[Source]: The PapillomaVirus Episteme (PaVE)

[EmilyHaag]

Source Name

The PapillomaVirus Episteme (PaVE)

Source URL

https://pave.niaid.nih.gov/

Source Description

PaVE is a NIAID-funded, curated repository of annotated papillomavirus genomes. It also has a toolset for analysis of user-submitted genomes. PaVE currently contains 853 annotated papillomavirus genomes, 11338 genes and regions, 6687 protein sequences, and 108 protein structures, which users can explore, analyze or download from the site.

Source Access

No access issue, account not needed

Source Funding

NIAID

Source Relevance

PaVE is a valuable resource for HPV research, offering genomic, proteomic, and functional data for papillomaviruses. Including PaVE in the NIAID Data Ecosystem will centralize access to high-quality, curated HPV datasets and tools. Additionally, this resource was prioritized for inclusion by ODSET.

Related WBS task

• Check here if this repository is funded by NIAID (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/11)
• Check here if this repository only has IID data (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/12)
• Check here if this is a generalist repository with IID data (https://github.com/NIAID-Data-Ecosystem/nde-roadmap/issues/12)

For internal use only. Assignee, please select the status of this issue

• Not yet started
• In process
• Blocked
• Will not include

Status Description

No response

Source to-do list

• License check- Can this source be included?
• Class check- Does this source have the right class of research output for inclusions?
• NIAID Review- Does NIAID approve of the inclusion of this source?
• Data access check- Have data access issues been resolved?
• Structured data check- Does this source have structured data?
• Mapping check- Has the properties from this source been mapped to the schema?
• Parser check- Has the parser been written?
• Parsed data check- Has a sanity check on the data obtained from this source been performed?
• Merge data- Has the crawler/plugin been successfully integrated with the system?
• Issues could not be resolved - Add as a single record via the DDE

[gtsueng]

@rshabman, The record types (Genome, Gene, Protein, GeneVariant) in this resource don't appear to be compatible with the Discovery Portal at this point in time. This resource has been queued to be added as a ResourceCatalog

[rshabman]

@gtsueng thank you. Please proceed with PAVE as a ResourceCatalog. If you can also provide a short summary (1-2 paragraphs), I can share this with the NIAID developers of PAVE.

[gtsueng]

@rshabman, @sudvenk The following resources have been added as ResourceCatalogs and are on the staging server awaiting approval for production:

• https://pave.niaid.nih.gov/ (2024.01.30)
• https://www.iddo.org/ (2024.01.30)
• https://www.iddo.org/wwarn (2024.01.30)

Regarding the summary of why PAVE has been added as a resource catalog, we are developing a report template for all Resource Catalogs which will be discussed at the next bi-weekly meeting.