information.

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Chan, Lili ;

Beers, Kelly

2 2020 | Kidney Int. 97(2):383-392

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Symptoms are common in patients on maintenance hemodialysis but identification is challenging. New informatics approaches including natural language p...
Contextualized Medication Information Extraction Using Transformer-based Deep Learning Architectures

CITE Title : Contextualized Medication Information Extraction Using Transformer-based Deep Learning Architectures Personal Author(s) : Chen, Aokun;Yu, Zehao;Yang, Xi;Guo, Yi;Bian, Jiang;Wu, Yonghui; Published Date : 6 2023;6-2023; Source : J Biomed Inform. 142:104370 URL : https://stacks.cdc.gov/view/cdc/153621 Chen, Aokun et al. (2023). Contextualized Medication Information Extraction Using Transformer-based Deep Learning Architectures. 142 Chen, Aokun et al. "Contextualized Medication Information Extraction Using Transformer-based Deep Learning Architectures" 142 (2023) Chen, Aokun et al. "Contextualized Medication Information Extraction Using Transformer-based Deep Learning Architectures" vol. 142, 2023 Export RIS Citation Information.

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Chen, Aokun ;

Yu, Zehao

6 2023 | J Biomed Inform. 142:104370

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ObjectiveTo develop a natural language processing (NLP) system to extract medications and contextual information that help understand drug changes. Th...
Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review

CITE Title : Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review Personal Author(s) : Kreimeyer, Kory;Foster, Matthew;Pandey, Abhishek;Arya, Nina;Halford, Gwendolyn;Jones, Sandra F;Forshee, Richard;Walderhaug, Mark;Botsis, Taxiarchis; Published Date : July 17 2017 Source : J Biomed Inform. 73:14-29 URL : https://stacks.cdc.gov/view/cdc/83255 Kreimeyer, Kory et al. (2017). Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review. 73 Kreimeyer, Kory et al. "Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review" 73 (2017) Kreimeyer, Kory et al. "Natural language processing systems for capturing and standardizing unstructured clinical information: A systematic review" vol. 73, 2017 Export RIS Citation Information.

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Kreimeyer, Kory ;

Foster, Matthew

July 17 2017 | J Biomed Inform. 73:14-29

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We followed a systematic approach based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses to identify existing clinical natura...
A UMLS-based spell checker for natural language processing in vaccine safety

CITE Title : A UMLS-based spell checker for natural language processing in vaccine safety Personal Author(s) : Tolentino, Herman D.;Matters, Michael D.;Walop, Wikke;Law, Barbara;Tong, Wesley;Liu, Fang;Fontelo, Paul;Kohl, Katrin;Payne, Daniel C.; Published Date : Feb 12 2007 Source : BMC Med Inform Decis Mak. 2007; 7:3. URL : https://stacks.cdc.gov/view/cdc/3476 Tolentino, Herman D. et al. (2007). A UMLS-based spell checker for natural language processing in vaccine safety. 7 Tolentino, Herman D. et al. "A UMLS-based spell checker for natural language processing in vaccine safety" 7 (2007) Tolentino, Herman D. et al. "A UMLS-based spell checker for natural language processing in vaccine safety" vol. 7, 2007 Export RIS Citation Information.

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Tolentino, Herman D. ;

Matters, Michael D.

Feb 12 2007 | BMC Med Inform Decis Mak. 2007; 7:3.

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BackgroundThe Institute of Medicine has identified patient safety as a key goal for health care in the United States. Detecting vaccine adverse events...
ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research

CITE Title : ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research Personal Author(s) : Oniani, David;Parmanto, Bambang;Saptono, Andi;Bove, Allyn;Freburger, Janet;Visweswaran, Shyam;Cappella, Nickie;McLay, Brian;Silverstein, Jonathan C.;Becich, Michael J.;Delitto, Anthony;Skidmore, Elizabeth;Wang, Yanshan; Published Date : 9 2023;9-2023; Source : Int J Med Inform. 177:105144 URL : https://stacks.cdc.gov/view/cdc/133513 Oniani, David et al. (2023). ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research. 177 Oniani, David et al. "ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research" 177 (2023) Oniani, David et al. "ReDWINE: A Clinical Datamart with Text Analytical Capabilities to Facilitate Rehabilitation Research" vol. 177, 2023 Export RIS Citation Information.

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Oniani, David ;

Parmanto, Bambang

9 2023 | Int J Med Inform. 177:105144

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Rehabilitation research focuses on determining the components of a treatment intervention, the mechanism of how these components lead to recovery and ...
Class Imbalance in Out-of-Distribution Datasets: Improving the Robustness of the TextCNN for the Classification of Rare Cancer Types

CITE Title : Class Imbalance in Out-of-Distribution Datasets: Improving the Robustness of the TextCNN for the Classification of Rare Cancer Types Personal Author(s) : De Angeli, Kevin;Gao, Shang;Danciu, Ioana;Durbin, Eric B.;Wu, Xiao-Cheng;Stroup, Antoinette;Doherty, Jennifer;Schwartz, Stephen;Wiggins, Charles;Damesyn, Mark;Coyle, Linda;Penberthy, Lynne;Tourassi, Georgia D.;Yoon, Hong-Jun; Published Date : 1 2022;1-2022; Source : J Biomed Inform. 125:103957 URL : https://stacks.cdc.gov/view/cdc/123189 De Angeli, Kevin et al. (2022). Class Imbalance in Out-of-Distribution Datasets: Improving the Robustness of the TextCNN for the Classification of Rare Cancer Types. 125 De Angeli, Kevin et al. "Class Imbalance in Out-of-Distribution Datasets: Improving the Robustness of the TextCNN for the Classification of Rare Cancer Types" 125 (2022) De Angeli, Kevin et al. "Class Imbalance in Out-of-Distribution Datasets: Improving the Robustness of the TextCNN for the Classification of Rare Cancer Types" vol. 125, 2022 Export RIS Citation Information.

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De Angeli, Kevin ;

Gao, Shang

1 2022 | J Biomed Inform. 125:103957

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In the last decade, the widespread adoption of electronic health record documentation has created huge opportunities for information mining. Natural l...
Optimal Vocabulary Selection Approaches for Privacy-Preserving Deep NLP Model Training for Information Extraction and Cancer Epidemiology

CITE Title : Optimal Vocabulary Selection Approaches for Privacy-Preserving Deep NLP Model Training for Information Extraction and Cancer Epidemiology Personal Author(s) : Yoon, Hong-Jun;Stanley, Christopher;Christian, J. Blair;Klasky, Hilda B.;Blanchard, Andrew E.;Durbin, Eric B.;Wu, Xiao-Cheng;Stroup, Antoinette;Doherty, Jennifer;Schwartz, Stephen;Wiggins, Charles;Damesyn, Mark;Coyle, Linda;Tourassi, Georgia D.; Published Date : 2022;2022; Source : Cancer Biomark. 33(2):185-198 URL : https://stacks.cdc.gov/view/cdc/120302 Yoon, Hong-Jun et al. (2022). Optimal Vocabulary Selection Approaches for Privacy-Preserving Deep NLP Model Training for Information Extraction and Cancer Epidemiology. 33(2). Yoon, Hong-Jun et al. "Optimal Vocabulary Selection Approaches for Privacy-Preserving Deep NLP Model Training for Information Extraction and Cancer Epidemiology" 33, no. 2 (2022) Yoon, Hong-Jun et al. "Optimal Vocabulary Selection Approaches for Privacy-Preserving Deep NLP Model Training for Information Extraction and Cancer Epidemiology" vol. 33, no. 2, 2022 Export RIS Citation Information.

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Yoon, Hong-Jun ;

Stanley, Christopher

2022 | Cancer Biomark. 33(2):185-198

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BACKGROUND:With the use of artificial intelligence and machine learning techniques for biomedical informatics, security and privacy concerns over the ...
Leveraging Automated Approaches to Categorize Birth Defects from Abstracted Birth Hospitalization Data

CITE Title : Leveraging Automated Approaches to Categorize Birth Defects from Abstracted Birth Hospitalization Data Personal Author(s) : Newton, Suzanne M.;Distler, Samantha;Woodworth, Kate R.;Chang, Daniel;Roth, Nicole M.;Board, Amy;Hutcherson, Hailee;Cragan, Janet D.;Gilboa, Suzanne M.;Tong, Van T.; Published Date : 1 2024;1-2024; Source : Birth Defects Res. 116(1):e2267 URL : https://stacks.cdc.gov/view/cdc/175209 Newton, Suzanne M. et al. (2024). Leveraging Automated Approaches to Categorize Birth Defects from Abstracted Birth Hospitalization Data. 116(1). Newton, Suzanne M. et al. "Leveraging Automated Approaches to Categorize Birth Defects from Abstracted Birth Hospitalization Data" 116, no. 1 (2024) Newton, Suzanne M. et al. "Leveraging Automated Approaches to Categorize Birth Defects from Abstracted Birth Hospitalization Data" vol. 116, no. 1, 2024 Export RIS Citation Information.

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Newton, Suzanne M. ;

Distler, Samantha

1 2024 | Birth Defects Res. 116(1):e2267

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Background:The Surveillance for Emerging Threats to Pregnant People and Infants Network (SET-NET) collects data abstracted from medical records and bi...
Identifying Social Determinants of Health from Clinical Narratives: A Study of Performance, Documentation Ratio, and Potential Bias

CITE Title : Identifying Social Determinants of Health from Clinical Narratives: A Study of Performance, Documentation Ratio, and Potential Bias Personal Author(s) : Yu, Zehao;Peng, Cheng;Yang, Xi;Dang, Chong;Adekkanattu, Prakash;Patra, Braja Gopal;Peng, Yifan;Pathak, Jyotishman;Wilson, Debbie L.;Chang, Ching-Yuan;Lo-Ciganic, Wei-Hsuan;George, Thomas J.;Hogan, William R.;Guo, Yi;Bian, Jiang;Wu, Yonghui; Published Date : 5 2024;5-2024; Source : J Biomed Inform. 153:104642 URL : https://stacks.cdc.gov/view/cdc/157107 Yu, Zehao et al. (2024). Identifying Social Determinants of Health from Clinical Narratives: A Study of Performance, Documentation Ratio, and Potential Bias. 153 Yu, Zehao et al. "Identifying Social Determinants of Health from Clinical Narratives: A Study of Performance, Documentation Ratio, and Potential Bias" 153 (2024) Yu, Zehao et al. "Identifying Social Determinants of Health from Clinical Narratives: A Study of Performance, Documentation Ratio, and Potential Bias" vol. 153, 2024 Export RIS Citation Information.

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Yu, Zehao ;

Peng, Cheng

5 2024 | J Biomed Inform. 153:104642

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ObjectiveTo develop a natural language processing (NLP) package to extract social determinants of health (SDoH) from clinical narratives, examine the ...
The use of natural language processing to identify Tdap-related local reactions at five health care systems in the Vaccine Safety Datalink

CITE Title : The use of natural language processing to identify Tdap-related local reactions at five health care systems in the Vaccine Safety Datalink Personal Author(s) : Zheng, Chengyi;Yu, Wei;Xie, Fagen;Chen, Wansu;Mercado, Cheryl;Sy, Lina S.;Qian, Lei;Glenn, Sungching;Lee, Gina;Tseng, Hung Fu;Duffy, Jonathan;Jackson, Lisa A.;Daley, Matthew F.;Crane, Brad;McLean, Huong Q.;Jacobsen, Steven J.; Published Date : 7 2019;7-2019; Source : Int J Med Inform. 127:27-34 URL : https://stacks.cdc.gov/view/cdc/80063 Zheng, Chengyi et al. (2019). The use of natural language processing to identify Tdap-related local reactions at five health care systems in the Vaccine Safety Datalink. 127 Zheng, Chengyi et al. "The use of natural language processing to identify Tdap-related local reactions at five health care systems in the Vaccine Safety Datalink" 127 (2019) Zheng, Chengyi et al. "The use of natural language processing to identify Tdap-related local reactions at five health care systems in the Vaccine Safety Datalink" vol. 127, 2019 Export RIS Citation Information.

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Zheng, Chengyi ;

Yu, Wei

7 2019 | Int J Med Inform. 127:27-34

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Objective:Local reactions are the most common vaccine-related adverse event. There is no specific diagnosis code for local reaction due to vaccination...
What Do You Think Caused Your ALS? An Analysis of the CDC National Amyotrophic Lateral Sclerosis Patient Registry Qualitative Risk Factor Data Using Artificial Intelligence and Qualitative Methodology

CITE Title : What Do You Think Caused Your ALS? An Analysis of the CDC National Amyotrophic Lateral Sclerosis Patient Registry Qualitative Risk Factor Data Using Artificial Intelligence and Qualitative Methodology Personal Author(s) : Boyce, Danielle;Raymond, Jaime;Larson, Theodore C.;Kirkland, Eddie;Horton, D. Kevin;Mehta, Paul; Published Date : 8-2024 Source : Amyotroph Lateral Scler Frontotemporal Degener. 25(5-6):615-624 URL : https://stacks.cdc.gov/view/cdc/159581 Boyce, Danielle et al. (2024). What Do You Think Caused Your ALS? An Analysis of the CDC National Amyotrophic Lateral Sclerosis Patient Registry Qualitative Risk Factor Data Using Artificial Intelligence and Qualitative Methodology. 25 Boyce, Danielle et al. "What Do You Think Caused Your ALS? An Analysis of the CDC National Amyotrophic Lateral Sclerosis Patient Registry Qualitative Risk Factor Data Using Artificial Intelligence and Qualitative Methodology" 25 (2024) Boyce, Danielle et al. "What Do You Think Caused Your ALS? An Analysis of the CDC National Amyotrophic Lateral Sclerosis Patient Registry Qualitative Risk Factor Data Using Artificial Intelligence and Qualitative Methodology" vol. 25, 2024 Export RIS Citation Information.

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Boyce, Danielle ;

Raymond, Jaime

8-2024 | Amyotroph Lateral Scler Frontotemporal Degener. 25(5-6):615-624

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Objective:Amyotrophic lateral sclerosis (ALS) is an incurable progressive neurodegenerative disease with a significant health burden and poorly unders...