METPO node-class proposal cohort metpo_traitmech_v3 (6 classes, local-only) by realmarcin · Pull Request #69 · CultureBotAI/TraitMech

realmarcin · 2026-05-24T04:43:15Z

Replaces #68 (auto-closed when its stacked base branch ground-causal-nodes-v1 was deleted on merge of #66). Same content + Copilot review fixes applied.

Summary

Scope-D follow-on to v1 (causal-graph scaffolding, #63) and v2 (causal-graph predicates, #65). Lifts 6 microbe-trait-specific node-class abstractions (METPO:1007500–METPO:1007505) that the node-grounding pipeline in #66 cannot reach because no clean CHEBI / GO / ENVO / PRO upstream home exists.

Not filed upstream in this PR — cohort lives in this repo only, matching the v1+v2 pattern.

Cohort (`proposals/metpo_traitmech_v3/`)

METPO ID	Label	Nodes	Cluster
`METPO:1007500`	proton motive force	16	bioenergetic state — electrochemical proton gradient
`METPO:1007501`	microbial biomass	16	material entity — carbon-assimilation sink
`METPO:1007502`	inorganic electron donor	7	class-of-chemicals — lithotrophic substrates
`METPO:1007503`	reducing power	4	metabolic capacity — reduced-cofactor pool
`METPO:1007504`	terminal electron acceptor	5	role-of-chemical — end of ETC (dual CHEMICAL + MF node-type uses)
`METPO:1007505`	membrane fluidity	6	membrane quality — modulated by temperature / lipid composition

The 6 classes ground 54 nodes; an accompanying GO mapping (carotenoid biosynthesis → GO:0016117) grounds 4 more, for 58 newly-grounded nodes total. Each candidate's rejected upstream alternative is documented per-row in proposal.md.

Four of these are mis-typed in the corpus (PMF/biomass/membrane fluidity as BIOLOGICAL_PROCESS though semantically a state / material entity / quality; reducing power as CHEMICAL though semantically a capacity). The mapping TSV grounds them at the current typing so the type-cleanup migration can land separately.

Mapping expansion

mappings/node_grounding.tsv grows 39 → 47 rows:

6 new METPO mappings (METPO:1007500–METPO:1007505)
1 dual-typing alias for terminal electron acceptor as MOLECULAR_FUNCTION
1 GO mapping (carotenoid biosynthesis → GO:0016117)

Corpus impact

	Before v3	After v3
Nodes grounded	564	622 (+58, 45% → 50%)
Nodes residual	688	630 (−58)
Distinct (label, type) residuals	511	503 (−8)

Copilot fixes (from PR #68)

Mapping-row count corrected: "7 additions" → 8 rows (6 METPO + 1 GO + 1 dual-typing alias).
Mis-typed-node count corrected: "Three of these" → "Four" (matches the 4-item list).
Typo: dispoportionation → disproportionation.

Verification (local)

$ just verify-proposal metpo_traitmech_v3
  failures: 0
  status:   PASS

$ just robot-validate-proposal metpo_traitmech_v3
  merged.owl lines:    8425
  reasoned.owl lines:  8431
  delta:               +6
  status:              PASS (no UNSAT, ELK exited 0)

$ just validate-strict
  files scanned:      357
  files with ERROR:   0

Test plan

verify-proposal PASS
robot-validate-proposal PASS
validate-strict clean
Idempotency: ground-nodes --apply (2nd run) → 0 additional groundings
CI re-runs validate-strict on YAML diff

🤖 Generated with Claude Code

Scope-D follow-on to v1 (causal-graph scaffolding) and v2 (causal-graph predicates). Lifts 6 microbe-trait-specific node-class abstractions that the node-grounding pipeline (#66) cannot reach because no clean CHEBI/GO/ENVO/PRO upstream home exists. Cohort (proposals/metpo_traitmech_v3/, 6 class rows): - METPO:1007500 proton motive force (16 nodes) - METPO:1007501 microbial biomass (16 nodes) - METPO:1007502 inorganic electron donor (7 nodes) - METPO:1007503 reducing power (4 nodes) - METPO:1007504 terminal electron acceptor (5 nodes, dual CHEMICAL+MF typing) - METPO:1007505 membrane fluidity (6 nodes) The 6 classes ground 54 nodes; an accompanying GO mapping (carotenoid biosynthesis → GO:0016117) grounds 4 more for a total of 58 newly-grounded nodes. Each candidate's rejected upstream alternative documented per-row in proposal.md (PATO viscosity is generic, CHEBI lacks class-of role for electron-donor, GO has the PMF-generation process but not the gradient-as-state). Four of these are mis-typed in the corpus (PMF/biomass/membrane fluidity as BIOLOGICAL_PROCESS though semantically a state / material entity / quality; reducing power as CHEMICAL though semantically a capacity). The mapping TSV grounds them at the current typing so the type-cleanup migration can land separately. ID block: METPO:1007500-1007505 (fresh 1007500+ block per skill). Subset tag: metpo_traitmech_2026_07. All parented to METPO:1000000. Mapping additions (mappings/node_grounding.tsv, 39 → 47 rows): - 6 new METPO mappings (1007500-1007505) - 1 dual-typing alias for terminal electron acceptor as MOLECULAR_FUNCTION - 1 GO mapping for carotenoid biosynthesis → GO:0016117 Per-corpus impact: Nodes grounded: 564 → 622 (+58, 45% → 50%) Nodes residual: 688 → 630 (-58) Distinct keys: 511 → 503 (-8) NOT filed upstream in this PR (per established convention from v1+v2). Cohort committed in-repo only. Addresses Copilot review on the original PR #68 branch: - Mapping-row count corrected from "7" / "10" to actual 8 rows (6 METPO + 1 GO + 1 dual-typing alias). - Mis-typed-node count corrected from "Three" to "Four" (the four-item list now matches). - Typo "dispoportionation" → "disproportionation". Verified locally: - just verify-proposal metpo_traitmech_v3 → PASS (0 failures) - just robot-validate-proposal metpo_traitmech_v3 → PASS, ELK +6 - just validate-strict → 0 ERROR rows / 357 files - just ground-nodes --apply (second run) → 0 additional groundings (idempotent) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Copilot

Pull request overview

Adds a new local-only METPO proposal cohort (metpo_traitmech_v3) to lift 6 microbe-trait-specific node-class abstractions into METPO placeholder IDs, and expands node-grounding mappings to ground previously residual causal-graph nodes across the TraitMech corpus.

Changes:

Add proposals/metpo_traitmech_v3/ (narrative + ROBOT-template TSV) proposing 6 new METPO classes (METPO:1007500–METPO:1007505).
Extend mappings/node_grounding.tsv with 8 new mapping rows (6 METPO + 1 GO + 1 dual-typing alias) and apply them across trait YAML causal-graph nodes.
Update reports/node_grounding_residual.tsv to reflect newly grounded residual clusters.

Reviewed changes

Copilot reviewed 46 out of 46 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
reports/node_grounding_residual.tsv	Removes now-grounded residual keys from the residual report.
proposals/metpo_traitmech_v3/proposal.md	Documents rationale/scope/impact for the v3 METPO node-class cohort.
proposals/metpo_traitmech_v3/metpo_proposal_classes_robot.tsv	ROBOT-template TSV defining the 6 proposed METPO classes.
mappings/node_grounding.tsv	Adds GO + METPO mappings (incl. dual-typed terminal electron acceptor) for node grounding.
data/traits/physiology/phototrophic.yaml	Grounds the `reducing power` causal node to `METPO:1007503` and records curation history.
data/traits/physiology/photoorganoheterotrophic.yaml	Grounds `proton motive force`/`biomass` causal nodes to METPO and records curation history.
data/traits/physiology/photolithotrophic.yaml	Grounds `inorganic electron donor`/`biomass` causal nodes to METPO and records curation history.
data/traits/physiology/photolithoautotrophic.yaml	Grounds `inorganic electron donor`/`reducing power`/`biomass` causal nodes to METPO and records curation history.
data/traits/physiology/photoheterotrophic.yaml	Grounds `biomass` causal node to `METPO:1007501` and records curation history.
data/traits/physiology/photoautotrophic.yaml	Grounds `biomass` causal node to `METPO:1007501` and records curation history.
data/traits/physiology/organotrophic.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/physiology/organoheterotrophic.yaml	Grounds `biomass` causal node to `METPO:1007501` and records curation history.
data/traits/physiology/mixotrophic.yaml	Grounds `biomass` causal node to `METPO:1007501` and records curation history.
data/traits/physiology/lithotrophic.yaml	Grounds `inorganic electron donor` and `proton motive force` causal nodes to METPO and records curation history.
data/traits/physiology/lithoheterotrophic.yaml	Grounds `inorganic electron donor`/`biomass` causal nodes to METPO and records curation history.
data/traits/physiology/lithoautotrophic.yaml	Grounds `inorganic electron donor`/`reducing power` causal nodes to METPO and records curation history.
data/traits/physiology/hydrogenotrophic.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/physiology/heterotrophic.yaml	Grounds `biomass` causal node to `METPO:1007501` and records curation history.
data/traits/physiology/chemotrophic.yaml	Grounds `terminal electron acceptor`/`proton motive force` causal nodes to METPO and records curation history.
data/traits/physiology/chemoorganotrophic.yaml	Grounds `terminal electron acceptor`/`proton motive force`/`biomass` causal nodes to METPO and records curation history.
data/traits/physiology/chemoorganoheterotrophic.yaml	Grounds `biomass` causal node to `METPO:1007501` and records curation history.
data/traits/physiology/chemolithoheterotrophic.yaml	Grounds `proton motive force`/`biomass` causal nodes to METPO and records curation history.
data/traits/physiology/chemolithoautotrophic.yaml	Grounds `inorganic electron donor`/`proton motive force`/`reducing power`/`biomass` causal nodes to METPO and records curation history.
data/traits/physiology/chemoheterotrophic.yaml	Grounds `biomass` causal node to `METPO:1007501` and records curation history.
data/traits/physiology/chemoautolithotrophic.yaml	Grounds `inorganic electron donor`/`biomass` causal nodes to METPO and records curation history.
data/traits/physiology/carboxydotrophic.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/morphology/yellow_pigmented.yaml	Grounds `carotenoid biosynthesis` causal node to `GO:0016117` and records curation history.
data/traits/morphology/pink_pigmented.yaml	Grounds `carotenoid biosynthesis` causal node to `GO:0016117` and records curation history.
data/traits/morphology/orange_pigmented.yaml	Grounds `carotenoid biosynthesis` causal node to `GO:0016117` and records curation history.
data/traits/morphology/carotenoid_pigmentation.yaml	Grounds `carotenoid biosynthesis` causal node to `GO:0016117` and records curation history.
data/traits/morphology/gliding.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/metabolism/respiration.yaml	Grounds `terminal electron acceptor`/`proton motive force` causal nodes to METPO and records curation history.
data/traits/metabolism/oxidative_phosphorylation.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/metabolism/anaerobic_respiration.yaml	Grounds `terminal electron acceptor` (MF-typed) to `METPO:1007504`, wraps long text lines, and records curation history.
data/traits/metabolism/aerobic_respiration.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/environment/temperature_preference.yaml	Grounds `membrane fluidity` causal node to `METPO:1007505` and records curation history.
data/traits/environment/temperature_optimum.yaml	Grounds `membrane fluidity` causal node to `METPO:1007505` and records curation history.
data/traits/environment/psychrotolerant.yaml	Grounds `membrane fluidity` causal node to `METPO:1007505` and records curation history.
data/traits/environment/psychrophilic.yaml	Grounds `membrane fluidity` causal node to `METPO:1007505` and records curation history.
data/traits/environment/ph_optimum.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/environment/obligately_aerobic.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/environment/neutrophilic.yaml	Grounds `proton motive force` causal node to `METPO:1007500` and records curation history.
data/traits/environment/mesophilic.yaml	Grounds `membrane fluidity` causal node to `METPO:1007505` and records curation history.
data/traits/environment/facultative_psychrophilic.yaml	Grounds `membrane fluidity` causal node to `METPO:1007505` and records curation history.
data/traits/environment/aerobic.yaml	Grounds `terminal electron acceptor` (MF-typed) to `METPO:1007504`, wraps long text lines, and records curation history.

Comments suppressed due to low confidence (1)

proposals/metpo_traitmech_v3/proposal.md:152

The “Mappings TSV size” row appears to be using the mapping-row count (excluding the header), but the after value is listed as 49. mappings/node_grounding.tsv currently has 47 mapping rows (plus 1 header row), so this should read 39 → 47 to match the actual file.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

+`data/traits/**/causal_graphs[].nodes[]`. As of this proposal,
+**622 of 1252 causal-graph nodes are grounded** (50%) using 39
+CHEBI / GO / ENVO / PATO mappings from #66 plus the 7 additions in
+this cohort (6 METPO + 1 GO).


…0 nodes) Adds 14 mappings across ENVIRONMENTAL_FACTOR (PATO + ENVO), CHEMICAL (CHEBI), and PATHWAY (GO) to ground the top remaining groundable labels in reports/node_grounding_residual.tsv after #66 (39 base) + #69 (8 METPO) + #70 (27 UniProt) + #72 (biomass retype). Additions (mappings/node_grounding.tsv, 75 → 89 rows): ENVIRONMENTAL_FACTOR (5 rows, PATO + ENVO): acidic external ph → PATO:0001428 acidic pH (5 nodes) alkaline external ph → PATO:0001429 alkaline pH (5 nodes) near-neutral external ph → PATO:0001432 neutral pH (4 nodes) very high temperature → PATO:0001637 extremely high temperature (2 nodes) high-salt environment → ENVO:01000687 saline environment (2 nodes) CHEMICAL (3 rows, CHEBI): thiosulfate → CHEBI:33542 thiosulfate(2-) (2 nodes) electron donor → CHEBI:17499 electron donor (2 nodes) organic compound → CHEBI:50860 organic molecular entity (6 nodes) PATHWAY (6 rows, GO): membrane electron transport chain → GO:0022900 ETC (3 nodes) electron transport chain → GO:0022900 (1 node) electron transport system → GO:0022900 (1 node) co2-fixation pathway → GO:0015977 carbon fixation (3 nodes) autotrophic co2 fixation → GO:0015977 (3 nodes) co2 fixation pathway → GO:0015977 (1 node) The PATHWAY additions collapse 6 distinct corpus-paraphrased labels onto 2 GO terms, demonstrating that the (label, node_type) mapping convention supports multi-label-→-one-CURIE without conflict. Per-corpus impact: Mapping TSV: 75 → 89 rows (+14) Nodes grounded: ~704 (53%) → ~744 (59%) Verified: - just ground-nodes --apply → 40 newly grounded - just ground-nodes (idempotency) → 0 - just validate-strict → 0 ERROR rows / 357 files Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

…0 nodes) (#74) Adds 14 mappings across ENVIRONMENTAL_FACTOR (PATO + ENVO), CHEMICAL (CHEBI), and PATHWAY (GO) to ground the top remaining groundable labels in reports/node_grounding_residual.tsv after #66 (39 base) + #69 (8 METPO) + #70 (27 UniProt) + #72 (biomass retype). Additions (mappings/node_grounding.tsv, 75 → 89 rows): ENVIRONMENTAL_FACTOR (5 rows, PATO + ENVO): acidic external ph → PATO:0001428 acidic pH (5 nodes) alkaline external ph → PATO:0001429 alkaline pH (5 nodes) near-neutral external ph → PATO:0001432 neutral pH (4 nodes) very high temperature → PATO:0001637 extremely high temperature (2 nodes) high-salt environment → ENVO:01000687 saline environment (2 nodes) CHEMICAL (3 rows, CHEBI): thiosulfate → CHEBI:33542 thiosulfate(2-) (2 nodes) electron donor → CHEBI:17499 electron donor (2 nodes) organic compound → CHEBI:50860 organic molecular entity (6 nodes) PATHWAY (6 rows, GO): membrane electron transport chain → GO:0022900 ETC (3 nodes) electron transport chain → GO:0022900 (1 node) electron transport system → GO:0022900 (1 node) co2-fixation pathway → GO:0015977 carbon fixation (3 nodes) autotrophic co2 fixation → GO:0015977 (3 nodes) co2 fixation pathway → GO:0015977 (1 node) The PATHWAY additions collapse 6 distinct corpus-paraphrased labels onto 2 GO terms, demonstrating that the (label, node_type) mapping convention supports multi-label-→-one-CURIE without conflict. Per-corpus impact: Mapping TSV: 75 → 89 rows (+14) Nodes grounded: ~704 (53%) → ~744 (59%) Verified: - just ground-nodes --apply → 40 newly grounded - just ground-nodes (idempotency) → 0 - just validate-strict → 0 ERROR rows / 357 files Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

The grounding pipelines and audit scripts have been load-bearing infrastructure for the last 7 PRs (#61, #66, #67, #69, #70 — all of which rewrite causal-graph fields based on these scripts' output). They had zero unit-test coverage. A silent regression in idempotency, header validation, or self-suppression would not be caught by validate-strict (which only checks per-record schema conformance, not pipeline correctness). Test counts: tests/test_ground_causal_predicates.py 9 tests tests/test_ground_causal_nodes.py 12 tests tests/test_validate_strict.py 11 tests tests/test_audit_writers.py 11 tests --- total new 43 tests total suite 54 tests (was 11) Coverage highlights: ground_causal_predicates.py: - load_mapping: basic happy path, conflict detection (same label → different CURIEs raises ValueError), incomplete-row skipping, missing-file error. - ground_edges_in_doc: idempotency (second pass = 0 changes), existing predicate_id never overwritten, residual counting for unmapped labels, empty/missing-predicate edges skipped. ground_causal_nodes.py: - All of the predicate suite plus: - (label, node_type) keyed lookup — same label, different node_types map to different CURIEs without aliasing. - Header validation (Copilot fix from PR #66): TSV with `nodetype` / `targetcurie` typo'd headers raises ValueError naming both missing columns. - grounded_keys-on-validation-failure separability (Copilot fix from PR #66): caller can union residual + grounded_keys to recover the corpus-state residual after rolling back an invalid file write. validate_strict.py: - classify: parametrized over the 5 categories (unexpected_field, missing_required, enum_mismatch, pattern_mismatch, other) — the messages must match the actual jsonschema phrasings the validator emits. - validate_one: clean record produces 0 errors; unknown field surfaces unexpected_field (the G01 gate behavior); missing required field surfaces missing_required; YAML parse error surfaces as yaml_parse_error category. - iter_yaml_files: walks directories, filters .txt, picks up nested *.yaml. audit_writers.py: - looks_like_yaml_writer: yaml.safe_dump / yaml.dump positive, bare .write_text negative, .write_text near .yaml hint positive, arbitrary code negative. - audit: full-safeguards writer flagged yes/yes/yes/yes; no-safeguards writer flagged no/no/no; non-writer returns None; wired_into_just yes when justfile mentions the script stem. - Self-suppression (Copilot fix from PR #64): audit_writers.py itself returns None even though its own source matches yaml.safe_dump. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* Add tests for grounding pipeline + audit scripts (+43 tests) The grounding pipelines and audit scripts have been load-bearing infrastructure for the last 7 PRs (#61, #66, #67, #69, #70 — all of which rewrite causal-graph fields based on these scripts' output). They had zero unit-test coverage. A silent regression in idempotency, header validation, or self-suppression would not be caught by validate-strict (which only checks per-record schema conformance, not pipeline correctness). Test counts: tests/test_ground_causal_predicates.py 9 tests tests/test_ground_causal_nodes.py 12 tests tests/test_validate_strict.py 11 tests tests/test_audit_writers.py 11 tests --- total new 43 tests total suite 54 tests (was 11) Coverage highlights: ground_causal_predicates.py: - load_mapping: basic happy path, conflict detection (same label → different CURIEs raises ValueError), incomplete-row skipping, missing-file error. - ground_edges_in_doc: idempotency (second pass = 0 changes), existing predicate_id never overwritten, residual counting for unmapped labels, empty/missing-predicate edges skipped. ground_causal_nodes.py: - All of the predicate suite plus: - (label, node_type) keyed lookup — same label, different node_types map to different CURIEs without aliasing. - Header validation (Copilot fix from PR #66): TSV with `nodetype` / `targetcurie` typo'd headers raises ValueError naming both missing columns. - grounded_keys-on-validation-failure separability (Copilot fix from PR #66): caller can union residual + grounded_keys to recover the corpus-state residual after rolling back an invalid file write. validate_strict.py: - classify: parametrized over the 5 categories (unexpected_field, missing_required, enum_mismatch, pattern_mismatch, other) — the messages must match the actual jsonschema phrasings the validator emits. - validate_one: clean record produces 0 errors; unknown field surfaces unexpected_field (the G01 gate behavior); missing required field surfaces missing_required; YAML parse error surfaces as yaml_parse_error category. - iter_yaml_files: walks directories, filters .txt, picks up nested *.yaml. audit_writers.py: - looks_like_yaml_writer: yaml.safe_dump / yaml.dump positive, bare .write_text negative, .write_text near .yaml hint positive, arbitrary code negative. - audit: full-safeguards writer flagged yes/yes/yes/yes; no-safeguards writer flagged no/no/no; non-writer returns None; wired_into_just yes when justfile mentions the script stem. - Self-suppression (Copilot fix from PR #64): audit_writers.py itself returns None even though its own source matches yaml.safe_dump. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Address Copilot review on PR #71 Add explicit `assert "b.yml" not in names` to test_iter_yaml_files_walks_directory_and_filters — the prior test documented the .yml-skipping behavior in a comment but never asserted it, so a regression that started picking up .yml during directory walks would have slipped through silently. Also add test_iter_yaml_files_accepts_yml_file_passed_directly to lock in the asymmetry that the previous test only hinted at: iter_yaml_files() does accept .yml when passed as a file argument (only the rglob('*.yaml') walk is .yaml-only). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * Update audit_writers tests to match #75's tightened heuristic PR #75 changed `looks_like_yaml_writer` to require that the yaml-serializer call feed directly into write_text on the same line (instead of the looser "any .write_text + any .yaml token" heuristic, which produced false positives for scripts that only READ trait YAMLs). The pre-#75 test asserted that `path.write_text(content) # .yaml` counted as a YAML writer. That returned True under the old heuristic and False under the new (correct) one. Replace it with two tests that lock in the new contract: test_looks_like_yaml_writer_write_text_of_yaml_dump Positive: write_text(yaml.safe_dump(...)) / write_text(yaml.dump(...)) both count. test_looks_like_yaml_writer_write_text_of_json_is_false Negative: a script that reads *.yaml then writes JSON via write_text is NOT a YAML writer — this is the false-positive case #75 explicitly fixed for scripts/build_embedding_index.py and scripts/render_trait_pages.py. Also rename test_looks_like_yaml_writer_write_text_without_yaml_hint_is_false to test_looks_like_yaml_writer_write_text_plain_is_false since the "yaml hint" phrasing was tied to the old heuristic. 56 tests pass (was 54; +2). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Copilot AI review requested due to automatic review settings May 24, 2026 04:43

Copilot started reviewing on behalf of realmarcin May 24, 2026 04:43 View session

realmarcin merged commit e713b68 into main May 24, 2026
3 checks passed

realmarcin deleted the metpo-proposal-traitmech-v3 branch May 24, 2026 04:44

Copilot AI reviewed May 24, 2026

View reviewed changes

This was referenced May 24, 2026

Tests for grounding pipeline + audit scripts (+43 tests) #71

Merged

Node grounding v2: PATO/CHEBI/GO/ENVO mapping expansion (+15 rows, +40 nodes) #74

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

METPO node-class proposal cohort metpo_traitmech_v3 (6 classes, local-only)#69

METPO node-class proposal cohort metpo_traitmech_v3 (6 classes, local-only)#69
realmarcin merged 1 commit into
mainfrom
metpo-proposal-traitmech-v3

realmarcin commented May 24, 2026

Uh oh!

Uh oh!

Copilot AI left a comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Conversation

realmarcin commented May 24, 2026

Summary

Cohort (proposals/metpo_traitmech_v3/)

Mapping expansion

Corpus impact

Copilot fixes (from PR #68)

Verification (local)

Test plan

Uh oh!

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Cohort (`proposals/metpo_traitmech_v3/`)