Patrick Ruch
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View article: DisProt in 2026: enhancing intrinsically disordered proteins accessibility, deposition, and annotation
DisProt in 2026: enhancing intrinsically disordered proteins accessibility, deposition, and annotation Open
DisProt (https://disprot.org/) is an open database integrating experimental evidence on intrinsically disordered proteins (IDPs), intrinsically disordered regions (IDRs), and their functions. Over the past two years, the database has grown…
View article: The Crete Declaration: Uniting Science for One Health
The Crete Declaration: Uniting Science for One Health Open
The interdependence of human, animal, plant and ecosystem health necessitates systemic, cross-domain collaboration to address global challenges, such as emerging diseases, climate change and biodiversity severe change. Through the Crete De…
View article: Manuscript Classification to Support the Analysis of Biases in Publication Opportunities
Manuscript Classification to Support the Analysis of Biases in Publication Opportunities Open
Diversity in the research workforce is essential for addressing complex problems. Female investigators, along with individuals from diverse backgrounds and identities, generate novel, impactful, and innovative research, whereas biases may …
View article: Foundation models for materials discovery – current state and future directions
Foundation models for materials discovery – current state and future directions Open
Large language models, commonly known as LLMs, are showing promise in tacking some of the most complex tasks in AI. In this perspective, we review the wider field of foundation models—of which LLMs are a component—and their application to …
View article: Unlocking the potential of PubMed Central supplementary data files
Unlocking the potential of PubMed Central supplementary data files Open
Motivation Biocuration workflows often rely on comprehensive literature searches for specific biological entities. However, standard search engines such as MEDLINE and PubMed Central provide an incomplete picture of the scientific literatu…
View article: Gender and geographical bias in the editorial decision-making process of biomedical journals: a case-control study
Gender and geographical bias in the editorial decision-making process of biomedical journals: a case-control study Open
Objectives To assess whether the gender (primary) and geographical affiliation (post-hoc) of the first and/or last authors are associated with publication decisions after peer review. Design Case-control study. Setting Biomedical journals.…
View article: A research data management (RDM) community for ELIXIR
A research data management (RDM) community for ELIXIR Open
Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and …
View article: Beyond BiCIKL: Towards Building an AI-Assisted “Biodiversity Supergraph”
Beyond BiCIKL: Towards Building an AI-Assisted “Biodiversity Supergraph” Open
BiCIKL ( Bi odiversity C ommunity I ntegrated K nowledge L ibrary) is a European Union (EU) Horizon 2020 project (2021–2024) building a new community of research infrastructures (RIs), researchers and other stakeholders, through improved a…
View article: BiotXplorer: Navigating Evidence-Based Biotic Interactions
BiotXplorer: Navigating Evidence-Based Biotic Interactions Open
BiotXplorer is an exploration tool to navigate biotic interactions in BiodiversityPMC (Pasche et al. 2023, Gobeill et al. 2020), a digitally native research library of articles for biomedical, biodiversity and environmental sciences stored…
View article: Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants
Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants Open
Assessing the pathogenicity of genetic variants is a critical aspect of genomic medicine and precision healthcare. Over the last decades, the identification of genetic variants and their characterization has become simpler (advent of high-…
View article: DOME Registry: Implementing community-wide recommendations for reporting supervised machine learning in biology
DOME Registry: Implementing community-wide recommendations for reporting supervised machine learning in biology Open
Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The DOME recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data …
View article: Liberate the power of biodiversity literature as FAIR digital objects
Liberate the power of biodiversity literature as FAIR digital objects Open
Knowledge about biodiversity is largely embedded in a daily growing corpus of over 500 million pages of biodiversity literature that is not machine-actionable. It is thus not open to building a biodiversity knowledge graph, or facilitating…
View article: A research data management (RDM) community for ELIXIR
A research data management (RDM) community for ELIXIR Open
Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have invested in RDM and …
View article: Assessment of gender and geographical bias in the editorial decision-making process of biomedical journals: A Case-Control study
Assessment of gender and geographical bias in the editorial decision-making process of biomedical journals: A Case-Control study Open
Objectives To assess whether the gender (primary) and geographical affiliation (post hoc) of the first and/or last authors of manuscripts is associated with publication decisions after controlling for known confounders. Design Case-control…
View article: DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology
DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology Open
Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recommendations aim to enhance the validation and reproducibility of ML research by establishing st…
View article: Exploring the Dual Role of LLMs in Cybersecurity: Threats and Defenses
Exploring the Dual Role of LLMs in Cybersecurity: Threats and Defenses Open
Large Language Models (LLMs) pose risks for cybersecurity since they facilitate minimal cost creation of malware, phishing messages, and malicious chatbots. At the same time, LLMs can help defend against cyberattacks. This chapter reviews …
View article: From SIBiLS to Biodiversity PMC: Foundations for the One Health Library
From SIBiLS to Biodiversity PMC: Foundations for the One Health Library Open
One Health is an integrated, unifying approach that aims to sustainably balance and optimize the health of people, animals and ecosystems in compliance with the United Nations development goals (Dye 2022). However, premier life and health …
View article: Towards "Biodiversity PMC"
Towards "Biodiversity PMC" Open
The Swiss Institute of Bioinformatics (SIB) Literature services (SIBiLS, Gobeill et al. 2020) provides powerful search capabilities to explore the life and health sciences literature by mirroring the United States National Institute of Hea…
View article: The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data
The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data Open
The Biodiversity Knowledge Hub (BKH) is a web platform acting as an integration point and broker of an open, FAIR (Findable, Accessible, Interoperable, Reusable) and interlinked corpora of biodiversity data, services and knowledge. It serv…
View article: The Ecosystem of Linked Biodiversity Publications: General Picture of Tools and Services Created by Plazi, Pensoft, MNHN, CETAF, Zenodo, and SIBiLS
The Ecosystem of Linked Biodiversity Publications: General Picture of Tools and Services Created by Plazi, Pensoft, MNHN, CETAF, Zenodo, and SIBiLS Open
A goal of natural history institutions is to contribute to the understanding of biodiversity and disseminate this knowledge through scholarly publications and other public activities. In today’s world, it is expected that this knowledge, i…
View article: ELIXIR-CONVERGE D4.3 Review of effectiveness of the Node Impact Assessment Toolkit
ELIXIR-CONVERGE D4.3 Review of effectiveness of the Node Impact Assessment Toolkit Open
An Impact Toolkit was created to support performance and impact evaluation in ELIXIR. The intended audience of this Toolkit is operators, developers and managers wishing to demonstrate and communicate the performance, impact, and ultimatel…
View article: Multilingual RECIST classification of radiology reports using supervised learning
Multilingual RECIST classification of radiology reports using supervised learning Open
Objectives The objective of this study is the exploration of Artificial Intelligence and Natural Language Processing techniques to support the automatic assignment of the four Response Evaluation Criteria in Solid Tumors (RECIST) scales ba…
View article: CINECA Curation-support application for care planning D5.4
CINECA Curation-support application for care planning D5.4 Open
This deliverable aims at designing and evaluating a curation support system to help clinicians to decide which treatments should be considered given a set of somatic/germline mutations and some particular clinical conditions (e.g. diagnosi…
View article: Assessing the use of supplementary materials to improve genomic variant discovery
Assessing the use of supplementary materials to improve genomic variant discovery Open
The curation of genomic variants requires collecting evidence not only in variant knowledge bases but also in the literature. However, some variants result in no match when searched in the scientific literature. Indeed, it has been reporte…
View article: COVoc and COVTriage: novel resources to support literature triage
COVoc and COVTriage: novel resources to support literature triage Open
Motivation Since early 2020, the coronavirus disease 2019 (COVID-19) pandemic has confronted the biomedical community with an unprecedented challenge. The rapid spread of COVID-19 and ease of transmission seen worldwide is due to increased…
View article: Recommendations for interoperability among infrastructures
Recommendations for interoperability among infrastructures Open
The BiCIKL project is born from a vision that biodiversity data are most useful if they are presented as a network of data that can be integrated and viewed from different starting points. BiCIKL’s goal is to realise that vision by linking…