New domain page about Virology

[NielsGeudens]

What topic do you wish to add?

A RDMkit domain page on virology. However, there is already (scattered) information available on RDMkit.

Are there existing pages in the RDMkit website related to the requested page?

The following sections from RDMKit could be relevant:

• COVID-19 Data Portal
• Collecting and processing pathogen genomic data: Your domain: Human pathogen genomics | RDMkit
• Sharing and preserving pathogen genomic data: Your domain: Human pathogen genomics | RDMkit

Quotes from existing RDMKit microbiology biotechnology domain:

• “Genomic information can be captured at the nucleotide level using the well-known European Nucleotide Archive (ENA) and submitted to the ENA database to allow the information to be shared.”
• “The database collection from the International Nucleotide Sequence Database Collaboration (INSDC) provides an umbrella for gathering and sharing a variety of sequence data from different sequence databases internationally.”
• “Other databases such as GenBank and the DNA Data Bank of Japan (DDBJ) also cater for sequence information.”

Existing information that could be referenced as “related pages”

• Data Publication
• Existing Data
• Data Security
• Data Sensitivity
• Human Data
• Data Analysis

Resources

If there are there resources that could be utilised for writing the new page, please list them below:

• General information regarding virus bioinformatics: Virus Bioinformatics - PMC
• Overview of databases and webtools: Database and Analytical Resources for Viral Research Community - PMC

Topics that could be included in a virology-oriented RDMKit domain page

1. Critical Resources:

• European Virus Archive
• International Committee on Taxonomy of Viruses (ICTV)

2. Standards and Vocabularies:

• EVORA vocabulary and ICTV ontologies (pending availability on OLS in M18/M24).

3. ISO Standards (though maybe not RDM-related enough?)

• ISO 35001 (Biorisk Management), which is currently under review by a Technical Committee, Kurt Zatloukal is participating
• ISO 20387 (Biobanking)
• ISO 17025 (Calibration and diagnostics);
• ISO 17034 (Ref material producers);
• ISO 9001 (Control of processes);
• ISO 15189 (Medical lab management);
• ISO 13485 (Medical devices)

4. Tools for Genomic Assembly:

• Address the gap in virology-specific genome assembly tools
• Virus Metagenomic classification methods: Frontiers | Overview of Virus Metagenomic Classification Methods and Their Biological Applications

Additional Tools:

• Biostudies: https://www.ebi.ac.uk/biostudies/

• ArrayExpress - Functional Genomics Data : https://www.ebi.ac.uk/biostudies/arrayexpress

• BioContainers can definitely have containers of interest, but need to be sorted out and a cookbook or tutorial from scratch will have to be provided for use by virologists:
  - https://biocontainers.pro/registry?all_fields_search=virus&sort_order=asc&sort_field=default&offset=0&limit=30
  - https://biocontainers.pro/registry?all_fields_search=assembly&sort_order=asc&sort_field=default&offset=0&limit=30
  - https://biocontainers.pro/registry?all_fields_search=metagenome&sort_order=asc&sort_field=default&offset=0&limit=30

• Same for biotools a selection of tools should be validated by virologists:
  - https://bio.tools/t?topicID=%22topic_0781%22

• COVID-19 Structural Hub https://3dbionotes.cnb.csic.es/ws/covid19

• disease-ontology https://www.disease-ontology.org/

• International Classification of Diseases https://icd.who.int/en

• Informed Consent Ontology https://raw.githubusercontent.com/ICO-ontology/ICO/master/ico.owl

• MolSSI - BioExcel COVID-19 therapeutics hub https://covid.bioexcel.eu/

• VirHostNet https://virhostnet.prabi.fr/

• ViralZone: https://viralzone.expasy.org/

• NCBI virus : https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide

• BV-BRC Bacterial and viral bioinformatics resource center: https://www.bv-brc.org/view/Virus/10239

• VIPERdb virus particle Explorer database https://viperdb.org/

• GBIF viruses : Global Biodiversity Information Facility https://www.gbif.org/search?q=virus

• GenBase for submission to INSDC: https://ngdc.cncb.ac.cn/genbase/?lang=en

• VirusSeq canadian data portal: https://virusseq-dataportal.ca/

• Sanger institute virus data: https://www.sanger.ac.uk/data/virus-data/

• VectorSurv for vector-borne diseases (USA) https://vectorsurv.org/

• IDDO Infectious Diseases data observatory: https://www.iddo.org/

• INFRAVEC https://infravec2.eu/

Key tools and databases that are already referenced in other parts of RDMKit, but that could also be relevant for the virology domain page:

• Data Repositories and Submission:
  - ENA Browser
  - ENA Upload Tool
  - INSDC (Essential for virology community engagement)
  - /!\GenBank is probably so obvious that it might be not required to list it https://www.ncbi.nlm.nih.gov/genbank/
• Analysis Tools:
  - Nextstrain for real-time pathogen evolution tracking
  - Nextclade (hosted by nextstrain) for clade assignment and quality checks
• COVID-19 Data Resources:
  - COVID-19 Data Portal
• The Pathogen Portal
  - https://www.pathogensportal.org/
• General:
  - Zenodo for data deposition
  - OpenAIRE Explore for open data

Context

About the EVORA project:
Building on previous collaborations, three key research infrastructures—EVA partner network, along with two major European infrastructures, ERINHA and ELIXIR —have joined forces as the European Viral Outbreak Research Alliance (EVORA). Together, we aim to integrate parts of their operations to create a sustainable platform for research on epidemic- and pandemic-prone viruses.
To promote discovery and adoption of best practices in data management for the virology community (D7.3 in the project), we aim to build on the ELIXIR RDMkit. Our goal is to create a framework that presents research data management practices tailored to the virology community. This framework should provide access to guidelines, best practices, and relevant services, including those offered by EVORA partners and public repositories.
In the project, we will work in two steps: we wish to create a ‘basic’ Virology domain page, which will be introduced to project members. In the course of the project (estimated, start of 2026), we will also organise a ‘contentathon’ event to expand existing RDM resources, including the basis domain page.
Note: poster of the issue is not a domain expert. Any assistance regarding validation of content would be greatly appreciated.