# Verdicts of the pre-registered OpenScientist batch (selection.yaml), read
# 2026-10-15 after all 16 reports were written. verdict is the report's own
# executive verdict; agrees compares it with review_action_at_selection
# (frozen at 1b7f8f330): ACCEPT agrees with SUPPORTED; UNDECIDED rows have no
# prior call, so "resolves" says what the run suggests. Runs marked
# max_iterations: 2 timed out at the 7200 s ceiling with 3 iterations and were
# retried once at 2 (a deviation from the pre-registered protocol).
# action_after_rereview: the row's action after the 2026-10-15 re-review that
# used these reports as evidence (with their claims checked against repo data).
batch: openscientist-controls-2026-10-14
results:
  - {gene: PP_1969, note: "The report gives PP_1969 vs E. coli MoaA as 40.9% in its Executive Judgment and 40.0% (126/315) in its Active-Site section; 126/315 is 40.0%. This run wrote no openscientist.md.citations.md sidecar.", action_after_rereview: 'UNDECIDED (ACCEPT on 2026-10-15, reverted 2026-10-16: below the NCBIfam TIGR02666 trusted cutoff and HAMAP MF_01225 level 0)', group: undecided, prior: UNDECIDED, verdict: SUPPORTED, resolves: ACCEPT, max_iterations: 3, report: genes/PSEPK/PP_1969/PP_1969-hypotheses/function-hypothesis-go-0061798/openscientist.md}
  - {gene: PP_2482, action_after_rereview: 'UNDECIDED (ACCEPT on 2026-10-15, reverted 2026-10-16: below the NCBIfam TIGR02666 trusted cutoff and HAMAP MF_01225 level 0)', group: undecided, prior: UNDECIDED, verdict: SUPPORTED, resolves: ACCEPT, max_iterations: 2, report: genes/PSEPK/PP_2482/PP_2482-hypotheses/function-hypothesis-go-0061798/openscientist.md}
  - {gene: PP_3571, action_after_rereview: 'MODIFY GO:0016811', group: undecided, prior: UNDECIDED, verdict: PARTIALLY_SUPPORTED, failure_mode: granularity (too general) with paralog confusion, resolves: "MODIFY to GO:0016811 pending assay; PANTHER places it in PTHR43808:SF31 (N-acetyl-L-citrulline deacetylase, GO:0043909), the true ArgE ortholog being PP_5186 (SF1)", max_iterations: 3, report: genes/PSEPK/PP_3571/PP_3571-hypotheses/function-hypothesis-go-0008777/openscientist.md}
  - {gene: PP_4594, action_after_rereview: 'UNDECIDED', group: undecided, prior: UNDECIDED, verdict: PARTIALLY_SUPPORTED, failure_mode: granularity (sibling activity within the gamma subfamily unresolved), resolves: "stays UNDECIDED (low-confidence sibling call; gamma-subfamily activities not separable by sequence)", max_iterations: 2, report: genes/PSEPK/PP_4594/PP_4594-hypotheses/function-hypothesis-go-0004123/openscientist.md}
  - {gene: ptxD, action_after_rereview: 'UNDECIDED', group: undecided, prior: UNDECIDED, verdict: PARTIALLY_SUPPORTED, failure_mode: granularity (too specific), resolves: "keep GO:0030267 and add GO:0016618 hydroxypyruvate reductase (GhrB-type dual activity); refutes the phosphite dehydrogenase reading of the ptxD symbol", max_iterations: 3, report: genes/PSEPK/ptxD/ptxD-hypotheses/function-hypothesis-go-0030267/openscientist.md}
  - {gene: gabD-II, action_after_rereview: 'UNDECIDED', group: undecided, prior: UNDECIDED, verdict: PARTIALLY_SUPPORTED, failure_mode: granularity (cofactor too specific), resolves: "MODIFY to succinate-semialdehyde dehydrogenase [NAD(P)+], the cofactor not being NAD+-specific", max_iterations: 3, report: genes/PSEPK/gabD-II/gabD-II-hypotheses/function-hypothesis-go-0004777/openscientist.md}
  - {gene: eryCIV, action_after_rereview: 'MODIFY GO:0019179', group: undecided, prior: UNDECIDED, verdict: PARTIALLY_SUPPORTED, failure_mode: granularity (too general), resolves: "keep; a more specific dTDP-sugar aminotransferase term is wanted (nearest neighbour DesI, PMID:17630700)", max_iterations: 3, report: genes/SACEN/eryCIV/eryCIV-hypotheses/function-hypothesis-go-0008483/openscientist.md}
  - {gene: ADAR2, note: 'GO:0003726 is the only source of the defining activity, but ADAR2 also has a related InterPro2GO row (GO:0004000, MODIFY), so it is a less clean control than relA, Cgas or TAS1R3.', group: accepted_control, prior: ACCEPT, verdict: SUPPORTED, agrees: true, max_iterations: 3, report: genes/DOROP/ADAR2/ADAR2-hypotheses/function-hypothesis-go-0003726/openscientist.md}
  - {gene: Cgas, group: accepted_control, prior: ACCEPT, verdict: SUPPORTED, agrees: true, max_iterations: 3, report: genes/HETGA/Cgas/Cgas-hypotheses/function-hypothesis-go-0061501/openscientist.md}
  - {gene: relA, group: accepted_control, prior: ACCEPT, verdict: SUPPORTED, agrees: true, max_iterations: 2, report: genes/PSEPK/relA/relA-hypotheses/function-hypothesis-go-0008728/openscientist.md}
  - {gene: TAS1R3, group: accepted_control, prior: ACCEPT, verdict: PARTIALLY_SUPPORTED, agrees: partly, failure_mode: subunit carries the heterodimer's function; hummingbird has no TAS1R2, note: "the run itself cites Baldwin et al. 2014 (PMID:25146290): hummingbird T1R1-T1R3 senses sugar, so the percept is real; the disagreement is how GO should attach a complex function to a subunit", max_iterations: 3, report: genes/9AVES/TAS1R3/TAS1R3-hypotheses/function-hypothesis-go-0033041/openscientist.md}
  - {gene: fadB, group: rule_test, rule: ec_contradiction, prior: ACCEPT, verdict: SUPPORTED, agrees: true, rule_vindicated: false, max_iterations: 3, report: genes/PSEPK/fadB/fadB-hypotheses/function-hypothesis-go-0016509/openscientist.md}
  - {gene: metZ, action_after_rereview: 'REMOVE (new term request O-succinylhomoserine sulfhydrylase activity)', group: rule_test, rule: ec_contradiction, prior: ACCEPT, verdict: REFUTED, agrees: false, rule_vindicated: true, failure_mode: within-superfamily mis-placement (lyase term on a transferase; EC 2.5.1.-), note: "GO has no O-succinylhomoserine sulfhydrylase term; the nearest, GO:0051009 O-acetylhomoserine sulfhydrylase activity (RHEA:27822), is a transferase, so the review's 'available parent' reasoning does not hold. The 2026-10-15 re-review changed the row to REMOVE (see action_after_rereview).", max_iterations: 2, report: genes/PSEPK/metZ/metZ-hypotheses/function-hypothesis-go-0016846/openscientist.md}
  - {gene: DDO, group: rule_test, rule: outside_ibd_clade, prior: ACCEPT, verdict: SUPPORTED, agrees: true, rule_vindicated: false, max_iterations: 3, report: genes/OCTVU/DDO/DDO-hypotheses/function-hypothesis-go-0019478/openscientist.md}
  - {gene: PP_2320, group: rule_test, rule: treegrafter_over_arba, prior: ACCEPT, verdict: SUPPORTED, agrees: true, max_iterations: 3, report: genes/PSEPK/PP_2320/PP_2320-hypotheses/function-hypothesis-go-0071972/openscientist.md}
  - {gene: pdxH, group: rule_test, rule: treegrafter_over_interpro2go, prior: ACCEPT, verdict: SUPPORTED, agrees: true, max_iterations: 2, report: genes/PSEPK/pdxH/pdxH-hypotheses/function-hypothesis-go-0042823/openscientist.md}