stitch

Name: stitch
Author: QSong-github

132stars4forks

How to install stitch?

qsong-github/drugclaw/stitch

$npx -y skills add QSong-github/DrugClaw --skill stitch

Installs into the current project.

Summary

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.

Files · 1

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SKILL.md

1	# STITCH Query Skill
2
3	Search STITCH for chemical–protein interactions via REST API. Auto-detects input type:
4
5	\| Input Pattern \| Detected As \| Example \|
6	\|---\|---\|---\|
7	\| `CIDm00002244` / `CIDs00002244` \| STITCH chemical ID \| direct lookup \|
8	\| `9606.ENSP00000352121` \| STRING protein ID \| direct lookup \|
9	\| anything else \| free text \| resolved via `/resolve` first \|
10
11	## API
12
13	\| Function \| Input \| Returns \|
14	\|---\|---\|---\|
15	\| `resolve(name, species)` \| chemical / protein name \| `list[dict]` with stringId, preferredName \|
16	\| `resolve_batch(names, species)` \| list of names \| `list[dict]` (via `/resolveList`) \|
17	\| `get_interactors(id, species, limit, required_score)` \| single ID \| `list[dict]` with partner IDs + scores \|
18	\| `get_actions(id, species, limit, required_score)` \| single ID \| `list[dict]` with mode (activation/inhibition/binding…) \|
19	\| `get_interactions(ids, species, required_score)` \| list of IDs \| `list[dict]` pairwise interactions among inputs \|
20	\| `search(entity, species, limit, required_score)` \| single entity (any type) \| `dict` with resolved_id, interactors, actions \|
21	\| `search_batch(entities, species, limit, required_score)` \| list or comma-separated string \| `dict[str, dict]` \|
22	\| `summarize(result, entity)` \| search() result + label \| compact text \|
23	\| `to_json(result)` \| any result \| JSON string \|
24
25	## Key Fields
26
27	Interactors — `stringId_A`, `stringId_B`, `preferredName_A`, `preferredName_B`, `score`, `nscore`, `fscore`, `pscore`, `ascore`, `escore`, `dscore`, `tscore`
28
29	Actions — `stringId_A`, `stringId_B`, `preferredName_A`, `preferredName_B`, `mode` (activation / inhibition / binding / catalysis / reaction / expression / ptmod), `action`, `is_directional`, `a_is_acting`, `score`
30
31	## Score Channels
32
33	\| Abbrev \| Meaning \|
34	\|---\|---\|
35	\| nscore \| neighborhood (genomic context) \|
36	\| fscore \| gene fusion \|
37	\| pscore \| phylogenetic co-occurrence \|
38	\| ascore \| co-expression \|
39	\| escore \| experimental evidence \|
40	\| dscore \| curated database evidence \|
41	\| tscore \| text mining \|
42	\| score \| combined score (0–1000; 400=medium, 700=high, 900=highest) \|
43
44	## Usage
45
46	See `if __name__ == "__main__"` block in `45_STITCH.py` for runnable examples covering: free-text name, STITCH CID, batch search, and JSON output.
47
48	## Data Source
49
50	- Provider: STITCH / STRING Consortium (EMBL, CPR, SIB, KU)
51	- Primary URL: `http://stitch.embl.de/api`
52	- Fallback URL: `https://string-db.org/api` (STITCH data merged into STRING 12+)
53	- Auth: None (public API; rate-limited — avoid parallel bulk requests)
54	- Species: Default 9606 (Homo sapiens); pass NCBI taxonomy ID for other organisms

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stitch

132stars4forks

View on GitHub

How to install stitch?

qsong-github/drugclaw/stitch

$npx -y skills add QSong-github/DrugClaw --skill stitch

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# STITCH Query Skill
2
3	Search STITCH for chemical–protein interactions via REST API. Auto-detects input type:
4
5	\| Input Pattern \| Detected As \| Example \|
6	\|---\|---\|---\|
7	\| `CIDm00002244` / `CIDs00002244` \| STITCH chemical ID \| direct lookup \|
8	\| `9606.ENSP00000352121` \| STRING protein ID \| direct lookup \|
9	\| anything else \| free text \| resolved via `/resolve` first \|
10
11	## API
12
13	\| Function \| Input \| Returns \|
14	\|---\|---\|---\|
15	\| `resolve(name, species)` \| chemical / protein name \| `list[dict]` with stringId, preferredName \|
16	\| `resolve_batch(names, species)` \| list of names \| `list[dict]` (via `/resolveList`) \|
17	\| `get_interactors(id, species, limit, required_score)` \| single ID \| `list[dict]` with partner IDs + scores \|
18	\| `get_actions(id, species, limit, required_score)` \| single ID \| `list[dict]` with mode (activation/inhibition/binding…) \|
19	\| `get_interactions(ids, species, required_score)` \| list of IDs \| `list[dict]` pairwise interactions among inputs \|
20	\| `search(entity, species, limit, required_score)` \| single entity (any type) \| `dict` with resolved_id, interactors, actions \|
21	\| `search_batch(entities, species, limit, required_score)` \| list or comma-separated string \| `dict[str, dict]` \|
22	\| `summarize(result, entity)` \| search() result + label \| compact text \|
23	\| `to_json(result)` \| any result \| JSON string \|
24
25	## Key Fields
26
27	Interactors — `stringId_A`, `stringId_B`, `preferredName_A`, `preferredName_B`, `score`, `nscore`, `fscore`, `pscore`, `ascore`, `escore`, `dscore`, `tscore`
28
29	Actions — `stringId_A`, `stringId_B`, `preferredName_A`, `preferredName_B`, `mode` (activation / inhibition / binding / catalysis / reaction / expression / ptmod), `action`, `is_directional`, `a_is_acting`, `score`
30
31	## Score Channels
32
33	\| Abbrev \| Meaning \|
34	\|---\|---\|
35	\| nscore \| neighborhood (genomic context) \|
36	\| fscore \| gene fusion \|
37	\| pscore \| phylogenetic co-occurrence \|
38	\| ascore \| co-expression \|
39	\| escore \| experimental evidence \|
40	\| dscore \| curated database evidence \|
41	\| tscore \| text mining \|
42	\| score \| combined score (0–1000; 400=medium, 700=high, 900=highest) \|
43
44	## Usage
45
46	See `if __name__ == "__main__"` block in `45_STITCH.py` for runnable examples covering: free-text name, STITCH CID, batch search, and JSON output.
47
48	## Data Source
49
50	- Provider: STITCH / STRING Consortium (EMBL, CPR, SIB, KU)
51	- Primary URL: `http://stitch.embl.de/api`
52	- Fallback URL: `https://string-db.org/api` (STITCH data merged into STRING 12+)
53	- Auth: None (public API; rate-limited — avoid parallel bulk requests)
54	- Species: Default 9606 (Homo sapiens); pass NCBI taxonomy ID for other organisms

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6 picks

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