Framework for a Protein Ontology. - Darren A. Natale; Cecilia N. Arighi; Winona C. Barker; Judith A. Blake; Ti-Cheng Chang; Zhang-Zhi Hu; Hongfang Liu; Barry Smith 001; Cathy H. Wu (BMC Bioinform., 2007)

Functional Annotation of Protein Isoforms and Modified Forms. - Harold J. Drabkin; Cecilia N. Arighi; Cathy H. Wu; Judith A. Blake (BIOCOMP, 2008)

TGF-beta signaling proteins and the Protein Ontology. - Cecilia N. Arighi; Hongfang Liu; Darren A. Natale; Winona C. Barker; Harold J. Drabkin; Judith A. Blake; Barry Smith 001; Cathy H. Wu (BMC Bioinform., 2009)

An improved ontological representation of dendritic cells as a paradigm for all cell types. - Anna Maria Masci; Cecilia N. Arighi; Alexander D. Diehl; Anne E. Lieberman; Chris Mungall; Richard H. Scheuermann; Barry Smith 001; Lindsay G. Cowell (BMC Bioinform., 2009)

An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents. - Luis D. Lopez; Jingyi Yu; Cecilia N. Arighi; Hongzhan Huang; Hagit Shatkay; Cathy H. Wu (BIBM, 2011)

Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools. - Cecilia N. Arighi; Darren A. Natale; Judith A. Blake; Carol J. Bult; Michael Caudy; Alexander D. Diehl; Harold J. Drabkin; Peter D'Eustachio; Alexei V. Evsikov; Hongzhan Huang; Natalia V. Roberts; Alan Ruttenberg; et al. (ICBO, 2011)

Overview of the BioCreative III Workshop. - Cecilia N. Arighi; Zhiyong Lu; Martin Krallinger; Kevin Bretonnel Cohen; W. John Wilbur; Alfonso Valencia; Lynette Hirschman; Cathy H. Wu (BMC Bioinform., 2011)

BioCreative III interactive task: an overview. - Cecilia N. Arighi; Phoebe M. Roberts; Shashank Agarwal; Sanmitra Bhattacharya; Gianni Cesareni; Andrew Chatr-aryamontri; Simon Clematide; Pascale Gaudet; Michelle G. Giglio; Ian Harrow; Eva Huala; Martin Krallinger; et al. (BMC Bioinform., 2011)

The Representation of Protein Complexes in the Protein Ontology (PRO). - Carol J. Bult; Harold J. Drabkin; Alexei V. Evsikov; Darren A. Natale; Cecilia N. Arighi; Natalia V. Roberts; Alan Ruttenberg; Peter D'Eustachio; Barry Smith 001; Judith A. Blake; Cathy H. Wu (BMC Bioinform., 2011)

The Protein Ontology: a structured representation of protein forms and complexes. - Darren A. Natale; Cecilia N. Arighi; Winona C. Barker; Judith A. Blake; Carol J. Bult; Michael Caudy; Harold J. Drabkin; Peter D'Eustachio; Alexei V. Evsikov; Hongzhan Huang; Jules Nchoutmboube; Natalia V. Roberts; et al. (Nucleic Acids Res., 2011)

Robust segmentation of biomedical figures for image-based document retrieval. - Luis D. Lopez; Jingyi Yu; Catalina O. Tudor; Cecilia N. Arighi; Hongzhan Huang; K. Vijay-Shanker; Cathy H. Wu (BIBM, 2012)

Pathway curation: Application of text-mining tools eGIFT and RLIMS-P. - Carl J. Schmidt; Liang Sun; Cecilia N. Arighi; Keith Decker; K. Vijay-Shanker; Manabu Torii; Catalina O. Tudor; Cathy H. Wu; Peter D'Eustachio (BIBM Workshops, 2012)

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. - Pascale Gaudet; Cecilia N. Arighi; Frederic B. Bastian; Alex Bateman; Judith A. Blake; J. Michael Cherry; Peter D'Eustachio; Robert D. Finn; Michelle G. Giglio; Lynette Hirschman; Renate Kania; William Klimke; et al. (Database J. Biol. Databases Curation, 2012)

Text mining for the biocuration workflow. - Lynette Hirschman; Gully A. P. C. Burns; Martin Krallinger; Cecilia N. Arighi; K. Bretonnel Cohen; Alfonso Valencia; Cathy H. Wu; Andrew Chatr-aryamontri; Karen G. Dowell; Eva Huala; Anália Lourenço; Robert S. Nash; et al. (Database J. Biol. Databases Curation, 2012)

The eFIP system for text mining of protein interaction networks of phosphorylated proteins. - Catalina O. Tudor; Cecilia N. Arighi; Qinghua Wang 003; Cathy H. Wu; K. Vijay-Shanker (Database J. Biol. Databases Curation, 2012)

Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees. - Qinghua Wang 003; Cecilia N. Arighi; Benjamin L. King; Shawn W. Polson; James Vincent; Chuming Chen; Hongzhan Huang; Brewster F. Kingham; Shallee T. Page; Marc Farnum Rendino; William Kelley Thomas; Daniel W. Udwary; et al. (Database J. Biol. Databases Curation, 2012)

BioCreative-2012 Virtual Issue. - Cathy H. Wu; Cecilia N. Arighi; Kevin Bretonnel Cohen; Lynette Hirschman; Martin Krallinger; Zhiyong Lu; Carolyn J. Mattingly; Alfonso Valencia; Thomas C. Wiegers; W. John Wilbur (Database J. Biol. Databases Curation, 2012)

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature. - Luis D. Lopez; Jingyi Yu; Cecilia N. Arighi; Manabu Torii; K. Vijay-Shanker; Hongzhan Huang; Cathy H. Wu (BCB, 2013)

Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. - Manabu Torii; Cecilia N. Arighi; Qinghua Wang 003; Cathy H. Wu; K. Vijay-Shanker (BCB, 2013)

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task. - Cecilia N. Arighi; Ben Carterette; K. Bretonnel Cohen; Martin Krallinger; W. John Wilbur; Petra Fey; Robert J. Dodson; Laurel Cooper; Ceri E. Van Slyke; Wasila M. Dahdul; Paula M. Mabee; Donghui Li; et al. (Database J. Biol. Databases Curation, 2013)

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint. - Karen Ross; Cecilia N. Arighi; Jia Ren; Hongzhan Huang; Cathy H. Wu (Database J. Biol. Databases Curation, 2013)

A framework for biomedical figure segmentation towards image-based document retrieval. - Luis D. Lopez; Jingyi Yu; Cecilia N. Arighi; Catalina O. Tudor; Manabu Torii; Hongzhan Huang; K. Vijay-Shanker; Cathy H. Wu (BMC Syst. Biol., 2013)

Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis. - Karen Ross; Catalina O. Tudor; Gang Li 021; Ruoyao Ding; Irem Çelen; Julie Cowart; Cecilia N. Arighi; Darren A. Natale; Cathy H. Wu (ICBO, 2014)

BioCreative-IV virtual issue. - Cecilia N. Arighi; Cathy H. Wu; Kevin Bretonnel Cohen; Lynette Hirschman; Martin Krallinger; Alfonso Valencia; Zhiyong Lu; W. John Wilbur; Thomas C. Wiegers (Database J. Biol. Databases Curation, 2014)

BC4GO: a full-text corpus for the BioCreative IV GO task. - Kimberly Van Auken; Mary L. Schaeffer; Peter McQuilton; Stanley J. F. Laulederkind; Donghui Li; Shur-Jen Wang; G. Thomas Hayman; Susan Tweedie; Cecilia N. Arighi; James Done; Hans-Michael Müller; Paul W. Sternberg; et al. (Database J. Biol. Databases Curation, 2014)

Overview of the gene ontology task at BioCreative IV. - Yuqing Mao; Kimberly Van Auken; Donghui Li; Cecilia N. Arighi; Peter McQuilton; G. Thomas Hayman; Susan Tweedie; Mary L. Schaeffer; Stanley J. F. Laulederkind; Shur-Jen Wang; Julien Gobeill; Patrick Ruch; et al. (Database J. Biol. Databases Curation, 2014)

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. - Sylvain Poux; Michele Magrane; Cecilia N. Arighi; Alan J. Bridge; Claire O'Donovan; Kati Laiho (Database J. Biol. Databases Curation, 2014)

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. - Manabu Torii; Gang Li 021; Zhiwen Li; Rose Oughtred; Francesca Diella; Irem Çelen; Cecilia N. Arighi; Hongzhan Huang; K. Vijay-Shanker; Cathy H. Wu (Database J. Biol. Databases Curation, 2014)

Protein Ontology: a controlled structured network of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Carol J. Bult; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; Olivia Helfer; Hongzhan Huang; Anna Maria Masci; et al. (Nucleic Acids Res., 2014)

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. - Catalina O. Tudor; Karen E. Ross; Gang Li 021; K. Vijay-Shanker; Cathy H. Wu; Cecilia N. Arighi (Database J. Biol. Databases Curation, 2015)

miRTex: A Text Mining System for miRNA-Gene Relation Extraction. - Gang Li 021; Karen E. Ross; Cecilia N. Arighi; Yifan Peng 002; Cathy H. Wu; K. Vijay-Shanker (PLoS Comput. Biol., 2015)

RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. - Manabu Torii; Cecilia N. Arighi; Gang Li 021; Qinghua Wang 003; Cathy H. Wu; K. Vijay-Shanker (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology. - Karen E. Ross; Darren A. Natale; Cecilia N. Arighi; Sheng-Chih Chen; Hongzhan Huang; Gang Li 021; Jia Ren; Michael Wang; K. Vijay-Shanker; Cathy H. Wu (ICBO/BioCreative, 2016)

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - Sun Kim; Rezarta Islamaj Dogan; Andrew Chatr-aryamontri; Christie S. Chang; Rose Oughtred; Jennifer M. Rust; Riza Batista-Navarro; Jacob Carter; Sophia Ananiadou; Sérgio Matos; André Santos; David Campos 001; et al. (Database J. Biol. Databases Curation, 2016)

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. - Yifan Peng 002; Cecilia N. Arighi; Cathy H. Wu; K. Vijay-Shanker (Database J. Biol. Databases Curation, 2016)

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. - Ayush Singhal; Robert Leaman; Natalie L. Catlett; Thomas Lemberger 001; Johanna R. McEntyre; Shawn W. Polson; Ioannis Xenarios; Cecilia N. Arighi; Zhiyong Lu (Database J. Biol. Databases Curation, 2016)

Overview of the interactive task in BioCreative V. - Qinghua Wang 003; Shabbir Syed-Abdul; Lara Almeida; Sophia Ananiadou; Yalbi I. Balderas-Martínez; Riza Batista-Navarro; David Campos 001; Lucy Chilton; Hui-Jou Chou; Gabriela Contreras; Laurel Cooper; Hong-Jie Dai; et al. (Database J. Biol. Databases Curation, 2016)

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. - Ruoyao Ding; Emmanuel Boutet; Damien Lieberherr; Michel Schneider; Michael Tognolli; Cathy H. Wu; K. Vijay-Shanker; Cecilia N. Arighi (Database J. Biol. Databases Curation, 2017)

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. - Sylvain Poux; Cecilia N. Arighi; Michele Magrane; Alex Bateman; Chih-Hsuan Wei; Zhiyong Lu; Emmanuel Boutet; Hema Bye-A-Jee; Maria Livia Famiglietti; Bernd Roechert; UniProt Consortium (Bioinform., 2017)

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. - Darren A. Natale; Cecilia N. Arighi; Judith A. Blake; Jonathan P. Bona; Chuming Chen; Sheng-Chih Chen; Karen R. Christie; Julie Cowart; Peter D'Eustachio; Alexander D. Diehl; Harold J. Drabkin; William D. Duncan; et al. (Nucleic Acids Res., 2017)

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. - Jia Ren; Gang Li 021; Karen Ross; Cecilia N. Arighi; Peter B. McGarvey; Shruti Rao; Julie Cowart; Subha Madhavan; K. Vijay-Shanker; Cathy H. Wu (Database J. Biol. Databases Curation, 2018)

iPTMnet: an integrated resource for protein post-translational modification network discovery. - Hongzhan Huang; Cecilia N. Arighi; Karen E. Ross; Jia Ren; Gang Li 021; Sheng-Chih Chen; Qinghua Wang 003; Julie Cowart; K. Vijay-Shanker; Cathy H. Wu (Nucleic Acids Res., 2018)

PIRSitePredict for protein functional site prediction using position-specific rules. - Chuming Chen; Qinghua Wang 003; Hongzhan Huang; Cholanayakanahalli R. Vinayaka; John S. Garavelli; Cecilia N. Arighi; Darren A. Natale; Cathy H. Wu (Database J. Biol. Databases Curation, 2019)

An effective biomedical document classification scheme in support of biocuration: addressing class imbalance. - Xiangying Jiang; Martin Ringwald; Judith A. Blake; Cecilia N. Arighi; Gongbo Zhang; Hagit Shatkay (Database J. Biol. Databases Curation, 2019)

Modality-Classification of Microscopy Images Using Shallow Variants of Deep Networks. - Juan Trelles Trabucco; Pengyuan Li 001; Cecilia N. Arighi; Hagit Shatkay; G. Elisabeta Marai (BIBM, 2020)

UPCLASS: a deep learning-based classifier for UniProtKB entry publications. - Douglas Teodoro; Julien Knafou; Nona Naderi; Emilie Pasche; Julien Gobeill; Cecilia N. Arighi; Patrick Ruch (Database J. Biol. Databases Curation, 2020)

ANIMO: Annotation of Biomed Image Modalities. - Juan Trelles Trabucco; Pengyuan Li 001; Cecilia N. Arighi; Daniela Raciti; Hagit Shatkay; G. Elisabeta Marai (BIBM, 2021)

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. - Franziska Hufsky; Kevin Lamkiewicz; Alexandre Almeida; Abdel Aouacheria; Cecilia N. Arighi; Alex Bateman; Jan Baumbach; Niko Beerenwinkel; Christian Brandt; Marco Cacciabue; Sara Chuguransky; Oliver Drechsel; et al. (Briefings Bioinform., 2021)

emiRIT: a text-mining-based resource for microRNA information. - Debarati Roychowdhury; Samir Gupta; Xihan Qin; Cecilia N. Arighi; K. Vijay-Shanker (Database J. Biol. Databases Curation, 2021)

Corrigendum to: Utilizing image and caption information for biomedical document classification. - Pengyuan Li 001; Xiangying Jiang; Gongbo Zhang; Juan Trelles Trabucco; Daniela Raciti; Cynthia L. Smith; Martin Ringwald; G. Elisabeta Marai; Cecilia N. Arighi; Hagit Shatkay (Bioinform., 2021)

Utilizing image and caption information for biomedical document classification. - Pengyuan Li 001; Xiangying Jiang; Gongbo Zhang; Juan Trelles Trabucco; Daniela Raciti; Cynthia L. Smith; Martin Ringwald; G. Elisabeta Marai; Cecilia N. Arighi; Hagit Shatkay (Bioinform., 2021)

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase. - Alistair MacDougall; Vladimir Volynkin; Rabie Saidi; Diego Poggioli; Hermann Zellner; Emma Hatton-Ellis; Vishal Joshi; Claire O'Donovan; Sandra E. Orchard; Andrea H. Auchincloss; Delphine Baratin; Jerven T. Bolleman; et al. (Bioinform., 2021)

UniProt: the universal protein knowledgebase in 2021. - Alex Bateman; Maria Jesus Martin; Sandra E. Orchard; Michele Magrane; Rahat Agivetova; Shadab Ahmad; Emanuele Alpi; Emily H. Bowler-Barnett; Ramona Britto; Borisas Bursteinas; Hema Bye-A-Jee; Ray Coetzee; et al. (Nucleic Acids Res., 2021)

The Gene Ontology resource: enriching a GOld mine. - Seth Carbon; Eric Douglass; Benjamin M. Good; Deepak R. Unni; Nomi L. Harris; Christopher J. Mungall; Siddartha Basu; Rex L. Chisholm; Robert J. Dodson; Eric Hartline; Petra Fey; Paul D. Thomas; et al. (Nucleic Acids Res., 2021)

BioRED: A Comprehensive Biomedical Relation Extraction Dataset. - Ling Luo 001; Po-Ting Lai; Chih-Hsuan Wei; Cecilia N. Arighi; Zhiyong Lu (AMIA, 2022)

BioRED: a rich biomedical relation extraction dataset. - Ling Luo 001; Po-Ting Lai; Chih-Hsuan Wei; Cecilia N. Arighi; Zhiyong Lu (Briefings Bioinform., 2022)

Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII. - Andrew Chatr-aryamontri; Lynette Hirschman; Karen E. Ross; Rose Oughtred; Martin Krallinger; Kara Dolinski; Mike Tyers; Tonia Korves; Cecilia N. Arighi (Database J. Biol. Databases Curation, 2022)

A roadmap for the functional annotation of protein families: a community perspective. - Valérie de Crécy-Lagard; Rocio Amorin de Hegedus; Cecilia N. Arighi; Jill Babor; Alex Bateman; Ian Blaby; Crysten Blaby-Haas; Alan J. Bridge; Stephen K. Burley; Stacey Cleveland; Lucy J. Colwell; Ana Conesa; et al. (Database J. Biol. Databases Curation, 2022)

MouseScholar: Evaluating an Image+Text Search System for Biocuration. - Juan Trelles Trabucco; Carla Floricel; Cecilia N. Arighi; Hagit Shatkay; Daniela Raciti; Martin Ringwald; G. Elisabeta Marai (BIBM, 2023)

Annotation of biologically relevant ligands in UniProtKB using ChEBI. - Elisabeth Coudert; Sebastien Gehant; Edouard De Castro; Monica Pozzato; Delphine Baratin; Teresa Batista Neto; Christian J. A. Sigrist; Nicole Redaschi; Alan J. Bridge; Lucila Aimo; Ghislaine Argoud-Puy; Andrea H. Auchincloss; et al. (Bioinform., 2023)

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. - Karina Martinez; Jon Agirre; Yukie Akune; Kiyoko F. Aoki-Kinoshita; Cecilia N. Arighi; Kristian B. Axelsen; Evan Bolton; Emily Bordeleau; Nathan J. Edwards; Elisa Fadda; Ten Feizi; Catherine A. Hayes; et al. (Database J. Biol. Databases Curation, 2024)