SYMBIONIC: A European Initiative on the Systems Biology of the Neuronal Cell. - Ivan Arisi; Paola Roncaglia; Vittorio Rosato; Antonino Cattaneo (Trans. Comp. Sys. Biology, 2006)

The Apoptosis Gene Ontology project and the IntAct-Apoptosis dataset: updating the conceptual representation of apoptosis. - Pablo Porras; Paola Roncaglia; Emily Dimmer; Jane Lomax; Rachael P. Huntley; Sandra E. Orchard; Marine Dumousseau; Samuel Kerrien; Henning Hermjakob (IWBBIO, 2013)

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. - Paola Roncaglia; Maryann E. Martone; David P. Hill; Tanya Z. Berardini; Rebecca E. Foulger; Fahim T. Imam; Harold J. Drabkin; Christopher J. Mungall; Jane Lomax (J. Biomed. Semant., 2013)

TermGenie - A web application for pattern-based ontology class generation. - Heiko Dietze; Tanya Z. Berardini; Rebecca E. Foulger; David P. Hill; Jane Lomax; David Osumi-Sutherland; Paola Roncaglia; Christopher J. Mungall (J. Biomed. Semant., 2014)

Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. - Sejal Patel; Paola Roncaglia; Ruth C. Lovering (BMC Bioinform., 2015)

Extending gene ontology in the context of extracellular RNA and vesicle communication. - Kei-Hoi Cheung; Shivakumar Keerthikumar; Paola Roncaglia; Sai Lakshmi Subramanian; Matthew E. Roth; Monisha Samuel; Sushma Anand; Lahiru Gangoda; Stephen Gould; Roger Alexander; David Galas; Mark B. Gerstein; et al. (J. Biomed. Semant., 2016)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2016)

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. - Kent A. Shefchek; Nomi L. Harris; Michael A. Gargano; Nicolas Matentzoglu; Deepak R. Unni; Matthew H. Brush; Dan Keith; Tom Conlin; Nicole A. Vasilevsky; Xingmin Aaron Zhang; James P. Balhoff; Larry Babb; et al. (Nucleic Acids Res., 2020)

A Community Effort for COVID-19 Ontology Harmonization. - Asiyah Yu Lin; Yuki Yamagata; William D. Duncan; Leigh C. Carmody; Tatsuya Kushida; Hiroshi Masuya; John Beverley; Biswanath Dutta; Michael DeBellis; Zoë May Pendlington; Paola Roncaglia; Yongqun He (ICBO, 2021)

Open Targets Genetics: systematic identification of trait-associated genes using large-scale genetics and functional genomics. - Maya Ghoussaini; Edward Mountjoy; Miguel Carmona; Gareth Peat; Ellen M. Schmidt; Andrew Hercules; Luca Fumis; Alfredo Miranda; Denise Carvalho-Silva; Annalisa Buniello; Tony Burdett; James D. Hayhurst; et al. (Nucleic Acids Res., 2021)

A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology. - Yongqun He; Hong Yu 014; Anthony Huffman; Asiyah Yu Lin; Darren A. Natale; John Beverley; Ling Zheng; Yehoshua Perl; Zhigang Wang; Yingtong Liu; Edison Ong; Yang Wang; et al. (J. Biomed. Semant., 2022)

COVoc and COVTriage: novel resources to support literature triage. - Déborah Caucheteur; Zoë May Pendlington; Paola Roncaglia; Julien Gobeill; Luc Mottin; Nicolas Matentzoglu; Donat Agosti; David Osumi-Sutherland; Helen E. Parkinson; Patrick Ruch (Bioinform., 2023)

The Cell Ontology in the age of single-cell omics. - Shawn Zheng Kai Tan; Aleix Puig-Barbe; Damien Goutte-Gattat; Caroline Eastwood; Brian D. Aevermann; Alida Avola; James P. Balhoff; Ismail Ugur Bayindir; Jasmine Belfiore; Anita R. Caron; David S. Fischer; Nancy George; et al. (CoRR, 2025)