This study is divided into four Work Packages (WP). The first three aim to survey the biodiversity data domain and catalogue and assess relevant research data management elements (WP1), analysis tools, services, and infrastructures (WP2), as well as active and planned projects and stakeholders (WP3).
WP4 aims to grow the ELIXIR Biodiversity Community by collating resources and materials for training and knowledge transfer amongst ELIXIR members and the wider research community.
WP1: Research data management and data interoperability
The aim of WP1 is to survey and catalogue Research Data Management (RDM) elements relevant to the biodiversity domain, with a focus on molecular data but not excluding other relevant data collection activities. By focusing on data management and not data analysis it remains distinct from WP2.
It is aligned with WP3 through the mapping of RDM-related activities being performed as part of ongoing projects (e.g. BGE, BiCIKL, TETTRIs), and will provide some of the substrate for discussions as part of WP3’s planned network event, contributing to creating connections with the wider community (particularly active ELIXIR Nodes).
It will also highlight current capacities and gaps in RDM practices that will feed into WP4’s activities. Development and adoption of best practices in RDM for the biodiversity research domain remain extremely variable, hence the focus here on assessing the current status and collating existing best practices. This will strengthen ELIXIR’s position in the biodiversity domain by leveraging ELIXIR’s RDM-related strengths in other research domains including other ELIXIR Communities.
Lead
Josie Burgin (EMBL-EBI)
Tasks
- Task 1.1: Collate existing data and metadata standards used to record biodiversity data and metadata, maintaining interoperability beyond genomics (taxonomy, ecological data, traits etc.) including gap identification on FAIRsharing and create or add to an existing Collection.
- Task 1.2: Develop implementable best practice recommendations for management of biodiversity molecular data in line ongoing projects (e.g. BGE, BiCIKL), connecting this to a dedicated RDMkit domain, at least one hybrid workshop to bring RDMkit to publishable status
- Task 1.3: Create FAIR Cookbook recipes on recommendations for tools associated with data management (e.g. applications of RO-crate and Ecological Metadata Language-oriented tools).
- Task 1.4: Build recommendations for recording taxonomic annotation of archived samples and sequences working with NCBI/GBIF/CoL/DiSSCo.
- Example Case Study: GlobalFungi Database metadata collection and curation to make published data findable and reusable in a research context.
Milestones and deliverables
- M1.1: List of existing standards and gap analysis in FAIRsharing
- M1.2: First draft of RDMkit for biodiversity molecular data management
- M1.3: Linking FAIR Cookbook recipes and RDMkit page/s
- M1.4: Publish taxonomic recommendations on RDMkit
- D1.1: Final cross-linked RDMkit and FAIR Cookbook content, standards in FAIRsharing and taxonomic recommendations
WP2: Services, tools, and analysis
The main aims of WP2 are to catalogue, review, and categorise tools, services, and analytical workflows currently in use by ELIXIR Nodes and the wider community, that process and analyse biodiversity-related data, with an emphasis on molecular data. This will include ELIXIR and non-ELIXIR tools.
It remains distinct from WP1 by focusing on data analysis tools, services, and infrastructures and not on data management in research. It will benefit from WP3’s surveys of stakeholders/projects to help identify key tools and services that should be prioritised for review and cataloguing. These priorities can feed into WP4’s training activities by identifying community needs with respect to the usability of important tools and services.
The outputs will ensure that ELIXIR is playing a leading role in identifying and exposing high-quality biodiversity-related analysis tools and services to the wider community of users, as well as fostering the development of such tools and services through connecting ELIXIR Nodes which are active in the domain.
Lead
Toni Gabaldón and Matúš Kalaš
Tasks
- Task 2.1: Development and population of a curated biodiversity subdomain in Bio.tools, especially for computational tools and workflows applicable to biodiversity research, particularly biodiversity genomics and biodiversity informatics
- Task 2.2: Review biodiversity-related workflows available in Galaxy and WorkflowHub, a curation effort to maintain a list of biodiversity-relevant workflows, working with Galaxy, the EuroScienceGateway EOSC project, and others, to support the inclusion of key tools
- Task 2.3: Collate community-wide usage of pipelines for biodiversity data analyses including tools to visualise and promote the data and publish the tools and workflows, connecting to the user communities to capture the steps considered critical for analysis workflows
- Task 2.4: Identify and fill gaps in the EDAM Ontology to enable cataloguing of biodiversity-relevant tools/services/workflows and other materials in Bio.tools, Galaxy, TeSS (WP4), WorkflowHub, and others (working closely with Tasks 2.1-2-3)
- Example Case Study: ITSoneWB profiling global taxonomic diversity of eukaryotic communities on Galaxy, and the GlobalFungi Database analysis workflows
Milestones and deliverables
- M2.1: Overview of main components of community-accepted biodiversity workflows
- M2.2: A prioritisation list of workflows for inclusion in Galaxy and WorkflowHub
- M2.3: EDAM concepts related to biodiversity research refined, updated, and added
- D2.1: Bio.tools, WorkflowHub, and Galaxy subdomains, populated with tools and workflows for biodiversity research
WP3: Outreach, networking, and communications
Biodiversity is a very broad and diverse domain of research, in which many networks of infrastructures and initiatives are involved. The main aims of WP3 are to better describe the landscape of stakeholders ELIXIR is working with or needs to better engage with and to establish a “network of networks” for biodiversity research.
It will feed into WP1 and WP2 by identifying ongoing or planned work directly relevant for improving RDM practices, and by exposing tools, services, and analysis workflows that the wider community are developing. It will also help to link training and knowledge transfer activities of various projects and stakeholders to the ELIXIR Training Platform and WP4.
By leveraging ELIXIR’s federated structure, these network growing activities will support biodiversity research by improving connections between existing projects and communities, as well as by promoting synergies and aligning data and tools to the needs of researchers. This will also strengthen ELIXIR’s position as a partner in the planning and development of new projects and initiatives in the biodiversity data/research domain.
Lead
Henrik Lantz
Tasks
- Task 3.1: Stakeholder and project (ongoing and planned) mapping exercise including a series of online questionnaires and idea gathering both within ELIXIR Nodes and externally in the form of funded local, national, regional, etc. projects and infrastructures or initiatives.
- Task 3.2: Build the “network of networks” by reaching out to and connecting with: infrastructures or initiatives (e.g. DiSSCo, GBIF, Lifewatch-ERIC, Geo-BON, Planetary Biology at EMBL) operating both transnationally and nationally; Ongoing European Commission funded projects (e.g. BGE, BiCIKL, BIODT, BioDiversa+), Platforms (e.g. Data Platform) and relevant ELIXIR Communities (e.g. Galaxy, Metagenomics, and System Biology). This will provide the critical mass, as well as the lines of communication, that will be required to effectively run the efforts in the other WPs (such as the community-accepted workflows, relevant biodiversity terms, as well as data management aspects).
- Task 3.3: Support meaningful interactions and exchanges through networking events, e.g. mini symposium at ELIXIR All Hands, online meetings for biodiversity-relevant projects to present themselves and discuss synergies, in-person meetings as satellites of other meetings, possibly also reaching out to connect with small and medium-sized enterprises working in the biodiversity domain.
Milestones and deliverables
- D3.1: A prioritised list of international and national stakeholders and partners that will drive the “network of networks”
- M3.1: Engagement and communication plan with priorities and actions
- M3.2: Diverse networking events, with different focus, that bring stakeholders together
- D3.2: An ELIXIR Biodiversity Community page, pointing to the collections of collated resources and further relevant pages/documents, highlighting the work of WP1, 2, and 4
WP4: Training and knowledge transfer
The overarching aim of WP4 is to leverage the strengths of ELIXIR’s training experience to help support the growth of the ELIXIR Biodiversity Community through network-driven sharing of training experiences and knowledge transfer and materials.
The work will be developed in close collaboration with the ELIXIR Training Platform and extensively use the methods already developed. Activities in Work Packages 1, 2, and 3 will help to connect to a wide range of relevant stakeholders and thereby feed WP4 with information about ongoing or planned training-related activities on the broader biodiversity community.
Lead
Patricia Palagi and Anne-Françoise Adam-Blondon
Tasks
- Task 4.1: Based on the relevant communities and stakeholders, define the appropriate learning pathways that can be used to upskill researchers in the context of biodiversity studies, and by connecting this with WP2, also allow for the identification of potential gaps in tools, services and training, so that this can be prioritised by the relevant initiatives.
- Task 4.2: Review, improve, and maintain a curated collection of biodiversity-relevant training resources (e.g. Galaxy for Ecology initiative), including materials (aiming for FAIR and open materials) and training and knowledge transfer events, published and made accessible through TeSS , GTN, etc.. and shared through the networks being mapped by activities in WP3.
- Task 4.3: In collaboration with WP3 and the ELIXIR Training Platform, sustain and increase training capacity in the community by raising awareness and organising events to exchange knowledge and information in best practices, methods and datasets for training, on Train-the-Trainer (TtT) pedagogical training activities.
Milestones and deliverables
- D4.1: Learning pathway(s), co-designed and co-created with the relevant communities
- M4.1: A list of gaps and priorities for new training materials/topics to be developed
- D4.2: A collection of training resources, as a TeSS Collection / GTN group links
- D4.3: Project Mid-term reporting (for contractual purposes); to be provided by funded Nodes
- D4.4: Scientific end report and Node-specific end report of the Implementation Study