tooluniverse-plant-genomics

Search PlantReactome with a keyword using PlantReactome_search_pathways, or query KEGG with plant organism codes like ath for Arabidopsis. For example, KEGG_get_pathway_genes with pathway_id ath00941 returns genes in Arabidopsis flavonoid biosynthesis.

Common codes include ath for Arabidopsis, osa for rice, zma for maize, tae for wheat, gmx for soybean, and sly for tomato. Confirm availability by querying kegg_search_pathway with the species name rather than assuming codes.

Use EnsemblCompara_get_orthologues to retrieve orthologs across plant species, then check functional annotation via UniProt. Account for whole-genome duplications, since one Arabidopsis gene may have multiple diverged paralogs in crop species.

Yes, the workflow explicitly addresses polyploidy, noting wheat is hexaploid (AABBDD) with three homeologous copies of most genes. It advises against inferring function from sequence similarity alone and recommends UniProt reviewed entries or PlantReactome for validation evidence.

TAIR has no public REST API, so Arabidopsis data comes from Ensembl Plants and UniProt instead. PlantReactome coverage centers on rice with Arabidopsis cross-references, and the skill does not cover marker-assisted selection or breeding simulation.

Use tooluniverse-systems-biology for general pathway analysis in human or mouse, and tooluniverse-phylogenetics for phylogenetic tree work. The plant genomics skill is specific to plant pathways, crop species, and plant taxonomy.