ECA-PP: From Public Data to Consistent Inputs

ECA-PP: From Public Data to Consistent Inputs A workflow diagram generated by Archify. 01 / Prepare and hand off 02 / Evidence and exceptions UPSTREAM ECA-PP ECA-RSI Input H5AD · Files converted by agents · Prepare and hand off › UPSTREAM Input H5AD Files converted by agents Standardize · Counts · species · genes · QC · Prepare and hand off › ECA-PP Standardize Counts · species · genes · QC Prepared data · standardized.h5ad + report · Prepare and hand off › ECA-PP Prepared data standardized.h5ad + report Identify metadata · Profile · rank · validate · Prepare and hand off › ECA-PP Identify metadata Profile · rank · validate Recorded decision · Batch · cell type · evidence · Prepare and hand off › ECA-PP Recorded decision Batch · cell type · evidence ECA-RSI · Iterative data governance · Prepare and hand off › ECA-RSI ECA-RSI Iterative data governance Reject dataset · Invalid input / failed gates · Evidence and exceptions › UPSTREAM · exit 2 Reject dataset Invalid input / failed gates exit 2 Needs a choice · Unresolved counts / species · Evidence and exceptions › ECA-PP · exit 3 · review Needs a choice Unresolved counts / species exit 3 · review Integration trial · Harmony · mixing · cell types · Evidence and exceptions › ECA-PP · bounded trial budget Integration trial Harmony · mixing · cell types bounded trial budget test candidate conclude read inspect evaluate evidence passed unsuitable ambiguous handoff Legend Processing Checks / review Data / evidence External system

One scientific standard

  • • Counts validation and recovery where supported
  • • Gene mapping, QC and normalization share a final gene set
  • • Minimum: 100 cells and 5,000 detected genes per dataset, not per cell

A decision with evidence

  • • Batch: recommend correction, unnecessary, or null
  • • Cell type: existing author annotation, or null
  • • Model unavailable: built-in policy continues; all submissions are checked

Keep outcomes distinct

  • • Successful output may carry non-blocking review notes
  • • exit 1: technical failure; never disguised as a successful null
  • • Source unchanged; formal files written atomically, old outputs archived