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Query KG-Microbe for organism information, growth media preferences, and metabolic capabilities
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Based on SOC occupation classification
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 | kg-query |
| description | Query KG-Microbe for organism information, growth media preferences, and metabolic capabilities |
Query the KG-Microbe knowledge graph for organism information including taxonomy, phenotypic traits, growth media, and media composition.
poetry run kg query-organism "Eggerthella lenta"
poetry run kg query-organism "Corynebacterium glutamicum" -o report.md
--db-path PATH: Custom database location (default: data/merged/kg-microbe.duckdb)--force-reload: Rebuild database from TSV files--nodes-path PATH: Custom nodes.tsv location--edges-path PATH: Custom edges.tsv location--output FILE: Save report to file instead of printingbiolink:located_in) and carry the METPO semantics in the relation column — METPO:2000517 (grows in) and METPO:2000518 (doesn't grow in). Filter on relation when querying.