A skill for the Codex CLI that provides access to the WheatOmics wheat multi-omics bioinformatics database via its REST API.
- Gene details: description, chromosome, protein length, MW, pI, annotations, JBrowse/Ensembl links
- Expression profiles: query across 60+ projects (tissue development, abiotic/biotic stress, hormone treatment)
- Coexpression networks: PCC-based coexpression pairs from grain and multi-tissue databases
- PPI networks: protein-protein interaction pairs
- Sequence retrieval: CDS, protein FASTA, batch retrieval, genomic interval extraction
- Comparative genomics: Triticeae homologs, wheat-rice-Arabidopsis orthologs, synteny blocks
- Literature search: indexed wheat literature with tags
- Primer design: CAPS/KASP primer design
- ID conversion: IWGSC v1/v2/v3 gene ID conversion
$skill-installer install https://github.com/CropCoder/wheatomics-skillOr clone the repository and copy files to $CODEX_HOME/skills/wheatomics/.
In Codex CLI, trigger by mentioning $wheatomics followed by your query:
$wheatomics 查一下 TraesCS5A02G391700 的表达量
$wheatomics find coexpression partners for this gene
$wheatomics get the protein sequence
https://wheatomics.sdau.edu.cn/api
API docs: https://wheatomics.sdau.edu.cn/api/docs
- v1:
Traes_5AL_XXXXXXXX - v2:
TraesCS5A02G391700(most common) - v3: Similar to v2
wheatomics/
├── SKILL.md # Skill definition and workflow
├── scripts/
│ └── wheatomics.py # curl wrapper for API queries
├── references/
│ └── api_reference.md # Complete endpoint schemas
└── agents/
└── openai.yaml # Agent configuration
WheatOmics paper: Ma S. et al., WheatOmics: A platform combining multiple omics data to accelerate functional genomics studies in wheat, Molecular Plant (2021). doi:10.1016/j.molp.2021.10.006
This skill is provided for use with Codex CLI. The WheatOmics database is developed by Shandong Agricultural University.