geneontologygeneontology/go-skills/skills/amigo/SKILL.md

amigo

Skill1 starsChanged 32 days agoBSD-3-ClauseView on GitHub

Use whenever you need to access existing standard annotations OR bioentities (genes, gene products) in the ID space used by Noctua

In this repository11 other files it gives its agents.
- CLAUDE.mdCLAUDE.md
- annotate-functionSkill
- gene-reviewSkill
- gocam-best-practiceSkill
- gocam-reviewSkill
- noctuaSkill
- pubmed-eutilsSkill
- reportSkill
- save-to-drop-boxSkill
- summarySkill
- uniprot-databaseSkill

The file

We split this skill into the rules it gives an agent

4 rules. About 0 are common, 3 are distinctive, and 1 is very specific to this project.

≈0
Common · estimate
Many files like this have a rule of this kind.
≈3
Distinctive · estimate
This author's own choices. Worth a look.
1
Very specific
Tied to their project's names, files or tools. Probably skip.

Common
Distinctive
Very specific

Distinctive:
Use for finding gene products and annotations
line 13
Very specific:
When these docs say amigo this can be expanded to noctua amigo if the alias is not set.
line 25
Distinctive:
All annotations for an entity:
line 84
Distinctive:
Search for GO annotations with filtering:
line 99

≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.

Files

SKILL.md

About

Use for finding gene products and annotations

Command Line Client

This uses the noctua command line tool, which should have been installed when we ran uv tool install noctua

I recommend:

alias amigo='noctua amigo'

When these docs say amigo this can be expanded to noctua amigo if the alias is not set.

You can get help at any time

amigo --help

subcommands also have help

Bioentities

Note that in AmiGO and in the GO-CAM store, MOD IDs are used for MODs, ComplexPortal for complexes, with UniProtKB (or RNA Central) IDs used for gene products in human and other species

Search bioentities

amigo search-bioentities --help

By text (eg gene symbol)

amigo search-bioentities -t P53

yields:

BIOENTITY       LABEL   NAME    TAXON   TYPE    SOURCE
FB:FBgn0039044  p53     p53     Drosophila melanogaster protein FB
ComplexPortal:CPX-663   p53-mdmx_human  p53-MDM4 transcriptional regulation complex     Homo sapiens    protein_complex ComplexPortal
ComplexPortal:CPX-759   p53-mdm2_human  p53-MDM2 transcriptional regulation complex     Homo sapiens    protein_complex ComplexPortal
ComplexPortal:CPX-6093  p53-mdm2_human-1        p53-MDM2-MDM4 transcriptional regulation complex        Homo sapiens    protein_complex ComplexPortal
UniProtKB:A0A9L0SIC9    TP53    Cellular tumor antigen p53      Equus caballus  protein UniProtKB

Restricting by taxon:

amigo search-bioentities -t P53 --taxon NCBITaxon:9606

Viewing more entities

amigo search-bioentities -t P53 -l 300

Fetching info on an entity or checking it exists:

amigo get-bioentity UniProtKB:P04637

Annotations

All annotations for an entity:

amigo bioentity-annotations UniProtKB:P04637
Found 100 annotations for UniProtKB:P04637:
GO_TERM GO_NAME ASPECT  EVIDENCE        REFERENCE       WITH    QUALIFIER       ASSIGNED_BY     DATE
GO:0008285      negative regulation of cell population proliferation    P       ISS     ['PMID:30514107']       -       -       ARUK-UCL        20210810
GO:0051726      regulation of cell cycle        P       ISS     ['PMID:30514107']       -       -       ARUK-UCL        20210810
GO:1902749      regulation of cell cycle G2/M phase transition  P       IMP     ['PMID:10962037']       -       -       UniProt 20210802
GO:0006974      DNA damage response     P       IDA     ['PMID:14744935']       -       -       MGI     20101109
GO:0006983      ER overload response    P       IDA     ['PMID:14744935']       -       -       MGI     20101109

Note that this is truncated. Use -l 9999 to fetch all

Search for GO annotations with filtering:

amigo search-annotations [OPTIONS]

╭─ Options ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ --bioentity -b TEXT Bioentity ID to filter by │ │ --go-term -g TEXT GO term ID to filter by │ │ --closure -c TEXT GO terms including closure (can repeat) │ │ --evidence -e TEXT Evidence types to filter by (can repeat) │ │ --taxon TEXT Organism filter │ │ --aspect -a TEXT GO aspect (C, F, or P) │ │ --assigned-by TEXT Annotation source filter │ │ --limit -l INTEGER Maximum number of results [default: 10] │ │ --base-url TEXT Custom GOlr endpoint URL │ │ --help Show this message and exit. │ ╰────────────────────────────────────────────────────────────────────────────────────

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