Minutes – 24 Jan 2025 – PDN All-Hands Meeting (3)

by | Mar 5, 2025 | Minutes, Minutes Consortium meetings | 0 comments

Thirty two PDN members, representing all 12 institutions, were present at the virtual All Hands meeting on 24 January 2025.

General Updates

 

  • Workstreams 5 (Training and Outreach) and Workstream 6 (Community) have merged into a single WS5 Training, Outreach and Community.
  • In-person event will take place in Lausanne, Switzerland, on 17-18 March, with around 30 PDN members from the US, South Africa and Europe.
  • RPPR guidelines were provided to PDN members.
  • WHO open consultation on “Attributes and principles for genomic data sharing platforms supporting surveillance of pathogens with epidemic and pandemic potential”: it was agreed that PDN will provide a consolidated response with a subgroup of members.

Workstream Updates

  • WS1: Pathogens Portals
      • Central Pathogens Portal
        • Indexing technology research to support very large datasets through SOLR, in addition to current Lucene-based backend indexing engine
        • Initiated more fine-grained access tracking to support impact reporting (based on BV-BRC metrics reporting). To be discussed how to disseminate it.
      • Pathogens Portal Nodes
        • Reference software:
          • First version of public repository for PPN software to be released in next few days
        • Community of Practice (CoP)
          • We have reached out and met those who had written letters of intent to collaborate with PDN. This will be the nucleus of the CoP. Others will be invited to join on an ongoing basis. Regular meetings will be set up.
          • Pathogens Portal Nodes: The 1st call for PP nodes seed money is open until 12th February, 1 application received so far. 
  • WS2: FAIR Data Management
      • Core Data Hubs and Archival Database
        • Data Hubs Portal
          • Included advanced searching feature for datasets which incorporates authenticated search.
          • Working on tidying up features and bugs in preparation for release (hopefully end of Feb/early March prior to Lausanne meeting).
          • Have had one or two further Data Hub requests and discussions – mainly to utilise the pre-release data sharing feature.
        • Working on incorporating the NIAID priority pathogens list into Pathogens Portal.
          • This includes updating GitHub of classifications that characterise content in the portal, tagging datasets accordingly ensuring that data content is presenting appropriately, and then updating the Pathogens Classification page to detail the sources.
          • Updates completed in Github. Tagging is automatic, and classifications page should update shortly.
        • Arbovirus data tagging
      • Pathogen Analysis System
        • Prototyping work with Galaxy platform – includes generating a Galaxy module to push data back to ENA.
          • Pilot with TB analysis pipeline
        • Working to arrange a call with BRC.analytics in order to better identify collaboration between the projects.
      • Capacity Framework
        • Planning strategy, work is ongoing and we are in contact with WHO IPSN to take into account their capacity framework – we want to align with them as much as possible. Planned work session on 18-19 March as follow-up of in-person meeting.
      • Metadata Standards
        • Working on respiratory viruses and AMR surveillance metadata.
        • Had a call with ELIXIR Biovalidator folks to discuss JSON schema validation using ontologies in more detail – understanding and taking forward what was learned and developed. 
  • WS3: Data Analyses
      • Outbreak response:
        • Working on priority pathogens list, to be presented at the next Executive Board meeting and the in-person event in Lausanne. 
      • Database: 
        • Started integrating global sewage analytical outputs
        • Improved database structure based on user feedback
      • Metagenomics:
        • Dark matter analysis: improved datasets by combining multiple datasets. Sequenced more wastewater samples with capture probes that also detect respiratory viruses. Meeting next week for discussing analysis pipeline.
        • Discussions on how to improve the binning to get more MAGs generated. Prediction of which MAGs are pathogenic or not, resulting tree was shown. 
  • WS4: Policy & Ethics
      • Developing Access Benefit Sharing (ABS) statement, to be further discussed at Lausanne meeting.
      • Outbreak response:
        • dynamic respond to other work streams
        • Prototype guidelines
        • Input on priority pathogen lists to reflect policy lists (e.g. IHR, PABS working definitions)
      • Working to identify areas for engagement around World Health Assembly (WHA)
        • Including policy briefing from WHO Secretariat (hopefully) – also related to EVORA project.
        • Deciding how to engage with negotiators
      • Working to schedule a policy workshop for PDN/BRC members– need input on dates. Does the first or second week of June work better?
      • Conducting wastewater ethics and regulatory assessments to inform PDN data management practices
      • Developing literature review on international guidance and policy documents on wastewater surveillance
      • Developing WWE Ethics Framework (PHA4GE) 
  • WS5: Training, Outreach & Community
      • Internal survey was sent out to the project members with questions about products, services, and users that we should support. The survey received 16 answers. We are in the process of analysing the results.
      • Preparing a survey around the same questions for the external community.
        • Potential survey participants: 
      • Support Centre for the Pathogens Portal: first working sprint to develop the website infrastructure happening in February.
      • Interview requests have gone out to PDN PIs, interview requests will go out to others on a rolling basis starting mid-next week. 
      • Preparing a survey around the same questions for the external community.
  • Outreach to Public Health stakeholders
        • Meeting with CDC Enteric Branch, Enterobase, CDC wastewater (5 Feb), cgMLST work session (13 Feb), other in planning
  • OCF and website
      • Internal interviews status: please respond to Lily’s emails
      • Working on 1-pager with SIB Comms team to accompany requests for interviews (for OCF) 
      • Website: being improved with SIB Comm
      • LinkedIn: retaken by SIB Comm
      • Started discussing the format of roundtable discussions focusing on what we want people to know, think, and feel after attending these – Kim and Lily will work on an initial draft and then circulate for comment