Systems biology (SB) is a new ELIXIR Community, utilising different ELIXIR resources, such as the Training eSupport System (TeSS) and bio.tools, a registry of software tools and data resources for life sciences. One of the main initial objectives of the SB Community is to create a SB-themed domain hosted by TeSS, encompassing SB-related ELIXIR services and events, in a fully automated way.
Most content in TeSS is sourced through automated aggregation (“scraping”) of external sources containing resources marked up with semantic metadata, like Bioschemas. Currently, TeSS cannot recognize references to bio.tools identifiers from a Bioschemas-annotated resource, so the number of resources linked to bio.tools is relatively low.
In this project, TeSS’ Bioschemas parser will be extended to recognize bio.tools identifier references, and documentation produced advising training resource maintainers how they can add these references to their Bioschemas markup. In collaboration with TeSS and bio.tools, we will focus on selected SB disciplines from the priority areas of the SB Community to integrate and cross-link related ELIXIR products - training events, training materials, computational and bioinformatics tools, databases and services from the bio.tools registry.
This will be achieved using suitable ontologies identified by the SB community and by careful curation of SB-related materials. We aim to extend this work to other ELIXIR products such as lists of trainers, related ELIXIR Innovation and Industry events and publications. This will serve as a pilot project leading to broader integration with other SB disciplines, and will be of interest to several other ELIXIR Communities.
- The short-term goal is to conduct a pilot study at the Biohackathon, the long-term goal is to extend the automated frame-work to other SB-related ELIXIR domains and services.
- (1) Adapting ontologies and explore ontology mappings (e.g., between EDAM and SBO), to annotate SB-related products by a set of controlled and relational vocabularies. (2) Using selected SB disciplines and related TeSS and bio.tools products (training events, training materials, computational, bioinformatics tools, databases, services), to integrate TeSS and bio.tools by extending TeSS’ Bioschemas parser. We will aim to explore: (3) Compliance with FAIR principles. (4) Extension to other ELIXIR resources.
- The preparation for the Biohackathon will start well before November to ensure we have a balanced and well-prepared team of curators and software developers, a minimum of 2-3 from both groups.
- We will leverage expertise of both curators and software developers, by alternating group meetings and the actual development of the project.
Barbara Szomolay, Brane Leskosek, Herve Menager