amigo

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.

AmiGO — GO Bioentity and Annotation Search

Use as a complement to gocam search when you need to:

• Resolve an MGI ID or other MOD ID to a gene symbol
• Find the canonical bioentity ID used in Noctua (MOD IDs for MODs, UniProtKB for human/other species)
• Cross-check GO annotations directly from the GO database
• Look up ComplexPortal entries for protein complexes

Invocation

# 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]

---

Resolve a gene product (find its bioentity ID and species)

# 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

---

Get all GO annotations for a gene product

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:

• Cross-check MF assignments (ASPECT=F) independently of gocam search
• Verify BP (ASPECT=P) and CC (ASPECT=C) annotations for part_of and occurs_in
• Check for NOT annotations that conflict with model claims

Filter 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

---

When to use AmiGO vs gocam search

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>