HetERogeneous sEmantic Data integratIon for the guT-bRain interplaY

Leistungen

Legal, ethical, and regulatory inventory

Preliminary overview of the legal and ethical requirements applicable to the HEREDITARY project.

Ontology and federated execution methods

Describe the ontology focusing on neurological diseases and the design of the query execution engine and optimizers (initial design of the architecture).

Guidelines and manual for applying the Health Social Labs methodology

Release of the guideline and manual for organizing and implementing Health Social Labs.

UNITO clinical studies documentation

Provide all the required approvals (e.g., regulatory, ethical, data access, material transfer agreements [if necessary and allowed by the data holder]) for the clinical studies led by UNITO.

RUMC clinical studies documentation

Provide all the required approvals (e.g., regulatory, ethical, data access, material and data transfer agreements [if necessary and allowed by the data holder]) for the clinical studies led by RUMC.

Visualization components for sequences, networks, text, and high-dimensional data

Concepts, initial conceptualization of the software libraries and documentation for visualization of these data types

Design of neurodegenerative use cases

Establish guidelines for data harmonization and provide evidence-based criteria for variable inclusion.

Medical terminology

Report describing the conceptual and linguistic systems that describe the medical terminology.

Federated infrastructure design

Report on Task 2.6, detailing the infrastructure design document outlining the architecture, components, and technologies used.

Linkage and feature extraction from gut-brain, initial evaluation

We will identify and provide integrated brain-gut linkage and behavioral phenotyping for use in feature extraction for federated learning. At M12, we will release an initial results evaluation. Data from this sample is very rich, and data will still need to be processed during the first year of the proposed project. We set intermediate evaluation windows to capitalize on this.

Evidence-based KBC: Initial results

Release of the methods for entity and relation extraction from the literature; methods for building iterative probabilistic KG.

UNIPD clinical studies documentation

Provide all the required approvals (e.g., regulatory, ethical, data access, material transfer agreements [if necessary and allowed by the data holder]) for the clinical studies led by UNIPD.

Ethical guidelines, data collection and sharing

"Results of Task 2.1 will describe legal and ethical aspects related to data transfer to other WPs for model training. In this deliverable, there will be a first assessment of the Ethics checks required in the ""Ethics Summary Report""."

Health Social Lab activities

First report on the first cycle of HSL (the idea creation and implementation of the defined activities).

Parkinson’s disease in the eye, first approach

Explore if eye images can predict PD development and biomarker associations. Description and outcomes of the first approach feeding in the images+clinical+demographic data directly into a deep learning classifier.

Visualization components for spatial, image, and simulation data

Concepts, initial conceptualization of the software libraries, and documentation for visualization of these additional data types.

Project website release

Official release of the project public website.

Computing infrastructures

Setting up the managed services and computational and storage facilities in the local medical centers

Veröffentlichungen

Binomial Confidence Intervals for Knowledge Graph Accuracy Estimation (Extended Abstract)

Autoren: Marchesin, Stefano; Silvello, Gianmaria
Veröffentlicht in: SEBD 2025, 2025
Herausgeber: Ceur-Ws
DOI: 10.5281/ZENODO.15745400

Utility-Oriented Knowledge Graph Accuracy Estimation with LimitedAnnotations: A Case Study on DBpedia

Autoren: Marchesin, Stefano; Silvello, Gianmaria; Alonso, Omar
Veröffentlicht in: HCOMP 2024, 2024
Herausgeber: AAAI
DOI: 10.1609/hcomp.v12i1.31605

Extending Nanopublications with Knowledge Provenance for Multi-Source Scientific Assertions

Autoren: Fabio Giachelle, Stefano Marchesin, Laura Menotti, and Gianmaria Silvello
Veröffentlicht in: IRCDL 2025, 2025
Herausgeber: CEUR

Constrained Linked Entity ANnotation using RAG (CLEANR)

Autoren: B. Kantz, S. Lengauer, P. Waldert, T. Schreck
Veröffentlicht in: CLEF 2025 BioASQ Report Paper for Task GutBrainIE on Gut-Brain Interplay Information Extraction, 2025
Herausgeber: CEUR Workshop Proceedings

Doctron: A Web-based Collaborative Annotation Tool for Ground Truth Creation in IR

Autoren: Ornella Irrera, Stefano Marchesin, Farzad Shami, Gianmaria Silvello
Veröffentlicht in: Proceedings of the 48th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2025
Herausgeber: ACM
DOI: 10.1145/3726302.3730286

MetaTron: Streamlining Collaborative Annotation for Biomedical Documents

Autoren: Irrera, Ornella; Marchesin, Stefano; Silvello, Gianmaria
Veröffentlicht in: SWAT4HCLS, 2025
Herausgeber: Arxiv
DOI: 10.5281/ZENODO.15656043

Advancing Inclusivity in a Medical Terminology Resource concerning the Gut-Brain Interplay: Insights from the HEREDITARY Project

Autoren: Vanessa Bonato, Federica Vezzani, Giorgio Maria Di Nunzio
Veröffentlicht in: Semmelweis Medical Linguistics Conference 2025 Inclusivity and Diversity in Healthcare Communication Research, 2025
Herausgeber: in press

Reusability of Biomedical Annotations for Gut-Brain Interplay Information Extraction as Terminological Data

Autoren: Vanessa Bonato
Veröffentlicht in: MDTT 2025, 2025
Herausgeber: CEUR-WS

Consumer-Centered Technology-Assisted Review: Insights and Challenges from the CLEF eHealth Tasks

Autoren: Giorgio Maria Di Nunzio
Veröffentlicht in: Semmelweis Medical Linguistics Conference 2025 Inclusivity and Diversity in Healthcare Communication Research, 2025
Herausgeber: in press

Reproducibility and Analysis of Scientific Dataset Recommendation Methods

Autoren: Ornella Irrera; Matteo Lissandrini; Daniele Dell'Aglio; Gianmaria Silvello
Veröffentlicht in: 18th ACM Conference on Recommender Systems, 2024
Herausgeber: ACM Press
DOI: 10.1145/3640457.3688071

Publishing CoreKB Facts as Nanopublications

Autoren: Fabio Giachelle; Stefano Marchesin; Laura Menotti; Gianmaria Silvello
Veröffentlicht in: IRCDL 2024, 2024, ISSN 1613-0073
Herausgeber: CEUR

Exploring Terminological Collocations in Biomedical Texts

Autoren: Costa, Rute; Ramos, Margarida; Canelas, Matilde; Mouro, Ana
Veröffentlicht in: MDTT 2025, 2025
Herausgeber: Ceur-Ws
DOI: 10.5281/ZENODO.15863151

BioASQ at CLEF2025: The Thirteenth Edition of the Large-Scale Biomedical Semantic Indexing and Question Answering Challenge

Autoren: Anastasios Nentidis, Georgios Katsimpras, Anastasia Krithara, Martin Krallinger, Miguel Rodriguez Ortega, Natalia Loukachevitch, Andrey Sakhovskiy, Elena Tutubalina, Grigorios Tsoumakas, George Giannakoulas, Alexandra Bekiaridou, Athanasios Samaras, Giorgio Maria Di Nunzio, Nicola Ferro, Stefano Marchesin, Laura Menotti, Gianmaria Silvello, Georgios Paliouras
Veröffentlicht in: Lecture Notes in Computer Science, Advances in Information Retrieval, 2025
Herausgeber: Springer Nature Switzerland
DOI: 10.1007/978-3-031-88720-8_61

Veracity Estimation for Entity-Oriented Search with Knowledge Graphs

Autoren: Marchesin, Stefano; Silvello, Gianmaria; Alonso, Omar
Veröffentlicht in: CIKM 2024, 2024
Herausgeber: ACM
DOI: 10.1145/3627673.3679561

FAIR Terminology Meets CLEAR Global

Autoren: Giorgio Maria Di Nunzio, Eszter Papp, Federica Vezzani, Ellie Kemp
Veröffentlicht in: Lecture Notes in Computer Science, Linking Theory and Practice of Digital Libraries, 2024
Herausgeber: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72440-4_17

Fact Verification in Knowledge Graphs Using LLMs

Autoren: Farzad Shami, Stefano Marchesin, and Gianmaria Silvello
Veröffentlicht in: SIGIR 2025, 2025
Herausgeber: THE 48TH INTERNATIONAL ACM SIGIR CONFERENCE ON RESEARCH AND DEVELOPMENT IN INFORMATION RETRIEVAL
DOI: 10.1145/3726302.3730142

The Elephant in the Room: The Impact of Domain-Expert (Dis)agreement. A Case Study on Cryptic Species

Autoren: Giorgio Maria Di Nunzio, Lucia Manni, Emanuela De Lisa, Federica Vezzani
Veröffentlicht in: MDTT 2025, 2025
Herausgeber: CEUR-WS

A Marker Design for visually enhancing Local Cluster Association

Autoren: S. Lengauer, P. Waldert, T. Schreck
Veröffentlicht in: IEEE VIS 2024 Bio+MedVis Challenge, 2024
Herausgeber: Zenodo

OnSET: Ontology and Semantic Exploration Toolkit

Autoren: B. Kantz, K. Innerebner, P. Waldert, S. Lengauer, E. Lex, T. Schreck
Veröffentlicht in: ACM SIGIR 2025 Proceedings, 2025
Herausgeber: ACM

Behavioral Clusters and Lesion Distributions in Ischemic Stroke, Based on NIHSS Similarity Network

Autoren: Louis Fabrice Tshimanga; Andrea Zanola; Silvia Facchini; Antonio Luigi Bisogno; Lorenzo Pini; Manfredo Atzori; Maurizio Corbetta
Veröffentlicht in: Journal of Healthcare Informatics Research, 2023, ISSN 2509-498X
Herausgeber: Journal of Healthcare Informatics Research
DOI: 10.1101/2023.11.08.23297808

BMC Bioinformatics

Autoren: Ornella Irrera; Stefano Marchesin; Gianmaria Silvello
Veröffentlicht in: BMC Bioinformatics, Ausgabe 25(112), 2024, ISSN 1471-2105
Herausgeber: BioMed Central
DOI: 10.1186/S12859-024-05730-9

Efficient and Reliable Estimation of Knowledge Graph Accuracy

Autoren: Stefano Marchesin; Gianmaria Silvello
Veröffentlicht in: PVLDB, Ausgabe 17(9), 2024, ISSN 2150-8097
Herausgeber: VLDB Endowment
DOI: 10.14778/3665844.3665865

Changes to Average Survival of Patients With Amyotrophic Lateral Sclerosis (1995–2018)

Autoren: Rosario Vasta, Filippo De Mattei, Salvatore Tafaro, Antonio Canosa, Umberto Manera, Maurizio Grassano, Francesca Palumbo, Sara Cabras, Enrico Matteoni, Francesca Di Pede, Grazia Zocco, Giorgio Pellegrino, Emilio Minerva, Daniela Pascariu, Barbara Iazzolino, Stefano Callegaro, Giuseppe Fuda, Paolina Salamone, Fabiola De Marchi, Letizia Mazzini, Cristina Moglia, Andrea Calvo, Adriano Chiò
Veröffentlicht in: Neurology, Ausgabe 104, 2025, ISSN 0028-3878
Herausgeber: Ovid Technologies (Wolters Kluwer Health)
DOI: 10.1212/WNL.0000000000213467

Credible Intervals for Knowledge Graph Accuracy Estimation

Autoren: Stefano Marchesin, Gianmaria Silvello
Veröffentlicht in: Proceedings of the ACM on Management of Data, Ausgabe 3, 2025, ISSN 2836-6573
Herausgeber: Association for Computing Machinery (ACM)
DOI: 10.1145/3725279

The More, the Better? Evaluating the Role of EEG Preprocessing for Deep Learning Applications

Autoren: Federico Del Pup, Andrea Zanola, Louis Fabrice Tshimanga, Alessandra Bertoldo, Manfredo Atzori
Veröffentlicht in: IEEE Transactions on Neural Systems and Rehabilitation Engineering, Ausgabe 33, 2025, ISSN 1534-4320
Herausgeber: Institute of Electrical and Electronics Engineers (IEEE)
DOI: 10.1109/TNSRE.2025.3547616

An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology

Autoren: Guglielmo Faggioli, Laura Menotti, Stefano Marchesin, Adriano Chió, Arianna Dagliati, Mamede de Carvalho, Marta Gromicho, Umberto Manera, Eleonora Tavazzi, Giorgio Maria Di Nunzio, Gianmaria Silvello, Nicola Ferro
Veröffentlicht in: Journal of Biomedical Semantics, Ausgabe 15, 2024, ISSN 2041-1480
Herausgeber: Springer Science and Business Media LLC
DOI: 10.1186/S13326-024-00317-Y

Le rôle du référent en terminologie : enquête sur la perception du trouble dysmorphique corporel

Autoren: Federica Vezzani; Rute Costa
Veröffentlicht in: Roczniki Humanistyczne, 2024, ISSN 0035-7707
Herausgeber: Towarzystwo Naukowe Kul & Katolicki Uniwersytet Lubelski Jana Pawła II – Wydział Nauk Humanistycznych
DOI: 10.18290/RH24728.5

Variation in psychopathological terminology

Autoren: Federica Vezzani, Rute Costa
Veröffentlicht in: Terminology. International Journal of Theoretical and Applied Ausgabes in Specialized Communication, Terminology / International Journal of Theoretical and Applied Ausgabes in Specialized Communication, Terminology, Ausgabe 30, 2024, ISSN 0929-9971
Herausgeber: John Benjamins Publishing Company
DOI: 10.1075/TERM.00078.VEZ

Phosphatemia is an Independent Prognostic Factor in Amyotrophic Lateral Sclerosis

Autoren: Vasta, Rosario; Koumantakis, Emanuele; Canosa, Antonio; Manera, Umberto; Grassano, Maurizio; Palumbo, Francesca; Cabras, Sara; Matteoni, Enrico; Di Pede, Francesca; De Mattei, Filippo; Vergnano, Filippo; Mandrioli, Jessica; Simonini, Cecilia; Martinelli, Ilaria; De Marchi, Fabiola; Mazzini, Letizia; Moglia, Cristina; Calvo, Andrea; Chiò, Adriano
Veröffentlicht in: Annals of Neurology, 2025, ISSN 1531-8249
Herausgeber: Wiley
DOI: 10.1002/ANA.27252

When LMF and TMF meet

Autoren: Federica Vezzani, Giorgio Maria Di Nunzio, Ana Salgado, Rute Costa
Veröffentlicht in: Terminology. International Journal of Theoretical and Applied Ausgabes in Specialized Communication, Terminology / International Journal of Theoretical and Applied Ausgabes in Specialized Communication, Terminology, Ausgabe 31, 2025, ISSN 0929-9971
Herausgeber: John Benjamins Publishing Company
DOI: 10.1075/TERM.00084.VEZ

Exploring Publicly Accessible Optical Coherence Tomography Datasets: A Comprehensive Overview

Autoren: Anastasiia Rozhyna; Gábor Márk Somfai; Manfredo Atzori; Delia Cabrera DeBuc; Amr Saad; Jay Zoellin; Henning Müller
Veröffentlicht in: Diagnostics, 2024, ISSN 2075-4418
Herausgeber: MDPI
DOI: 10.3390/DIAGNOSTICS14151668

MetaTron: advancing biomedical annotation empowering relation annotation and collaboration

Autoren: Ornella Irrera, Stefano Marchesin, Gianmaria Silvello
Veröffentlicht in: BMC Bioinformatics, Ausgabe 25, 2024, ISSN 1471-2105
Herausgeber: Springer Science and Business Media LLC
DOI: 10.1186/S12859-024-05730-9

Toward improving reproducibility in neuroimaging deep learning studies

Autoren: Federico Del Pup; Federico Del Pup; Federico Del Pup; Manfredo Atzori; Manfredo Atzori; Manfredo Atzori
Veröffentlicht in: Frontiers in Neuroscience, 2024, ISSN 1662-453X
Herausgeber: Frontiers
DOI: 10.3389/FNINS.2024.1509358

SelfEEG: A Python library for Self-Supervised Learning in Electroencephalography

Autoren: Federico Del Pup; Andrea Zanola; Louis Fabrice Tshimanga; Paolo Emilio Mazzon; Manfredo Atzori
Veröffentlicht in: The Journal of Open Source Software, Ausgabe 9(95), 2024, ISSN 2475-9066
Herausgeber: Journal of Open Source Software
DOI: 10.48550/arxiv.2401.05405

BIDSAlign: a library for automatic merging and preprocessing of multiple EEG repositories

Autoren: Andrea Zanola; Federico Del Pup; Camillo Porcaro; Manfredo Atzori
Veröffentlicht in: Journal of Neural Engineering, 2024, ISSN 1741-2552
Herausgeber: Springer
DOI: 10.1088/1741-2552/AD6A8C

The role of data partitioning on the performance of EEG-based deep learning models in supervised cross-subject analysis: A preliminary study

Autoren: Federico Del Pup, Andrea Zanola, Louis Fabrice Tshimanga, Alessandra Bertoldo, Livio Finos, Manfredo Atzori
Veröffentlicht in: Computers in Biology and Medicine, Ausgabe 196, 2025, ISSN 0010-4825
Herausgeber: Elsevier BV
DOI: 10.1016/J.COMPBIOMED.2025.110608

Can We Measure the Impact of a Database?

Autoren: Peter Buneman, Dennis Dosso, Matteo Lissandrini, Gianmaria Silvello, He Sun
Veröffentlicht in: Communications of the ACM, Ausgabe 68, 2025, ISSN 0001-0782
Herausgeber: Association for Computing Machinery (ACM)
DOI: 10.1145/3704723

Content-Based Dataset Retrieval Methods: Reproducibility of the ACORDAR Test Collection

Autoren: Laura Menotti, Manuel Barusco, Riccardo Forzan, Gianmaria Silvello
Veröffentlicht in: Lecture Notes in Computer Science, Linking Theory and Practice of Digital Libraries, 2024
Herausgeber: Springer Nature Switzerland
DOI: 10.1007/978-3-031-72437-4_18

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