kg-microbe

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.

Render a GTDB phylogenetic diagram from a KG-Microbe merged release with each clade sized by the count of non-taxonomy edges (phenotypes, growth media, chemicals, etc.) incident on it. Folds NCBITaxon and kgmicrobe.strain edges onto their GTDB equivalent via in-graph close_match, GTDB metadata, and the published NCBI2GTDB tables. Persists the resolved mapping and a gap report. Use when you need to see *where in the GTDB tree the metadata is concentrated* — which clades are well-characterized vs sparse.

Generate a structured Markdown report on every post-transform and post-merge operation needed to take KG-Microbe from per-source TSVs to the final shipped data products (merged KG, RDF copy, release tarballs). Reports each operation's purpose, command, inputs, outputs, severity, and current freshness against the on-disk repo state. Use when planning a release, onboarding, auditing what is stale, or producing a "what's left to ship" punch list.

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.

Walk and validate multi-hop semantic paths in KG-Microbe transform outputs. Use to uncover modeling bugs where the KG does not accurately represent the raw data — cross-contamination, self-loops, phantom intermediates, false-majority emission, missing expected paths, cardinality outliers — by combining open-ended path exploration with built-in archetype checks calibrated against the raw source data.

Audit code + curation files for hardcoded ontology mappings, dead files, schema heterogeneity, and repeated-callsite "data masquerading as code" patterns

Produce a standardized semantic-modeling diff report between two KG-Microbe merged-KG releases. Use when comparing KG versions to quantify changes in biolink/METPO categories, predicates, relations, CURIE prefixes, knowledge sources, and predicate × category signatures.

Cut an official KG-Microbe GitHub release. Bundles merged-KG + transformed + raw, links a review verdict, splits assets that exceed GitHub's 2 GiB per-file limit, and falls back to Zenodo for very large payloads. Use when publishing a new merged KG to Knowledge-Graph-Hub/kg-microbe releases.

Address unresolved Copilot review threads on a GitHub PR and mark each one resolved (equivalent to clicking the "Resolve conversation" button in the GitHub UI). Use when the user asks to "address copilot", "fix copilot comments", "resolve copilot conversations", or similar on a PR.

Query KG-Microbe for organism information, growth media preferences, and metabolic capabilities

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.

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.