Core Data Hubs hosted at EMBL-EBI will be extended to integrate the wastewater data use case and additional pathogens covered by the Pathogen Analysis System. A major functionality of the data hubs enables multiple collaborators and institutes to share data in private, pre-publication mode, prior to release publicly. We will develop interfaces to elements of the core data hubs at various levels: (1) data submission, maintaining metadata standards and appropriate data accreditation and authorisation, (2) data analysis via integration into the Pathogen Analysis System, (3) related visualizations and tools, (4) search and retrieval, with documented specifications.

Services will span all pathogens determined to be of interest to NIH-NIAID and will include coverage of publicly available data from public data resources, such as INSDC, UniProt and wwPDB. These data will be made discoverable through search tools through the indexing of metadata harvested from global data resources.

We will also provide a data sourcing toolkit, to (i) document and publish public data resource indexing and metadata retrieval workflows, and (ii) provide tools and/or code snippets to support the developers and operators of third party specialist data resources managers in their systematic access to data sets of relevance to their services.

A Capacity Framework for pathogen data platforms will be implemented as a web portal to support capacity building and continuous improvement towards FAIR data management and processing.

For the standards and analyses, we will focus on the wastewater use case and on highest priority pathogens.

Work stream co-leads:

• Nadim Rahman (EMBL-EBI)
• Sara Monzón (ISCIII)
  

PDN develops innovative computational methods, with benchmarking and implementation across PDN. A selected use case on wastewater data will serve to co-develop the infrastructure and governance, chosen as examples for the development of generic elements of a shared analytics system that tackles challenges across pathogens and diseases, and threading through the PDN project such that technical delivery and engagement of scientific communities is optimally tuned to the diversity of pathogens that exist.

PDN also provides outbreak response capabilities by integrating standard analysis workflows for some viruses, bacteria, fungi, parasites and vector-borne pathogens of interest to NIAID, into the Pathogen Analysis System. This also includes developing and integrating dedicated analysis pipelines on the Pathogen Analysis System in response to emerging threats to rapidly support the community.

Work stream co-leads:

• Miranda de Graaf (EMC)
• Peter Van Heusden (SANBI)

The PDN and its internal users, managers, and systems will be overseen through a transparent and effective governance structure that will develop and implement policies informed through a consultative process involving all constituencies, including community representatives from the Open Community Forum roundtable, experience from current archival databases and sharing platforms, international collaborations advancing FAIR Data Principles in pathogen genomic research (e.g. PHA4GE, GMI), and international and national policy decisions (e.g. WHO, CBD, CDC, ECDC, African CDC etc.).

These policies will be shaped in light of the need to protect sensitive data; promote trust and accountability between users and between the broader open data ecosystem and the public health and lay communities and decision makers; and do so through regular consultation and revision. Conversely, policy experts in the PDN Consortia will represent PDN interests and vision in various policy discussions.

The work will focus on the wastewater data use case but also consider broadly all the pathogens of interest to NIAID.

Work stream co-leads:

• Amber Scholz (DSMZ)
• Sam Halabi (GU)
  

PDN will provide:

1. Introductory training for newcomers with limited computational skills;
2. Community engagement that raises awareness of the platform among broader audiences;
3. A documentation and support desk that can support all levels of users, including those with advanced skills and use cases. Efforts will mainly focus on the wastewater use case. We will prioritize reaching audiences that could make use of the data and tools but may need assistance in overcoming data analysis skills gaps.
4. An Open Community Forum that will ensure community-driven developments that meet existing needs and have real impact. It is a forum to identify gaps, propose new ideas of features and suggest developments to be implemented. The forum’s ultimate goal is to facilitate widest use of pathogen biodata for research, management (including surveillance and informing policy) and learning, by enhancing the utility of open pathogen biodata to our stakeholders.

Work stream co-leads:

• Jason Williams (CSHL)
• Daniel Thomas Lopez (EMBL-EBI)
• Kim Gurwitz (EMBL-EBI)
• Aitana Neves (SIB)
• Lily Weissgold (DSMZ)