Cecilia N. Arighi

According to our database1, Cecilia N. Arighi authored at least 60 papers between 2007 and 2023.

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Bibliography

2023
Annotation of biologically relevant ligands in UniProtKB using ChEBI.
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Bioinform., January, 2023

MouseScholar: Evaluating an Image+Text Search System for Biocuration.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022
A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation, 2022

Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII.
Database J. Biol. Databases Curation, 2022

BioRED: a rich biomedical relation extraction dataset.
Briefings Bioinform., 2022

BioRED: A Comprehensive Biomedical Relation Extraction Dataset.
Proceedings of the AMIA 2022, 2022

2021
The Gene Ontology resource: enriching a GOld mine.
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Nucleic Acids Res., 2021

UniProt: the universal protein knowledgebase in 2021.
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Nucleic Acids Res., 2021

UniRule: a unified rule resource for automatic annotation in the UniProt Knowledgebase.
Bioinform., 2021

Utilizing image and caption information for biomedical document classification.
Bioinform., 2021

Corrigendum to: Utilizing image and caption information for biomedical document classification.
Bioinform., 2021

emiRIT: a text-mining-based resource for microRNA information.
Database J. Biol. Databases Curation, 2021

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Briefings Bioinform., 2021

ANIMO: Annotation of Biomed Image Modalities.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020
UPCLASS: a deep learning-based classifier for UniProtKB entry publications.
Database J. Biol. Databases Curation, 2020

Modality-Classification of Microscopy Images Using Shallow Variants of Deep Networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2020

2019
An effective biomedical document classification scheme in support of biocuration: addressing class imbalance.
Database J. Biol. Databases Curation, 2019

PIRSitePredict for protein functional site prediction using position-specific rules.
Database J. Biol. Databases Curation, 2019

2018
iPTMnet: an integrated resource for protein post-translational modification network discovery.
Nucleic Acids Res., 2018

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature.
Database J. Biol. Databases Curation, 2018

2017
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.
Nucleic Acids Res., 2017

On expert curation and scalability: UniProtKB/Swiss-Prot as a case study.
Bioinform., 2017

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality.
Database J. Biol. Databases Curation, 2017

2016
Overview of the interactive task in BioCreative V.
Database J. Biol. Databases Curation, 2016

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.
Database J. Biol. Databases Curation, 2016

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.
Database J. Biol. Databases Curation, 2016

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Database J. Biol. Databases Curation, 2016

Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
PLoS Comput. Biol., 2015

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.
Database J. Biol. Databases Curation, 2015

2014
Protein Ontology: a controlled structured network of protein entities.
Nucleic Acids Res., 2014

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.
Database J. Biol. Databases Curation, 2014

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data.
Database J. Biol. Databases Curation, 2014

Overview of the gene ontology task at BioCreative IV.
Database J. Biol. Databases Curation, 2014

BC4GO: a full-text corpus for the BioCreative IV GO task.
Database J. Biol. Databases Curation, 2014

BioCreative-IV virtual issue.
Database J. Biol. Databases Curation, 2014

Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis.
Proceedings of the 5th International Conference on Biomedical Ontology, 2014

2013
A framework for biomedical figure segmentation towards image-based document retrieval.
BMC Syst. Biol., 2013

Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint.
Database J. Biol. Databases Curation, 2013

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Database J. Biol. Databases Curation, 2013

Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach.
Proceedings of the ACM Conference on Bioinformatics, 2013

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
BioCreative-2012 Virtual Issue.
Database J. Biol. Databases Curation, 2012

Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees.
Database J. Biol. Databases Curation, 2012

The eFIP system for text mining of protein interaction networks of phosphorylated proteins.
Database J. Biol. Databases Curation, 2012

Text mining for the biocuration workflow.
Database J. Biol. Databases Curation, 2012

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference.
Database J. Biol. Databases Curation, 2012

Pathway curation: Application of text-mining tools eGIFT and RLIMS-P.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

Robust segmentation of biomedical figures for image-based document retrieval.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011
The Protein Ontology: a structured representation of protein forms and complexes.
Nucleic Acids Res., 2011

The Representation of Protein Complexes in the Protein Ontology (PRO).
BMC Bioinform., 2011

BioCreative III interactive task: an overview.
BMC Bioinform., 2011

Overview of the BioCreative III Workshop.
BMC Bioinform., 2011

Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools.
Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2011

2009
An improved ontological representation of dendritic cells as a paradigm for all cell types.
BMC Bioinform., 2009

TGF-beta signaling proteins and the Protein Ontology.
BMC Bioinform., 2009

2008
Functional Annotation of Protein Isoforms and Modified Forms.
Proceedings of the International Conference on Bioinformatics & Computational Biology, 2008

2007
Framework for a Protein Ontology.
BMC Bioinform., 2007


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