chembl-molecule-search

Name: chembl-molecule-search
Author: ma-compbio-lab

36stars5forks

How to install chembl-molecule-search?

ma-compbio-lab/skillfoundry/chembl-molecule-search

$npx -y skills add ma-compbio-lab/SkillFoundry --skill chembl-molecule-search

Installs into the current project.

Summary

Use this skill to search ChEMBL molecules by keyword and return a compact compound summary. Do not use it for local chemistry calculations or unsupported bulk export.

Files · 1

View on GitHub

SKILL.md

1	## Purpose
2	Search ChEMBL by free-text query and return compact compound summaries suitable for quick cheminformatics triage.
3
4	## When to use
5	- You need a ChEMBL identifier and basic compound summary for a known drug or molecule name.
6	- You want a lightweight compound lookup before deeper cheminformatics or screening workflows.
7
8	## When not to use
9	- You need local descriptor calculation or docking.
10	- You need bulk export of a large ChEMBL slice.
11	- You need offline execution.
12
13	## Inputs
14	- Query string
15	- Optional result limit and output path
16
17	## Outputs
18	- JSON payload with query metadata and compact molecule summaries
19
20	## Requirements
21	- Python 3.10+
22	- Network access to `www.ebi.ac.uk`
23
24	## Procedure
25	1. Run `python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1 --out skills/drug-discovery-and-cheminformatics/chembl-molecule-search/assets/chembl_imatinib.json`.
26	2. Inspect `molecules` for `chembl_id`, `preferred_name`, `molecule_type`, `max_phase`, `canonical_smiles`, and selected properties.
27	3. Use the returned ChEMBL IDs in downstream compound-knowledge workflows when needed.
28
29	## Validation
30	- Command exits successfully.
31	- `molecules` contains at least one ChEMBL result for a known query.
32	- The first result has a non-empty `chembl_id` and molecule summary fields.
33
34	## Failure modes and fixes
35	- No hits: refine the query or use a more canonical drug name.
36	- Too many hits: lower `--limit` and inspect the top results manually.
37	- HTTP errors: retry later and keep the query simple for smoke verification.
38
39	## Safety and limits
40	- Knowledge lookup only.
41	- This skill does not perform synthesis planning, structure optimization, or wet-lab decision making.
42
43	## Example
44	- `python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1`
45
46	## Provenance
47	- ChEMBL web services docs: https://www.ebi.ac.uk/chembl/api/data/docs
48	- ChEMBL API base path: https://www.ebi.ac.uk/chembl/api/data/
49
50	## Related skills
51	- `clinicaltrials-study-search`

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chembl-molecule-search

36stars5forks

View on GitHub

How to install chembl-molecule-search?

ma-compbio-lab/skillfoundry/chembl-molecule-search

$npx -y skills add ma-compbio-lab/SkillFoundry --skill chembl-molecule-search

Installs into the current project.

Summary

Use this skill to search ChEMBL molecules by keyword and return a compact compound summary. Do not use it for local chemistry calculations or unsupported bulk export.

Files · 1

View on GitHub

SKILL.md

1	## Purpose
2	Search ChEMBL by free-text query and return compact compound summaries suitable for quick cheminformatics triage.
3
4	## When to use
5	- You need a ChEMBL identifier and basic compound summary for a known drug or molecule name.
6	- You want a lightweight compound lookup before deeper cheminformatics or screening workflows.
7
8	## When not to use
9	- You need local descriptor calculation or docking.
10	- You need bulk export of a large ChEMBL slice.
11	- You need offline execution.
12
13	## Inputs
14	- Query string
15	- Optional result limit and output path
16
17	## Outputs
18	- JSON payload with query metadata and compact molecule summaries
19
20	## Requirements
21	- Python 3.10+
22	- Network access to `www.ebi.ac.uk`
23
24	## Procedure
25	1. Run `python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1 --out skills/drug-discovery-and-cheminformatics/chembl-molecule-search/assets/chembl_imatinib.json`.
26	2. Inspect `molecules` for `chembl_id`, `preferred_name`, `molecule_type`, `max_phase`, `canonical_smiles`, and selected properties.
27	3. Use the returned ChEMBL IDs in downstream compound-knowledge workflows when needed.
28
29	## Validation
30	- Command exits successfully.
31	- `molecules` contains at least one ChEMBL result for a known query.
32	- The first result has a non-empty `chembl_id` and molecule summary fields.
33
34	## Failure modes and fixes
35	- No hits: refine the query or use a more canonical drug name.
36	- Too many hits: lower `--limit` and inspect the top results manually.
37	- HTTP errors: retry later and keep the query simple for smoke verification.
38
39	## Safety and limits
40	- Knowledge lookup only.
41	- This skill does not perform synthesis planning, structure optimization, or wet-lab decision making.
42
43	## Example
44	- `python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1`
45
46	## Provenance
47	- ChEMBL web services docs: https://www.ebi.ac.uk/chembl/api/data/docs
48	- ChEMBL API base path: https://www.ebi.ac.uk/chembl/api/data/
49
50	## Related skills
51	- `clinicaltrials-study-search`

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6 picks

Type