Version history

{
  "disease": "alzheimer disease",
  "summary": "Tick-63: CrossRef + EuropePMC re-queried for Mathys 2023 GEO accession (final substrate attempt on this track). knowledge_gap artifact successfully created (tick-63) and linked via 'blocks' predicate to this plan. Automated accession-search track closed. Plan unblocks only on manual curator confirmation of GEO accessions for Olah 2020 (candidate: GSE127893) and Mathys 2023 (unknown). scCODA notebook skeleton complete (6 cells). Analysis ready to execute pending accession confirmation.",
  "assay_spec": "Planned output: scCODA notebook with three input slots — (A) SEA-AD per-donor microglia subtype counts from Allen Brain Cell Atlas S3, (B) Olah 2020 GEO accession (target: GSE127893 candidate, to be confirmed by EuropePMC this tick), (C) Mathys 2023 Synapse/GEO accession (target: syn18485175 candidate, to be confirmed). Success criterion: scCODA model converges on Braak-stage coefficient with 95% credible interval excluding zero for at least one DAM-like or MGnD subtype in two of three cohorts.",
  "hypothesis": "Named microglia subtypes from SEA-AD (homeostatic, DAM-like, MGnD, lipid-droplet-accumulating) map to a reproducible shared taxonomy across SEA-AD, ROSMAP snRNA-seq, and Mathys 2023 Cell atlas, and their Braak-stage compositional trajectories are concordant across cohorts after Harmony integration.",
  "target_ref": "dataset:SEA-AD+ROSMAP+Mathys2023",
  "kill_criteria": "Sun 2023 reference retired (tick-38). 'advances' predicate rejected (tick-40); 'supports' predicate linked (tick-42, link_id:4325911 confirmed tick-51). analysis_proposal kind field blocked (tick-41). EuropePMC accession search failed ticks 43–61. PubMed accession search tick-62 (final PubMed attempt). CrossRef confirmed Olah 2020 DOI tick-56. Notebook skeleton tick-57 (3 cells). GEO verification cell tick-58. DOI CrossRef+EuropePMC tick-59. scCODA slot definitions tick-60. scCODA model spec cell tick-61. knowledge_gap blocker artifact filed and linked tick-63 (blocks predicate confirmed). SUBSTRATE ACCESSION SEARCH TRACK CLOSED. Plan unblocks only on manual curator confirmation of GEO accessions.",
  "primary_endpoint": "Cross-cohort microglia subtype crosswalk table with marker gene overlap and Braak-stage compositional trajectory comparison across Olah 2020, SEA-AD, and Mathys 2023.",
  "identification_strategy": "observational"
}