metpo-proposal

name	metpo-proposal
description	Workflow for proposing new METPO terms from KG-Microbe transform output. Use when adding new METPO classes or properties, drafting an upstream submission to berkeleybop/metpo, or validating a proposal before sharing with curators.

METPO Proposal Workflow

Purpose

Produce a clean, ROBOT-validated, ELK-coherent METPO term proposal that can be filed against berkeleybop/metpo. A proposal must:

1. Not collide with any existing METPO term (label or exact synonym).
2. Use Aristotelian definitions (<genus>: <differentia>).
3. Cite the definition source (IAO:0000119 axiom annotation).
4. Reuse appropriate parent classes from existing METPO (avoid jumping straight to METPO:1000000 when a sibling parent exists).
5. Pass robot template ingestion and robot reason --reasoner ELK without unsatisfiable classes.
6. Be tagged with a stable subset identifier (oboInOwl:inSubset) so curators can filter by proposal cohort.

Authoritative artifacts

File	Format	Role
mappings/metpo_proposal_categorical.tsv	curation TSV (one header)	Human-edited proposal of categorical classes; emitted by scripts/extract_metpo_proposals.py
mappings/metpo_proposal_quantitative.tsv	curation TSV	Datatype properties + numeric tolerance class forms
mappings/metpo_existing_aliases.tsv	curation TSV	Proposed concepts that already exist in METPO (use these IDs instead)
mappings/metpo_label_corrections.tsv	curation TSV	Upstream label-fix requests for existing METPO terms whose rdfs:label disagrees with their numeric-threshold or other intrinsic synonyms. Each row cites a berkeleybop/metpo issue. Distinct from metpo_existing_aliases.tsv: aliases route a kg-microbe-side label to an existing METPO ID as-is; corrections request that the upstream record itself be amended.
mappings/metpo_proposal_classes_robot.tsv	ROBOT template (two header rows)	Class declarations submittable to METPO maintainers
mappings/metpo_proposal_properties_robot.tsv	ROBOT template	Property declarations submittable to METPO maintainers
kg_microbe/transform_utils/metatraits/mappings/metpo_alias_mappings.tsv	Tier-2 override	Consumed by metatraits transform to use existing METPO IDs
mappings/kgmicrobe_proposal_placeholders.tsv	curation TSV	Registry of kgmicrobe.*:* placeholder CURIEs that transforms emit while a METPO term is still under proposal — see "Placeholder policy" below

The *_robot.tsv files are the upstream-submittable artifacts. The plain metpo_proposal_*.tsv files are the curation/audit ledger.

Placeholder policy (transforms must not emit unminted METPO IDs)

Until a proposed METPO term is officially minted in the upstream berkeleybop/metpo release, KG-Microbe transforms MUST NOT emit the proposed METPO ID into nodes.tsv / edges.tsv. Instead the transform mapping points at a kgmicrobe.<sub>:<local_id> placeholder CURIE.

• Per-CURIE label / category / description live in kg_microbe/transform_utils/custom_curies.yaml under one of the kgmicrobe.activity / kgmicrobe.trait / kgmicrobe.compound / kgmicrobe.pathway blocks.
• The placeholder ↔ proposed-METPO swap table lives in mappings/kgmicrobe_proposal_placeholders.tsv. Every kgmicrobe.* CURIE that does correspond to a row in mappings/metpo_proposal_*.tsv MUST be listed there with status, used_by, and target proposed_metpo_id.

When a proposal lands upstream and the METPO ID is minted, swap the transform-side object_id from the kgmicrobe.* placeholder back to the METPO ID and update status=accepted in the placeholder registry.

Workflow

1. Generate / update curation TSVs

poetry run python scripts/extract_metpo_proposals.py

This:

• Validates against data/transformed/ontologies/metpo_nodes.tsv (no label/synonym collisions).
• Validates BacDive observation counts against data/raw/bacdive_strains.json if present (data-driven check, see compute_bacdive_observations).
• Emits the four curation TSVs above.

Run poetry run pytest tests/test_extract_metpo_proposals.py to confirm regenerate-and-diff cleanliness (artifact-as-source-of-truth gate).

2. Mirror into ROBOT-template format

After editing the curation TSVs, regenerate the ROBOT-shaped tables. Two header rows are required: row 1 is the human-readable column name; row 2 is the ROBOT directive.

Required ROBOT directives

Classes (metpo_proposal_classes_robot.tsv):

Column	Directive	Effect
proposed_id	ID	subject IRI
label	LABEL	rdfs:label
definition	A IAO:0000115	textual definition annotation
definition_source	>A IAO:0000119	axiom annotation on the definition (proper OBO citation pattern)
parent	SC %	rdfs:subClassOf
synonyms	A oboInOwl:hasExactSynonym SPLIT=|	exact synonyms (pipe-split)
xrefs	A oboInOwl:hasDbXref SPLIT=|	dbxrefs (pipe-split)
subset	A oboInOwl:inSubset	proposal cohort tag (e.g. metpo_proposal_2026_04)
priority, observations, traits_addressed	(empty)	curation metadata, ignored by ROBOT

Properties (metpo_proposal_properties_robot.tsv):

Column	Directive	Effect
proposed_id	ID	subject IRI
label	LABEL	rdfs:label
definition	A IAO:0000115	definition
definition_source	>A IAO:0000119	citation
type	TYPE	owl:DatatypeProperty or owl:ObjectProperty
domain	DOMAIN	rdfs:domain
range	RANGE	rdfs:range
xrefs	A oboInOwl:hasDbXref SPLIT=|	dbxrefs
subset	A oboInOwl:inSubset	cohort tag

All rows must be padded to the same column count (trailing tabs for empty cells), or ROBOT will reject the template.

3. Validate with ROBOT (REQUIRED before sharing)

# 3a. Compile each template into OWL — fails on syntax errors
robot template \
  --template mappings/metpo_proposal_classes_robot.tsv \
  --prefix "METPO: http://purl.obolibrary.org/obo/METPO_" \
  --prefix "biolink: https://w3id.org/biolink/vocab/" \
  --output /tmp/metpo_classes.owl

robot template \
  --template mappings/metpo_proposal_properties_robot.tsv \
  --prefix "METPO: http://purl.obolibrary.org/obo/METPO_" \
  --prefix "biolink: https://w3id.org/biolink/vocab/" \
  --output /tmp/metpo_props.owl

# 3b. Merge classes + properties into a single proposal artifact
robot merge \
  --input /tmp/metpo_classes.owl \
  --input /tmp/metpo_props.owl \
  --output /tmp/metpo_proposal_merged.owl

# 3c. ELK reason — fails on inconsistencies / unsatisfiable classes
robot reason \
  --reasoner ELK \
  --input /tmp/metpo_proposal_merged.owl \
  --axiom-generators "SubClass EquivalentClass" \
  --output /tmp/metpo_proposal_reasoned.owl

Pass criteria:

• All three commands exit zero with no UNSAT / inconsistent warnings on stderr.
• The reasoned output line count is close to the merged input line count (a small delta is just inferred subclass redundancy; a large delta or new equivalent-class assertions indicates unintended collapses).

Common failures and fixes:

Symptom	Cause	Fix
Number of columns ... does not match	directive row shorter than data rows	pad header row 2 with trailing tabs
Could not parse: <directive>	typo in directive (e.g. A IAO 0000115)	use space between directive code and CURIE: A IAO:0000115
UNSAT class: <CURIE>	conflicting parent/disjoint axioms	review parent chain; check if a sibling class is disjoint via PATO/OBI
Inconsistent ontology	conflicting domain/range vs. parent property	tighten domain/range or relax parent
New EquivalentClasses axiom in reasoned output	two children mapped to same parent + same definition pattern collapse	review definition uniqueness

4. Submit upstream

The submittable artifacts are:

• mappings/metpo_proposal_classes_robot.tsv
• mappings/metpo_proposal_properties_robot.tsv
• /tmp/metpo_proposal_reasoned.owl (for reviewers who prefer OWL)

File a PR or issue at berkeleybop/metpo with the TSVs attached. Reference the subset tag (e.g. metpo_proposal_2026_04) so reviewers can filter.

Definition style

Aristotelian convention (genus + differentia):

<term>: <existing parent class> with <distinguishing feature>.

Examples in current proposal:

• circular colony = "Colony shape with a regular round outline."
• fried-egg-shaped colony = "Colony shape with a raised opaque centre and translucent peripheral zone, resembling a fried egg."
• catalase positive = "Catalase activity phenotype in which the catalase test yields a positive result, characterised by visible bubbling on H2O2."

Avoid:

• Bare phrases without a genus anchor (e.g. "Multiple flagella per cell" — what kind of thing? add Flagellar arrangement in which ...).
• Definitions that only repeat the label (e.g. "polytrichous: polytrichous arrangement").
• References to other proposed siblings by ID (use labels — IDs may shift before publication).

Definition source citations

Every term needs IAO:0000119. Acceptable forms:

Source	CURIE pattern	Example
BacDive strain entry	BacDive:strain/<id>	BacDive:strain/13245
Bergey's Manual	ISBN:<isbn>	ISBN:9780470654958
Reused PATO/GO definition	the source CURIE itself	PATO:0000052
Peer-reviewed paper	PMID:<id> or DOI:<doi>	PMID:31123456
Working draft (placeholder)	TODO:add_citation	only acceptable in pre-submission drafts

A proposal with only TODO:add_citation placeholders should NOT be submitted upstream.

Parent class selection

Prefer the most specific existing METPO parent. Audit chain:

1. Search data/transformed/ontologies/metpo_nodes.tsv for sibling concepts.
2. If a sibling class exists (e.g. METPO:1000332 = pH tolerance), use it as parent.
3. Only fall back to METPO:1000000 for genuinely top-level new categories.

Mass SC METPO:1000000 is a code smell — flag it during review.

Numeric-ID range conventions

When you mint a new ID, place it in the range that already groups its kind. METPO splits into two families by leading digit:

Range	What lives there	Example
METPO:1000xxx	Classes (organism, environment, phenotype, enzyme, growth medium, …)	METPO:1000525 microbe, METPO:1000526 chemical entity, METPO:1000527 enzyme, METPO:1004005 growth medium
METPO:1004xxx	Growth-medium classes	METPO:1004005 growth medium and its children
METPO:1005xxx	Test-result / assay classes	METPO:1005010 indole test, METPO:1005011 indole test positive
METPO:1007xxx	KG-Microbe proposal classes (pre-mint cohort)	All proposed classes in this PR cohort
METPO:2000001-2000020	Object properties — chemical interaction, positive	METPO:2000002 assimilates, METPO:2000006 uses as carbon source
METPO:2000021-2000056	Object properties — chemical interaction, negative (paired with the matching positive ~25 IDs lower; gaps in 2000040-2000056 also hold positive extensions)	METPO:2000027 does not assimilate, METPO:2000031 does not use as carbon source
METPO:2000057, 2000064-2000070	Object-property gaps in the chemical-interaction range — use these for new pairs	METPO:2000064 tolerates / METPO:2000065 does not tolerate
METPO:2000101-2000103	High-level capability/phenotype predicates	METPO:2000102 has phenotype, METPO:2000103 capable of
METPO:2000202, 2000222	Production predicates	METPO:2000202 produces / METPO:2000222 does not produce
METPO:2000302/2000303	Enzyme-activity predicates	shows activity of / does not show activity of
METPO:2000517/2000518	Growth-medium predicates	grows in / does not grow in
METPO:2000601-2000606	Process predicates	denitrifies, ammonifies, oxidizes in darkness, …
METPO:2000701-2000709, 2000711-2000716, 2000721+	Datatype properties — observational values	METPO:2000702 has minimum temperature value, METPO:2000715 has GC percentage value
METPO:2000717-2000720	Datatype-property gaps in the value-property family — use these for new value/optimum properties	METPO:2000717 has growth temperature optimum value

Rules of thumb:

1. Match the family. A new chemical-interaction object property goes in the 2000001-2000056 range, not in 2000700+. A new optimum-value datatype property goes in 2000700+, not in 2000001+.
2. Find the gap, don't fork. Before minting, dump all ObjectProperty/DatatypeProperty IDs in the target family (grep -nE "metpo/2000[0-9]{3}\"" data/raw/metpo.owl | grep -E "DatatypeProperty|ObjectProperty") and pick the next free slot in the conceptual range. The current gaps as of metpo_proposal_2026_04:
   • Object-property gaps in the chemical-interaction range: 2000057, 2000064-2000070. Adjacent positive/negative pairs are preferred over the legacy "+25 offset" pattern when the offset would push you outside the conceptual range.
   • Datatype-property gaps in the value-property range: 2000710, 2000717-2000720.
   • Class gaps for proposal cohorts: 1007xxx is reserved for KG-Microbe proposals; pick the next unused 1007NNN slot in the relevant subrange.
3. Document the gap when you mint. In the term's definition or the surrounding comment in extract_metpo_proposals.py, note WHY this ID was picked ("placed in the 2000064-2000070 gap of the chemical-interaction object-property family because …"). Keeps future curators from re-shuffling.

Paired predicates: positive ↔ negative via shared synonym

The metatraits transform's _build_metpo_lookups (kg_microbe/transform_utils/metatraits/metatraits.py:919, helper _get_negative_predicate at metatraits.py:2103) auto-pairs METPO predicates so a downstream call like

self._get_negative_predicate("METPO:2000064")  # tolerates
# → "METPO:2000065"  # does not tolerate

resolves the partner without any hardcoded table. The pairing rule:

1. The negative member's rdfs:label MUST start with does not (lowercased). The loader uses this prefix to flag the entry as the negative half.
2. Both members MUST share at least one oboInOwl:hasRelatedSynonym (or label) so they end up under the same metpo_pattern_to_predicate key.

Worked example — METPO:2000002 / 2000027:

	METPO:2000002 (positive)	METPO:2000027 (negative)
label	assimilates	does not assimilate
synonym	assimilation	assimilation
Builds key assimilation	positive=METPO:2000002	negative=METPO:2000027

Result: metpo_pattern_to_predicate["assimilation"] = {positive: METPO:2000002, negative: METPO:2000027}. _get_negative_predicate(METPO:2000002) iterates the dict, finds the entry where positive==METPO:2000002, and returns its negative.

Counter-example (broken pairing) — METPO:2000517/2000518 in the current upstream release:

	METPO:2000517	METPO:2000518
label	grows in	does not grow in
synonyms	(none)	(none)
Built keys	positive["grows in"]=2000517	negative["does not grow in"]=2000518

No shared key → not paired → _get_negative_predicate("METPO:2000517") returns None → false-majority grows in observations are silently dropped. Fix: add a shared related synonym to both upstream (e.g. growth medium relation or growth in medium).

When proposing a new paired predicate, always:

• Use does not <stem> as the negative label.
• Give both members a shared oboInOwl:hasRelatedSynonym (a noun-form of the relation works well: tolerance, assimilation, production).
• Optionally give the negative additional synonyms for human readability (is susceptible to, is sensitive to) — these become extra entries in metpo_pattern_to_predicate keyed on those synonyms but, because they're only on the negative member, they don't interfere with the pairing.

Predicate vs class: when to model with which

The proposal occasionally has a choice: encode an organism-chemical relationship as a predicate-driven edge (organism --P--> chemical) or as a class-subdivision phenotype (organism --has phenotype--> "X-susceptible" class). Default to the predicate, not the class.

Modeling choice	Use when
Predicate-driven (mint or reuse a paired predicate; emit org --P--> chem/medium/enzyme/process)	The relationship is parametric over a chemical/medium/enzyme axis. New axis values shouldn't require new ontology mints. Examples: tolerates(org, chem), grows in(org, medium), shows activity of(org, enzyme).
Class-subdivision (mint a phenotype class per outcome and use biolink:has_phenotype / METPO:2000102)	The "outcome" is qualitative and not a function of a chemical/medium/enzyme. Examples: cell shape (rod-shaped, coccus-shaped), colony morphology (circular, irregular, fried-egg-shaped), Gram stain (positive/negative).

Smell: a class hierarchy whose name encodes a chemical or medium (bile acid susceptible, growth on MacConkey agar, catalase positive) is a candidate for collapse into a predicate-driven pattern. The METPO proposal in metpo_proposal_2026_04 removed three such hierarchies (growth on {MacConkey,blood,EMB} agar and bile acid response/susceptible) in favour of the predicate-driven equivalents (METPO:2000517 grows in and METPO:2000064/2000065 tolerates / does not tolerate).

Test-outcome classes are a special case — they encode a bench observation (catalase test positive) that is downstream of the underlying enzyme activity. Keep the test-outcome class AND assert the underlying predicate edge in parallel; the class records "the assay was performed and yielded outcome X", the predicate records "the organism has activity Y".

Subset tagging

All proposal rows must be tagged with a cohort identifier so curators can filter:

subset	A oboInOwl:inSubset
metpo_proposal_2026_04

Use a date-stamped string (metpo_proposal_<YYYY>_<MM>). On the next proposal cohort, mint a new value (don't reuse).

Skill checklist

When this skill is invoked, run through:

• scripts/extract_metpo_proposals.py exits clean
• pytest tests/test_extract_metpo_proposals.py tests/test_metatraits.py passes
• *_robot.tsv files have two header rows, consistent column counts
• Every row has a definition_source (no TODO:add_citation if submitting)
• Every row has a subset cohort tag
• robot template succeeds for both class + property TSVs
• robot merge produces a single OWL
• robot reason --reasoner ELK exits clean with no UNSAT classes
• No mass SC METPO:1000000 (>3 rows) without curator review
• Every minted ID lands in the conventional family range (see "Numeric-ID range conventions") and the choice of slot is documented in the surrounding source comment
• Every newly proposed paired predicate has the negative member labelled does not <stem> AND a shared oboInOwl:hasRelatedSynonym with its positive partner — verify by simulating _build_metpo_lookups against the proposal OWL
• Every class hierarchy whose name encodes a chemical / medium / enzyme has been audited against the "predicate vs class" rule; if a paired predicate already exists (or could be cheaply minted), prefer the predicate-driven edge
• Every entry in METPO_LABEL_CORRECTIONS cites a berkeleybop/metpo issue and the validate_label_corrections() freshness check passes (entries become stale once upstream fixes them — re-check before re-shipping)

See also

• metpo-ontology skill — for using existing METPO terms in transforms (the inverse direction)
• scripts/extract_metpo_proposals.py — proposal generation source
• berkeleybop/metpo — upstream repository
• ROBOT template docs — full directive reference