reactome-skill: Скилл для анализа путей и генов

--- name: reactome-skill description: Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list. license: MIT skill-author: AIPOCH --- ## When to Use - You have a list of genes/proteins and want to run pathway overrepresentation (enrichment) analysis against Reactome. - You need to retrieve curated pathway content (hierarchy, reactions, participants) by Reactome stable IDs (e.g., `R-HSA-69278`). - You want to map expression values onto pathways to support pathway-level interpretation. - You need to project pathways across species/organisms using Reactome’s species projection capabilities. - You are building a systems biology workflow that requires programmatic access to Reactome via its REST API. ## Key Features - **Pathway enrichment (overrepresentation)** for identifier lists. - **Expression analysis** by mapping expression data to Reactome pathways. - **Content retrieval** for pathways, reactions, and participating molecules. - **Pathway hierarchy access** to navigate curated pathway structures. - **Species projection** to map pathways across organisms. - **API documentation reference**: see `references/api_reference.md`. ## Dependencies - `python` (3.x) - `requests` (latest compatible) - `reactome2py` (latest compatible) Install: ```bash uv pip install reactome2py requests ``` ## Example Usage The following commands are runnable examples using the provided CLI script. ### 1) Query pathway content by Reactome ID ```bash python scripts/reactome_tool.py query_content --id "R-HSA-69278" ``` ### 2) Run overrepresentation analysis for a gene list ```bash python scripts/reactome_tool.py analyze_identifiers --identifiers "TP53,BRCA1" ``` ## Implementation Details - **API access pattern**: The skill uses the Reactome REST API (via `reactome2py` and/or direct HTTP calls with `requests`) to fetch pathway content and submit analyses. - **Identifier input**: Gene/protein identifiers are provided as a comma-separated string (e.g., `TP53,BRCA1`) and are submitted for overrepresentation analysis. - **Stable IDs**: Content retrieval expects Reactome stable identifiers (commonly formatted like `R-HSA-xxxxx` for human pathways). - **Outputs**: Results typically include pathway/reaction metadata and analysis outputs (e.g., enriched pathways with associated statistics), depending on the invoked action. - **Reference**: Reactome developer documentation is available at https://reactome.org/dev and the local API notes at `references/api_reference.md`.