[Source]: High Priority Resource Catalogs

[gtsueng]

Source Name

NIAID High Priority Resource Catalogs

Source URL

https://discovery.biothings.io/schema-playground

Source Description

These are repositories that are high priority for integration, but currently are not of the right type for integration, so they will be added as ResourceCatalogs

• https://dbaasp.org/home
• https://www.ebi.ac.uk/emdb/
• https://portal.hmpdacc.org/projects/t
• https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/
• http://www.peptideatlas.org/
• https://www.uniprot.org/

Source Access

Unknown

Source Funding

No response

Source Relevance

These are resources that were prioritized as high priority as of the end of April 2024

Related WBS task

• Check here if this repository is funded by NIAID
• Check here if this repository only has IID data
• 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]

As of 2024.05.14, The metadata for the following sources have been curated and are available here. They will be uploaded once issues with the batch upload feature in the DDE have been addressed.

• https://dbaasp.org/home
• https://www.ebi.ac.uk/emdb/
• http://www.peptideatlas.org/
• https://www.uniprot.org/

The curation of metadata about the remaining two sources continues to be underway:

• https://portal.hmpdacc.org/projects/t
• https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/

[gtsueng]

As of 2024.05.21, The metadata for the following sources have been uploaded to the NIAID Data Ecosystem entry point in the DDE:

• https://dbaasp.org/home
• https://www.ebi.ac.uk/emdb/
• http://www.peptideatlas.org/
• https://www.uniprot.org/
• https://portal.hmpdacc.org/projects/t
• https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/

The records can be viewed in the DDE at: https://discovery.biothings.io/dataset?template=nde:resourcecatalog

These records will be viewable on staging once a new data build has been created

[gtsueng]

@hartwickma, @rshabman, @lisa-mml, @sudvenk

These sources are now on Staging. Upon receiving the "go-ahead", we will move them to Production.

[gtsueng]

@DylanWelzel @jal347 Per an email dated 2024.06.21, these DDE-ingested resources have been approved for Production. The list of resources approved for production vs staging has been updated.

[gtsueng]

@hartwickma, @rshabman, @lisa-mml, @sudvenk as seen during the biweekly call dated 2024.06.25, these high priority resources are now on production.

I am changing the status of this issue to 'pending close out' and will close the issue after a week if there are no additional comments or concerns

[gtsueng]

Based on discussions initiated during the bi-weekly meeting dated 2024.06.25, the genre and abstract field for each ResourceCatalog may need to be updated such that any non-IID resources are categorized as generalist. For this reason, the status of this issue has been updated to in progress -- refinement

[gtsueng]

The genre field for these Resource Catalogs have been updated. I am marking this issue as pending close out and will close this issue after a week if there are no additional comments or changes to be made.

[rshabman]

Hi @gtsueng, @hartwickma, @rshabman, @lisa-mml, @sudvenk: Can the Scripps team evaluate PaVE? The Papillomavirus Episteme – under the direction of Dr. Alison McBride is a curated repository of annotated papillomavirus genomes. It also has a toolset for analysis of user-submitted genomes. https://pave.niaid.nih.gov/. Ideally we can integrate at the dataset level, if not, can you please map out an approach to bring online as a resource catalog for a shorter term solution? If this is already in a GH issue, apologies for cross posting.

[EmilyHaag]

An issue has been created for PaVE: #226