القائمة
Use whenever you need to access existing standard annotations OR bioentities (genes, gene products) in the ID space used by Noctua
يُحدَّد Prompt الذي يراجع المصدر أولًا بشكل افتراضي. يمكنك التبديل إلى أمر مباشر أو تنزيل نسخة محلية.
اقرأ SKILL.md وأي ملفات مرافقة يعرضها SkillsMP قبل أن تقرر التثبيت.
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
يتجاوز الأمر المباشر Prompt المخصّص للمراجعة. افحص المصدر قبل تشغيله.
npx skills add https://github.com/geneontology/go-jupyter --skill amigoيبقى الأمر في سطر واحد. مرّر أفقيًا لمراجعته كاملًا قبل النسخ.
تفضّل نسخة محلية؟ نزّل الملفات المتاحة حاليًا لدى SkillsMP.
عرض SKILL.md
| name | amigo |
| description | Use whenever you need to access existing standard annotations OR bioentities (genes, gene products) in the ID space used by Noctua |
Use for finding gene products and annotations
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
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
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. │ ╰────────────────────────────────────────────────────────────────────────────────────