Most cited papers in Biomedical Text Mining and Ontologies
What are the most cited papers in Biomedical Text Mining and Ontologies?
The most cited paper in Biomedical Text Mining and Ontologies is "Research electronic data capture (REDCap)—A metadata-driven methodology and workflow process for providing translational research informatics support" (Paul A. Harris, ROBERT J. TAYLOR, Robert J. Thielke et al., 2008), with 53,362 citations. Next come "Gene Ontology: tool for the unification of biology" (45,425) and "STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets" (19,535).
Showing 50 of 98 papers. Every paper with more than 1,514 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Research electronic data capture (REDCap)—A metadata-driven methodology and workflow process for providing translational research informatics support Paul A. Harris, ROBERT J. TAYLOR, Robert J. Thielke et al. · Journal of Biomedical Informatics | Oct 2008 | 53,362 |
| 2 | Gene Ontology: tool for the unification of biology Michael Ashburner, Catherine A. Ball, Judith A. Blake et al. · Nature Genetics | May 2000 | 45,425 |
| 3 | STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Damian Szklarczyk, Annika L. Gable, David B. Lyon et al. · Nucleic Acids Research | 16 Nov 2018 | 19,535 |
| 4 | Haploview: analysis and visualization of LD and haplotype maps Jeffrey C. Barrett, Ben N. Fry, Julian Maller et al. · Bioinformatics | 5 Aug 2004 | 14,838 |
| 5 | A translation approach to portable ontology specifications Thomas Olaf Gruber · Knowledge Acquisition | Jun 1993 | 12,728 |
| 6 | Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research Ana Conesa, Stefan Götz, Juan Miguel García-Gómez et al. · Bioinformatics | 4 Aug 2005 | 12,162 |
| 7 | STRING v10: protein–protein interaction networks, integrated over the tree of life Damian Szklarczyk, Andrea Franceschini, Stefan Wyder et al. · Nucleic Acids Research | 28 Oct 2014 | 11,220 |
| 8 | In silico prediction of protein-protein interactions in human macrophages Oussema Souiai, Fatma Zahra Guerfali, Slimane Ben Miled et al. · BMC Research Notes | 2014 | 10,946 |
| 9 | KEGG: new perspectives on genomes, pathways, diseases and drugs Minoru I. Kanehisa, Miho Furumichi, Mao Tanabe et al. · Nucleic Acids Research | 26 Oct 2016 | 9,650 |
| 10 | DAVID: Database for Annotation, Visualization, and Integrated Discovery Glynn Dennis, Brad T. Sherman, Douglas A Hosack et al. · Genome biology | 3 Apr 2003 | 9,558 |
| 11 | Toward principles for the design of ontologies used for knowledge sharing? Thomas Olaf Gruber · International Journal of Human-Computer Studies | Nov 1995 | 7,721 |
| 12 | The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible Damian Szklarczyk, John H. Morris, Helen Victoria Cook et al. · Nucleic Acids Research | 11 Oct 2016 | 7,527 |
| 13 | Improving Bioscience Research Reporting: The ARRIVE Guidelines for Reporting Animal Research Carol Kilkenny, William J. Browne, Innes C. Cuthill et al. · PLoS Biology | 29 Jun 2010 | 7,456 |
| 14 | BioBERT: a pre-trained biomedical language representation model for biomedical text mining Jinhyuk Lee, Wonjin Yoon, Sungdong Kim et al. · Bioinformatics | 5 Sep 2019 | 7,445 |
| 15 | REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms Fran Supek, Matko Bošnjak, Nives Škunca et al. · PLoS ONE | 18 Jul 2011 | 7,079 |
| 16 | ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks Gabriela Bindea, Bernhard Mlecnik, Hubert Hackl et al. · Bioinformatics | 23 Feb 2009 | 6,728 |
| 17 | The cochrane database of systematic reviews John Geddes · Journal of Psychosomatic Research | Apr 1996 | 6,126 |
| 18 | Finding scientific topics Thomas L. Griffiths, Mark Steyvers · Proceedings of the National Academy of Sciences | 6 Apr 2004 | 6,099 |
| 19 | The Reactome pathway Knowledgebase Antonio Fabregat et al. · Nucleic Acids Research | 9 Dec 2015 | 6,015 |
| 20 | User's guide to correlation coefficients Haldun Akoğlu · Turkish Journal of Emergency Medicine | 7 Aug 2018 | 5,925 |
| 21 | The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses Gil Stelzer, Naomi Rosen, Inbar Plaschkes et al. · Current Protocols in Bioinformatics | Jun 2016 | 5,762 |
| 22 | ShinyGO: a graphical gene-set enrichment tool for animals and plants Xijin Ge, Dongmin Jung, Runan Yao · Bioinformatics | 23 Dec 2019 | 5,631 |
| 23 | PubChem Substance and Compound databases Sunghwan Kim, Paul A Thiessen, Evan Bolton et al. · Nucleic Acids Research | 22 Sep 2015 | 5,614 |
| 24 | KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases Chen Xie, Xizeng Mao, Jiaju Huang et al. · Nucleic Acids Research | 27 Jun 2011 | 5,545 |
| 25 | The Gene Ontology Resource: 20 years and still GOing strong Consortium, The Gene Ontology · Nucleic Acids Research | 17 Oct 2018 | 5,260 |
| 26 | KEGG for integration and interpretation of large-scale molecular data sets Minoru I. Kanehisa, Susumu Goto, Yoko Sato et al. · Nucleic Acids Research | 10 Nov 2011 | 5,051 |
| 27 | Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses Matthew E. Falagas, Eleni I. Pitsouni, George A. Malietzis et al. · The FASEB Journal | 20 Sep 2007 | 5,038 |
| 28 | The Gene Ontology (GO) database and informatics resource Gene Ontology Consortium · Nucleic Acids Research | 17 Dec 2003 | 4,775 |
| 29 | Ontology Development 101: A Guide to Creating Your First Ontology Natalya Fridman Noy, Deborah L. McGuinness | 2002 | 4,635 |
| 30 | ClinVar: improving access to variant interpretations and supporting evidence Melissa Landrum et al. · Nucleic Acids Research | 17 Nov 2017 | 4,603 |
| 31 | STRING v9.1: protein-protein interaction networks, with increased coverage and integration Andrea Franceschini, Damian Szklarczyk, Sune Pletscher-Frankild et al. · Nucleic Acids Research | 29 Nov 2012 | 4,592 |
| 32 | The Unified Medical Language System (UMLS): integrating biomedical terminology Olivier Bodenreider · Nucleic Acids Research | 17 Dec 2003 | 4,474 |
| 33 | BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks Steven Maere, K. Heymans, Martin T. R. Kuiper · Computer applications in the biosciences | 21 Jun 2005 | 4,346 |
| 34 | BioGRID: a general repository for interaction datasets C. Stark · Nucleic Acids Research | 28 Dec 2005 | 4,162 |
| 35 | Yago Fabian M. Suchanek, Gjergji Kasneci, Gerhard Weikum | 8 May 2007 | 3,972 |
| 36 | Gene Set Knowledge Discovery with Enrichr Zhuorui Xie, Allison M. Bailey, Maxim V. Kuleshov et al. · Current Protocols | Mar 2021 | 3,895 |
| 37 | ClinVar: public archive of relationships among sequence variation and human phenotype Melissa Landrum, Jennifer M. Lee, George R. Riley et al. · Nucleic Acids Research | 14 Nov 2013 | 3,790 |
| 38 | CDD: NCBI's conserved domain database Aron Marchler‐Bauer, Myra K. Derbyshire, Noreen R. Gonzales et al. · Nucleic Acids Research | 20 Nov 2014 | 3,664 |
| 39 | PubChem 2023 update Sunghwan Kim, Jie Chen, Tiejun Cheng et al. · Nucleic Acids Research | 13 Oct 2022 | 3,434 |
| 40 | Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature Christophe Destrieux, Bruce R. Fischl, Anders Martin Dale et al. · NeuroImage | 14 Jun 2010 | 3,250 |
| 41 | Data, information, knowledge and principle: back to metabolism in KEGG Minoru I. Kanehisa, Susumu Goto, Yoko Sato et al. · Nucleic Acids Research | 7 Nov 2013 | 3,218 |
| 42 | Thinking about Mechanisms Peter K Machamer, Lindley Darden, Carl F. Craver · Philosophy of Science | Mar 2000 | 3,173 |
| 43 | Networks of Scientific Papers Derek J. de Solla Price · Science | 30 Jul 1965 | 3,165 |
| 44 | Deep learning for healthcare: review, opportunities and challenges Riccardo Miotto, Fei Wang, Shuang Wang et al. · Briefings in Bioinformatics | 5 Apr 2017 | 3,149 |
| 45 | SciBERT: A Pretrained Language Model for Scientific Text Iz Beltagy, Kyle Lo, Arman Cohan | 2019 | 3,130 |
| 46 | CDD/SPARCLE: functional classification of proteins via subfamily domain architectures Aron Marchler‐Bauer et al. · Nucleic Acids Research | 29 Nov 2016 | 2,954 |
| 47 | Feature-rich part-of-speech tagging with a cyclic dependency network Kristina Toutanova, Dan Klein, Christopher D. Manning et al. | 2003 | 2,890 |
| 48 | DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants Janet Piñero, Álex Bravo, Núria Queralt-Rosiñach et al. · Nucleic Acids Research | 18 Oct 2016 | 2,874 |
| 49 | The Gene Ontology knowledgebase in 2023 Suzi Aleksander et al. · Genetics | 3 Mar 2023 | 2,868 |
| 50 | Introduction to the CoNLL-2003 shared task Erik F. Tjong Kim Sang, Fien De Meulder | 2003 | 2,825 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.