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Look up pathway or GO/Reactome/KEGG term definitions and key genes.
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Based on SOC occupation classification
| name | pathway_lookup |
| description | Look up pathway or GO/Reactome/KEGG term definitions and key genes. |
| category | bio/literature |
| version | 1 |
| requires_tools | ["fetch_url","search_knowledge_base"] |
| requires_network | true |
| user_invocable | true |
| species | any |
| modality | literature |
| stage | utilities |
| stability | experimental |
| safety_level | low |
User asks what a pathway or GO/Reactome/KEGG term is, or which genes are in it.
Local first: Use search_knowledge_base with the term to find lab-curated definitions.
Online: Use fetch_url for public APIs:
https://reactome.org/ContentService/data/pathway/{id}/containedGenes or search.Synthesize: Definition of the pathway/term + list of key genes (if available) + optional link.
Manage the BioAPEX current-feature workflow from scoping through review and completion
Turn an analysis request into a Slurm-ready execution plan with commands, resource assumptions, and job structure.
Scale a buffer recipe to a target volume and compute component masses/volumes.
Save a fetched summary or document to the knowledge base for later retrieval (e.g. after PubMed/UniProt lookup).
Interpret scRNA clusters using marker genes and suggest cell type or state.
Critically evaluate a perturbation hypothesis — challenge assumptions, propose negative controls, and flag confounders.