Issues

• target_condition mismatch between *_sample.tsv and *_study.tsv

  bug
  waldronlab/curatedMetagenomicDataCuration#167 · Filter by author SvetlanaUP opened on Sep 22, 2026

• Use omicidx to fill in missing BioProjects and run accessions

  enhancement
  waldronlab/curatedMetagenomicDataCuration#166 · Filter by author lwaldron opened on Sep 18, 2026

• biomarker_value pattern rejects negatives, scientific notation and <0.01

  schema
  waldronlab/curatedMetagenomicDataCuration#165 · Filter by author lwaldron opened on Sep 18, 2026

• studies_status.csv splits on commas, so "Korea, Republic of" becomes two values

  bug
  waldronlab/curatedMetagenomicDataCuration#164 · Filter by author lwaldron opened on Sep 18, 2026
  

• age_group: dictionary says NCIT:C17600, curators used NCIT:C49685

  schema
  waldronlab/curatedMetagenomicDataCuration#163 · Filter by author lwaldron opened on Sep 18, 2026
  

• CI validator silently skips 11 curated studies (glob is *_sample.tsv only)

  bugschema
  waldronlab/curatedMetagenomicDataCuration#160 · Filter by author lwaldron opened on Sep 18, 2026
  2

  

• A Beginner’s Guide to curatedMetagenomicData Curation

  waldronlab/curatedMetagenomicDataCuration#156 · Filter by author SvetlanaUP opened on Sep 8, 2026

• Missing sample in Valles-ColomerM_2023_a

  waldronlab/curatedMetagenomicDataCuration#154 · Filter by author SvetlanaUP opened on Aug 25, 2026

• To sync curated metadata from the Parkinson's studies

  curation repo
  waldronlab/curatedMetagenomicDataCuration#152 · Filter by author SvetlanaUP opened on Jul 13, 2026
  

• Parkinson's studies to run through cMD Nextflow

  waldronlab/curatedMetagenomicDataCuration#150 · Filter by author lwaldron opened on Jun 30, 2026
  

• biomarker_name is listed as "dynamic_enum" under corpus.type but has "NA" under dynamic.enum

  schema
  waldronlab/curatedMetagenomicDataCuration#137 · Filter by author lwaldron opened on Mar 11, 2026
  4

• Document curation and downstream workflow on README.md

  waldronlab/curatedMetagenomicDataCuration#133 · Filter by author lwaldron opened on Mar 11, 2026
  1

  

• Feedback on Excel/Google Sheets curation tool

  help wanted
  waldronlab/curatedMetagenomicDataCuration#122 · Filter by author lwaldron opened on Dec 19, 2025
  6

  

• Template creating GitHub Action fails

  bug
  waldronlab/curatedMetagenomicDataCuration#116 · Filter by author shbrief opened on Nov 30, 2025
  

• Vignette creating curation template

  waldronlab/curatedMetagenomicDataCuration#110 · Filter by author shbrief opened on Sep 24, 2025
  

• [Study]: Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals

  study to curate
  waldronlab/curatedMetagenomicDataCuration#100 · Filter by author shbrief opened on Jul 22, 2025
  4

  

• Add curation template checking for presence of SRR accessions

  waldronlab/curatedMetagenomicDataCuration#94 · Filter by author seandavi opened on Jul 2, 2025
  1

  

• Add ZOE datasets as curated data

  study to curate
  waldronlab/curatedMetagenomicDataCuration#91 · Filter by author seandavi opened on Jul 1, 2025
  3

  

• Studies missing SRR accessions

  curation repo
  waldronlab/curatedMetagenomicDataCuration#90 · Filter by author seandavi opened on Jul 1, 2025
  2

  

• Request update in HallAB_2017_metadata

  waldronlab/curatedMetagenomicDataCuration#81 · Filter by author jarchana09 opened on Aug 15, 2024
  

• Add all HMP 1 healthy participants

  wishlist
  waldronlab/curatedMetagenomicDataCuration#71 · Filter by author lwaldron opened on Dec 6, 2022

• duplicate samples in NielsenHB_2014 & LeChatelierE_2013

  waldronlab/curatedMetagenomicDataCuration#62 · Filter by author lzhangxcode opened on Oct 30, 2021
  3