Irina Balaur

The development of computational approaches in systems biology has reached a state of maturity that allows their transition to systems medicine. Despite this progress, intuitive visualisation and context-dependent knowledge representation still present a major bottleneck. In this paper, we describe the Disease Maps Project, an effort towards a community-driven computationally readable comprehensive representation of disease mechanisms. We outline the key principles and the framework required for the success of this initiative, including use of best practices, standards and protocols. We apply a modular approach to ensure efficient sharing and reuse of resources for projects dedicated to specific diseases. Community-wide use of disease maps will accelerate the conduct of biomedical research and lead to new disease ontologies defined from mechanism-based disease endotypes rather than phenotypes.

The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).

Objectives: The continuous integration of artificial intelligence (AI) into clinical settings requires the development of up-to-date and robust guidelines and standard frameworks that consider the evolving challenges of AI implementation in medicine. This review evaluates the quality of these guideline and summarizes ethical frameworks, best practices, and recommendations. Materials and Methods: The Appraisal of Guidelines, Research, and Evaluation II tool was used to assess the quality of guidelines based on 6 domains: scope and purpose, stakeholder involvement, rigor of development, clarity of presentation, applicability, and editorial independence. The protocol of this review including the eligibility criteria, the search strategy data extraction sheet and methods, was published prior to the actual review with International Registered Report Identifier of DERR1-10.2196/47105. Results: The initial search resulted in 4975 studies from 2 databases and 7 studies from manual search. Eleven articles were selected for data extraction based on the eligibility criteria. We found that while guidelines generally excel in scope, purpose, and editorial independence, there is significant variability in applicability and the rigor of guideline development. Well-established initiatives such as TRIPOD+AI, DECIDE-AI, SPIRIT-AI, and CONSORT-AI have shown high quality, particularly in terms of stakeholder involvement. However, applicability remains a prominent challenge among the guidelines. The result also showed that the reproducibility, ethical, and environmental aspects of AI in medicine still need attention from both medical and AI communities. Discussion: Our work highlights the need for working toward the development of integrated and comprehensive reporting guidelines that adhere to the principles of Findability, Accessibility, Interoperability and Reusability. This alignment is essential for fostering a cultural shift toward transparency and open science, which are pivotal milestone for sustainable digital health research. Conclusion: This review evaluates the current reporting guidelines, discussing their advantages as well as challenges and limitations.

Summary: The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. Availability and Implementation: The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/ . The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework . Contact: ibalaur@eisbm.org. Supplementary information: Supplementary data are available at Bioinformatics online.