Stitch
Skill BioTender-max/awesome-bio-agent-skills/skills/drugclaw/stitch
Query the STITCH chemical-protein interaction database. Use whenever the user asks about chemical-protein interactions, drug-target binding, compound action modes, or wants to look up any entity (chemical name, STITCH CID, STRING protein ID) in STITCH.From its SKILL.md
npx -y skills add BioTender-max/awesome-bio-agent-skills --skill stitchAssembled from the repository path, not quoted from the project. Check it against their README if it does not work.
One thing to look at
- no licenseNo license file was found in the repository. Code published without one is not open source by default, so using it at work is a question for whoever answers licensing questions where you are.
SKILL.md
2.9 KB, 722 tokens by cl100k_base, as published. Nobody here has run it
STITCH Query Skill
Search STITCH for chemical–protein interactions via REST API. Auto-detects input type:
| Input Pattern | Detected As | Example |
|---|---|---|
CIDm00002244 / CIDs00002244 | STITCH chemical ID | direct lookup |
9606.ENSP00000352121 | STRING protein ID | direct lookup |
| anything else | free text | resolved via /resolve first |
API
| Function | Input | Returns |
|---|---|---|
resolve(name, species) | chemical / protein name | list[dict] with stringId, preferredName |
resolve_batch(names, species) | list of names | list[dict] (via /resolveList) |
get_interactors(id, species, limit, required_score) | single ID | list[dict] with partner IDs + scores |
get_actions(id, species, limit, required_score) | single ID | list[dict] with mode (activation/inhibition/binding…) |
get_interactions(ids, species, required_score) | list of IDs | list[dict] pairwise interactions among inputs |
search(entity, species, limit, required_score) | single entity (any type) | dict with resolved_id, interactors, actions |
search_batch(entities, species, limit, required_score) | list or comma-separated string | dict[str, dict] |
summarize(result, entity) | search() result + label | compact text |
to_json(result) | any result | JSON string |
Key Fields
Interactors — stringId_A, stringId_B, preferredName_A, preferredName_B, score, nscore, fscore, pscore, ascore, escore, dscore, tscore
Actions — stringId_A, stringId_B, preferredName_A, preferredName_B, mode (activation / inhibition / binding / catalysis / reaction / expression / ptmod), action, is_directional, a_is_acting, score
Score Channels
| Abbrev | Meaning |
|---|---|
| nscore | neighborhood (genomic context) |
| fscore | gene fusion |
| pscore | phylogenetic co-occurrence |
| ascore | co-expression |
| escore | experimental evidence |
| dscore | curated database evidence |
| tscore | text mining |
| score | combined score (0–1000; 400=medium, 700=high, 900=highest) |
Usage
See if __name__ == "__main__" block in 45_STITCH.py for runnable examples covering: free-text name, STITCH CID, batch search, and JSON output.
Data Source
- Provider: STITCH / STRING Consortium (EMBL, CPR, SIB, KU)
- Primary URL:
http://stitch.embl.de/api - Fallback URL:
https://string-db.org/api(STITCH data merged into STRING 12+) - Auth: None (public API; rate-limited — avoid parallel bulk requests)
- Species: Default 9606 (Homo sapiens); pass NCBI taxonomy ID for other organisms
What ships with it: 5 files
14.3 KB alongside SKILL.md, 4 of them executable
- example.pyruns9.0 KB
- __init__.pyruns130 B
- README.md939 B
- retrieve.pyruns771 B
- stitch_skill.pyruns3.5 KB