Q: Will the data be downloadable individually, or in large-scale, and in different formats? Will there be pre-computed data available?

The current bulk download system is described here . This will be evolved throughout the project in response to user requirements. Several pipelines will be integrated into the Pathogen Analysis System (PAS). For the data types and species covered by the PAS, pre-computed datasets will also be made available; for others primary (but validated) data will be presented.

Question 1

How do I access, search, and blast the data and data sets in the PDN?

clinbio-admin · Accepted Answer

The Pathogens Portal hosted at EMBL-EBI will let investigators access and search the data. Users may blast the data trough the ENA portal.

Question 2

How do I obtain information about the BRC releases and events?  Will there be newsletters, social media, and public forums that I can attend and participate discussions?

clinbio-admin · Accepted Answer

We will have a dedicated website to update regularly on the BRC releases and events. We will also make use of social media (e.g. LinkedIn, X). The Open Community Forum will be accessible from the website.

Question 3

I do not have background in bioinformatics.  Will the analytics tools be easy to use?  If I need help, how and where do I get help?

clinbio-admin · Accepted Answer

The PDN Community of Practice and Open Community Forum will be starting places to get help. The Pathogen Analysis System will also pre-compute datasets based on standard pipelines.

Question 4

I have restrictions on upload my data to compute.  Will I be able to use analytics software tools running on my laptop locally?

clinbio-admin · Accepted Answer

Yes, the analysis pipelines will be made publicly-available on code repositories; in this case users will be required to set up and operate the appropriate workflow management environments for their work.

Question 5

If I have feedback, suggestions, or requests for (new functionalities, data, and special services (e.g., conducting specialized analysis, assisting with data deposits, requesting specialized trainings etc.), to the PDN, how do I contact the PDN?

clinbio-admin · Accepted Answer

On our website (to be developed), we will have dedicated space for the Open Community Forum and for anyone to make suggestions or requests.

Question 6

What are data types (e.g., genomics, transcriptomics (bulk and scRNASeq), proteomics, orthologs, surveillance, etc.) and data sets that will be offered in the PDN?

clinbio-admin · Accepted Answer

PDN will cover diverse biodata types, including host and pathogen genomics, transcriptomics, proteins, pathways and networks, imaging and cohorts.

Question 7

What are the organisms and taxonomic groups available in the PDN?

clinbio-admin · Accepted Answer

The Data Portal services will span all pathogens determined to be of interest to NIH-NIAID, gradually also capturing host, intermediate host and vector species of relevance to the listed pathogen species and groups.

Question 8

Will I be able to bring my own data to analyze with the data in the PDN?  Will I be able to store my data privately and securely?  What is the limit of data storage? How long can I store my data?  Can I share my data with others?  Will there be different options to adjust the access to my data and analytics (e.g., privately, share with collaborator and make it public)?

clinbio-admin · Accepted Answer

The data should be submitted to INSDC. The Pathogens Portal offers the possibility to request a private data hub to host non-sensitive data, and share them privately within a group of collaborators for a limited time (up to 2 years in the first instance, but extensible). After this time, data are expected to be released fully openly in accordance with best open data practice.

Question 9

Will the data be curated, relevant and frequently updates?  And how often the database is updated in comparison to the INSDC?

clinbio-admin · Accepted Answer

Data will be routed into PDN through data submission tools and services appropriate for the data type concerned. This routing will assure that data type-appropriate validation, standards compliance, curation and integration are applied to data available through PDN services. The Portal will not host data directly, rather will provide a fully synchronous view on the underlying data resources upon whose data it serves. The core data resource, ENA, is refreshed on a daily basis; as soon as data have been through submission services, they are released into ENA and indexed on a daily basis, and hence become available for indexing in the Portal.

Question 10

Will the data be downloadable individually, or in large-scale, and in different formats? Will there be pre-computed data available?

clinbio-admin · Accepted Answer

The current bulk download system is described here. This will be evolved throughout the project in response to user requirements. Several pipelines will be integrated into the Pathogen Analysis System (PAS). For the data types and species covered by the PAS, pre-computed datasets will also be made available; for others primary (but validated) data will be presented.

Question 11

Will the new PDN support large-scale data download and large-scale analytics, and computation?  And what is considered large-scale (e.g., more than 100)? Will the analytic tools and computations run at adequate speed?

clinbio-admin · Accepted Answer

Bulk downloads will be supported. Scaling of downloads and analytics of many hundreds of thousands of datasets, or indeed entire collections will eventually be implemented based on existing technology.

Question 12

Will the PDN educational material (e.g., User Documentation, Webinars, YouTube Video, email help desk, on-line materials, MOOCs/Coursera, conference booths, etc.) be free and accessible broadly to investigator around the world?

clinbio-admin · Accepted Answer

All the training material will be freely accessible and comply with FAIR principles.

Question 13

Will the resources be free and accessible broadly to investigator around the world?

clinbio-admin · Accepted Answer

All the resources developed within PDN will be free and accessible to investigators (via web interfaces or by providing open source code under permissive licences on open repositories). All data will also be available for download, subject to data protection restrictions.

Question 14

Will there be a mechanism to incorporate my experimental results or findings into the data in the PDN (e.g., modify the annotated genomes)?

clinbio-admin · Accepted Answer

No. The appropriate routing for this information is via the owners of the genome records, who can consider incoming experimental data for incorporation into their annotations; we therefore recommend in these cases that experimentalists work with data owners to drive these annotation updates.

Question 15

Will there be a workspace with selections of tools for analyzing data?   Will the command-line interface and web interface GUI (click-and-drag) functions be available?  And if I have a tool that would be helpful for others, how do I share my tools with others in the PDN?

clinbio-admin · Accepted Answer

The tools integrated into the Pathogen Analysis System will run automatically for the matching data types and species. A standardised workflow template based on DSL2 Nextflow will also be available for users of local data hubs to run these workflows on their data. We consider providing a workflow repository to deposit analysis pipelines, share and collaborate, but we do not anticipate command-line or click and drag functions directly on arbitrary (user-selected) data sets in the Portal.

Question 16

Will there be experts in my field who understand the needs and where the field is going as part of the PDN?  And can I offer my suggestions on how to improve the PDN and how do I do that?

clinbio-admin · Accepted Answer

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The PDN comprises a large consortium with wide expertise. We however welcome suggestions and expertise from others, as part of the Open Community Forum and through the Community of Practice where we will reach out to domain experts. PDN will also liaise with other initiatives relevant to this topic (e.g. PHA4GE, GMI, ELIXIR…).

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Question 17

Will there be tools to help me submit my genomic data and metadata associated data to public repositories (e.g., NCBI, other INSDCs)?

clinbio-admin · Accepted Answer

We will provide and support the submission tools and services that ENA provides. There will not be PDN-specific tools, but the development cycles for the existing tools will be informed by what we hear and learn from their use by the PDN data provide community. In addition, PDN includes a Community of Practice where knowledge sharing on data brokering will be a central element, providing further streamlined options for those providing their data into PDN.

RESOURCES

Pathogens Portal

Pathogens Portal Nodes

Pathogen Data Platform Capacity Framework

Training material

Presentations

Minutes Consortium meetings

Minutes Executive Board meetings

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

Minutes – 22 Nov 2024 – PDN All-Hands Meeting (2)

Minutes – 20 Sept 2024 – PDN All-Hands Meeting (kick-off)

Minutes – 28 February 2025 – PDN Executive Board meeting

Minutes – 20 December 2024 – PDN Executive Board meeting

Minutes – 25 October 2024 – PDN Executive Board meeting

Frequenty Asked Questions

General

If I have feedback, suggestions, or requests for (new functionalities, data, and special services (e.g., conducting specialized analysis, assisting with data deposits, requesting specialized trainings etc.), to the PDN, how do I contact the PDN?

What are the organisms and taxonomic groups available in the PDN?

Will there be experts in my field who understand the needs and where the field is going as part of the PDN? And can I offer my suggestions on how to improve the PDN and how do I do that?

Training and Events

How do I obtain information about the BRC releases and events? Will there be newsletters, social media, and public forums that I can attend and participate discussions?

Will the PDN educational material (e.g., User Documentation, Webinars, YouTube Video, email help desk, on-line materials, MOOCs/Coursera, conference booths, etc.) be free and accessible broadly to investigator around the world?

FAIRness of data and resources

How do I access, search, and blast the data and data sets in the PDN?

I have restrictions on upload my data to compute. Will I be able to use analytics software tools running on my laptop locally?

What are data types (e.g., genomics, transcriptomics (bulk and scRNASeq), proteomics, orthologs, surveillance, etc.) and data sets that will be offered in the PDN?

Will the data be curated, relevant and frequently updates? And how often the database is updated in comparison to the INSDC?

Will the data be downloadable individually, or in large-scale, and in different formats? Will there be pre-computed data available?

Will the new PDN support large-scale data download and large-scale analytics, and computation? And what is considered large-scale (e.g., more than 100)? Will the analytic tools and computations run at adequate speed?

Will the resources be free and accessible broadly to investigator around the world?

Will there be a mechanism to incorporate my experimental results or findings into the data in the PDN (e.g., modify the annotated genomes)?

Will there be tools to help me submit my genomic data and metadata associated data to public repositories (e.g., NCBI, other INSDCs)?

Analyses

How do I access, search, and blast the data and data sets in the PDN?

I do not have background in bioinformatics. Will the analytics tools be easy to use? If I need help, how and where do I get help?

Will the data be downloadable individually, or in large-scale, and in different formats? Will there be pre-computed data available?

Will the new PDN support large-scale data download and large-scale analytics, and computation? And what is considered large-scale (e.g., more than 100)? Will the analytic tools and computations run at adequate speed?

Will there be a workspace with selections of tools for analyzing data? Will the command-line interface and web interface GUI (click-and-drag) functions be available? And if I have a tool that would be helpful for others, how do I share my tools with others in the PDN?

RESOURCES

Training material

Presentations

Minutes Consortium meetings

Minutes Executive Board meetings

Frequenty Asked Questions

General

If I have feedback, suggestions, or requests for (new functionalities, data, and special services (e.g., conducting specialized analysis, assisting with data deposits, requesting specialized trainings etc.), to the PDN, how do I contact the PDN?

What are the organisms and taxonomic groups available in the PDN?

Will there be experts in my field who understand the needs and where the field is going as part of the PDN? And can I offer my suggestions on how to improve the PDN and how do I do that?

Training and Events

How do I obtain information about the BRC releases and events? Will there be newsletters, social media, and public forums that I can attend and participate discussions?

Will the PDN educational material (e.g., User Documentation, Webinars, YouTube Video, email help desk, on-line materials, MOOCs/Coursera, conference booths, etc.) be free and accessible broadly to investigator around the world?

FAIRness of data and resources

How do I access, search, and blast the data and data sets in the PDN?

I have restrictions on upload my data to compute. Will I be able to use analytics software tools running on my laptop locally?

What are data types (e.g., genomics, transcriptomics (bulk and scRNASeq), proteomics, orthologs, surveillance, etc.) and data sets that will be offered in the PDN?

Will the data be curated, relevant and frequently updates? And how often the database is updated in comparison to the INSDC?

Will the data be downloadable individually, or in large-scale, and in different formats? Will there be pre-computed data available?

Will the new PDN support large-scale data download and large-scale analytics, and computation? And what is considered large-scale (e.g., more than 100)? Will the analytic tools and computations run at adequate speed?

Will the resources be free and accessible broadly to investigator around the world?

Will there be a mechanism to incorporate my experimental results or findings into the data in the PDN (e.g., modify the annotated genomes)?

Will there be tools to help me submit my genomic data and metadata associated data to public repositories (e.g., NCBI, other INSDCs)?

Analyses

How do I access, search, and blast the data and data sets in the PDN?

I do not have background in bioinformatics. Will the analytics tools be easy to use? If I need help, how and where do I get help?

Will the data be downloadable individually, or in large-scale, and in different formats? Will there be pre-computed data available?

Will the new PDN support large-scale data download and large-scale analytics, and computation? And what is considered large-scale (e.g., more than 100)? Will the analytic tools and computations run at adequate speed?

Will there be a workspace with selections of tools for analyzing data? Will the command-line interface and web interface GUI (click-and-drag) functions be available? And if I have a tool that would be helpful for others, how do I share my tools with others in the PDN?

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