// Search GO bioentities (genes, gene products, complexes) and their GO annotations directly from the GO database. Use to resolve MGI/MOD/ComplexPortal IDs, cross-check GO annotations independently of gocam search, or find MOD-specific gene product IDs needed in Noctua models.
| name | amigo |
| description | Search GO bioentities (genes, gene products, complexes) and their GO annotations directly from the GO database. Use to resolve MGI/MOD/ComplexPortal IDs, cross-check GO annotations independently of gocam search, or find MOD-specific gene product IDs needed in Noctua models. |
Use as a complement to gocam search when you need to:
# Same pattern as barista — requires uv in PATH
uv run noctua amigo <subcommand> [options]
Or if the amigo alias is set:
alias amigo='uv run noctua amigo'
amigo <subcommand> [options]
# Search by gene symbol + taxon
uv run noctua amigo search-bioentities -t Syt1 --taxon NCBITaxon:10090
# Returns: bioentity ID, label, name, taxon, type, source
# e.g. MGI:MGI:98777 Syt1 synaptotagmin I Mus musculus protein MGI
This is the authoritative source for which IDs Noctua actually uses. For mouse, expect MGI IDs. For human, expect UniProtKB IDs.
# Confirm a specific accession exists
uv run noctua amigo get-bioentity UniProtKB:P04637
uv run noctua amigo get-bioentity MGI:MGI:98777
uv run noctua amigo bioentity-annotations UniProtKB:P46096 -l 100
# Returns: GO_TERM, GO_NAME, ASPECT (F/P/C), EVIDENCE, REFERENCE, QUALIFIER, ASSIGNED_BY, DATE
Use this to:
gocam searchpart_of and occurs_inFilter by aspect:
# MF only
uv run noctua amigo search-annotations -b UniProtKB:P46096 -a F -l 100
# With evidence filter (experimental codes only)
uv run noctua amigo search-annotations -b UniProtKB:P46096 -a F -e IDA -e IMP -e IPI -l 100
| Situation | Use |
|---|---|
| Need UniProt ID for a mouse gene | gocam search (faster, CLI output) |
| Encountered an MGI ID, need the gene symbol | /amigo search-bioentities --taxon NCBITaxon:10090 |
| Need canonical Noctua bioentity ID | /amigo search-bioentities |
| Verify MF annotations, get SynGO | gocam search |
| Independent cross-check of GO annotations | /amigo bioentity-annotations |
| Look up ComplexPortal entry | /amigo search-bioentities -t <complex name> |
This skill should be used when creating, editing, or validating GO-CAM (Gene Ontology Causal Activity Model) models. It provides comprehensive annotation guidelines for molecular functions, biological processes, cellular components, and causal relationships following GO Consortium standards.
Independent blind evaluation of GO-CAM claims documents using Claude Explore subagents to read the PDFs. Reads expert_validation_claims.md and verifies every claim against primary PDFs from scratch, producing a structured evaluation report. Use after gocam-claims-pipeline has generated its output. Always run in a fresh session — never in the same session as the pipeline. For a Gemini-powered alternative, see /blind-review-gemini.
Independent blind evaluation of GO-CAM claims documents using Gemini. One Gemini instance per primary PDF reads the paper directly and returns PASS/FLAG/FAIL verdicts on every claim citing it. Use after gocam-claims-pipeline has generated its output. Always run in a fresh session — never in the same session as the pipeline. For a Claude-engine alternative, see /blind-review-claude.
Generate a .drawio pathway diagram from a GO-CAM claims document. Use after completing the annotation pipeline (Phase 7) to produce agent-output/pathway_sketch.drawio. Reads shape styles and the Shape Palette page from workflow/network_template_draw.drawio.
Launches two parallel Gemini instances per paper to review GO-CAM claims from two complementary perspectives — a peer reviewer (scientific accuracy) and a GO-CAM curator (annotation correctness). Each receives the full claim in claims_template format and responds as an expert with OK/WRONG/UNCERTAIN plus a corrected claim where needed. Collects both outputs into peer_review_claims.md alongside the original claim.
Run the full GO-CAM literature-backed annotation pipeline. Reads GO-CAM models (OWL/TTL), verifies all claims against primary research PDFs, and produces expert validation documents. Use when starting or continuing a GO-CAM curation project folder.