メニュー
Finds patterns so metatraits output follows KGX format and METPO semantics without adding extra terms. Use when working with unmapped traits, metatraits transform output, KGX format, trait ontology mapping, or label-to-CURIE resolution.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
Knowledge modeling review of KG-Microbe transforms and merged KG for alignment with METPO, Biolink Model, and KGX specification. Use when auditing transform output quality, validating categories/predicates, checking CURIE prefix registration, or preparing a release.
Add a new data source transform to KG-Microbe end-to-end — from "should we even ingest this?" through deep research, cross-reference analysis, semantic design, code scaffold, integration, verification, and shipping the PR. Bakes in the CLAUDE.md 7-step checklist plus the research + analysis + verify phases that keep the KG coherent. Use whenever the ask is "ingest X", "add source Y", or "integrate a new database into kg-microbe".
Ship a messy topic branch as a set of clean, focused PRs. Walks through triage of committed commits + working-tree modifications + untracked files, extracts misfiled commits to their own branches, splits orthogonal changes into separate PRs, gitignores build noise, opens follow-up issues for deferred items, and merges in the correct dependency order. Use when a working branch has accumulated mixed commits, uncommitted work, and dozens of untracked scratch files and needs to reach master.
Emit a Codex-ready review prompt for the KG-Microbe repository focused on code logic, consistency, robustness, bugs, bottlenecks, and scalability. Use before delegating a deep review pass to Codex (via the codex:rescue subagent) or another external code-review agent so the target is precisely scoped and the review dimensions are enforced.
Determine whether local KG-Microbe transform outputs (data/transformed/<source>/) and merged KG (data/merged/) are current relative to origin/master. Compares latest commit times on origin/master touching each transform's code directory against local output mtimes; also checks merge stage against merge_utils/, merge.yaml, and every transform output. Use before cutting a release, before running kg-release, or when triaging "why did my merged KG change".
Work with KG-Microbe's unified chemical mapping system (`mappings/kgmicrobe_unified_entity_mappings.sssom.tsv.gz` and `kg_microbe/utils/chemical_mapping_utils.py`). Use when adding a new mapping source, regenerating the unified file, debugging a missing ChEBI lookup, validating mappings against OLS, or reasoning about which source wins when sources disagree.
| name | metpo-ontology |
| description | Finds patterns so metatraits output follows KGX format and METPO semantics without adding extra terms. Use when working with unmapped traits, metatraits transform output, KGX format, trait ontology mapping, or label-to-CURIE resolution. |
Find patterns so metatraits output follows KGX format and METPO semantics. Do not add extra terms—use only existing ontology terms.
Allowed ontologies: Metatraits should express traits using GO, CHEBI, EC, METPO, and RHEA only.
Ontology data locations:
data/transformed/ontologies/ — nodes/edges for GO, CHEBI, EC, and METPOdata/transformed/rhea_mappings/ — RHEA reaction mappings (use for RHEA nodes/edges)Known unmapped relationship types: Reference docs/metatraits/unmapped_traits_unique.tsv for relationship types derived from unmapped_traits.tsv and taxa in data/transformed/metatraits/.
Label-to-CURIE mappings: https://metatraits.embl.de/traits shows relations between labels and CURIEs for chemicals, enzymes, etc. Use this to resolve unmapped traits—look up the mapping between term labels and term CURIEs.
Conformance: Ensure output conforms to KGX format and METPO semantics; do not introduce new terms.
data/transformed/ontologies/ (GO, CHEBI, EC, METPO)data/transformed/rhea_mappings/ (RHEA via rhea_mappings transform)