Project 33: Training Systems biology curators in building interoperable and reusable models following a learning path approach
Systems biology is an important area for ELIXIR, as illustrated by the emergence of the Systems Biology Community. Building on Project 9 from last year’s BioHackathon, and in collaboration with the ELIXIR’s Biocuration Focus Group and Training Platform, we aim to develop a learning path for systems biology biocurators (https://github.com/elixir-europe/biohackathon-projects-2021/tree/main/projects/9). This will support the creation and curation of interoperable and reusable models for precise hypotheses and predictions.
To this end, we will produce an overview of systems biology courses and training materials, and organize them in an ELIXIR TeSS Collection (https://tess.elixir-europe.org/collections). In this process, we will also identify training gaps and propose learning objectives to ensure the development of necessary competences.
Learning paths require a ‘roadmap’ for training units and modules (https://en.wikipedia.org/wiki/Learning_pathway). By reviewing the existing materials in the domains of knowledge annotation, diagrammatic representation and model building, we will catalog and harmonise available guidelines and training materials, exploring the following areas:
-how to annotate and encode bioentities and molecular interactions, building on experience of the Biocuration Focus Group and existing content for resources like UniProt, IMEx or MI2CAST;
-how to create systems biology diagrams, with emphasis on visual exploration and analytics, benefiting from experience of Reactome, WikiPathways and Disease Maps Community;
-how to enrich curated knowledge with text mining, benefiting from the development of the ELIXIR Data Platform literature annotation services and its Implementation Study on Scalable Curation;
-how to build systems biology models for analysis and simulations, in relation to BioModels, SABIO-RK and other resources for interoperable and reproducible models.
For all the topics above, we will evaluate available materials on relevant interdisciplinary aspects, in particular on FAIR principles and data management, such as RDMTollkit, and incorporate those with suitable coverage.
Data Platform Tools Platform Training Platform
Project Number: 33
Marek Ostaszewski, [email protected]
- A publication draft by mid 2023, deposited on biorxiv
- Necessary materials required for the deposition learning path for systems biology biocuration in a platform like TeSS
- One or several ELIXIR TeSS collections of training materials
- A comprehensive report of the systems biology curation areas in need of development of training materials
- Biocuration of molecular knowledge (entities and their interactions)
- Tools and standards for model building
- Graphical representation of biological models
- Web services and platforms for sharing models and annotations
- Learning paths methodology
Number of expected hacking days: 4