LungMAP missing DRS URLs in some cases

[bvizzier-ucsc]

Submitted via email by Josh Fortriede

TLDR;

• LM4 to TDR contained DRS_URIs for FASTQ files.
• File Manifest from Omics Data Browser does not have the DRS_URIs.
• Datasets that should have BDCat DRS URIs in TDR & Data Browser
  • Human distal airways contain a multipotent secretory cell that can regenerate alveoli : f899709c-ae2c-4bb9-88f0-131142e6c7ec
  • Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes : 20037472-ea1d-4ddb-9cd3-56a11a6f0f76

Preface:

I did a look at TDR snapshots and the information available in the data browser related to the DRS URIs generated by BioData Catalyst (BDCat) and then submitted in the file descriptor files to TDR. Below are my findings.

Dataset:

The following datasets have been submitted to BDCat and gotten DRS URI's that we have sent to TDR

• Human distal airways contain a multipotent secretory cell that can regenerate alveoli
  • f899709c-ae2c-4bb9-88f0-131142e6c7ec
  • Ingest Broker
  • Data Browser
  • TDR Snapshot
• Single-cell multiomic profiling of human lungs reveals cell-type-specific and age-dynamic control of SARS-CoV2 host genes
  • 20037472-ea1d-4ddb-9cd3-56a11a6f0f76
  • Ingest Broker
  • Data Browser
  • TDR Snapshot

TDR Snapshot LM4:

When Viewing the "sequence_file", the descriptor column shows the JSON content of the file descriptor. This shows the DRS URI.

File Manifest from Respiratory Airway Secretory Cells Submission - OMIC Data Browser

The DRS URI is missing.

[hannes-ucsc]

This is essentially a duplicate of https://github.com/DataBiosphere/azul/issues/3631 which is assigned to @bvizzier-ucsc (the author of this issue) in order to obtain an answer to my question regarding the expected level of support for these types of DRS URIs.

[dsotirho-ucsc]

Closing as dup of #3631