pharmgkb

Name: pharmgkb
Author: QSong-github

132stars4forks

How to install pharmgkb?

qsong-github/drugclaw/pharmgkb

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

Installs into the current project.

Summary

Query ClinPGx (PharmGKB) and CPIC for pharmacogenomics data. Use whenever the user asks about gene-drug interactions, pharmacogenomics clinical annotations, drug-metabolizing enzymes, CPIC guidelines, or variant-level PGx evidence for any gene symbol, drug name, rsID, or ClinPGx

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SKILL.md

1	# PharmGKB / ClinPGx Query Skill
2
3	Queries two complementary APIs:
4
5	- ClinPGx API (`api.clinpgx.org/v1`) — gene, chemical, variant detail
6	- CPIC API (`api.cpicpgx.org/v1`) — gene-drug pairs, CPIC guideline levels (PostgREST)
7
8	Auto-detects input entity type by pattern:
9
10	\| Input Pattern \| Detected As \| Data Sources \|
11	\|---\|---\|---\|
12	\| `PA128` \| ClinPGx accession \| gene or chemical detail + CPIC pairs \|
13	\| `rs4244285` \| dbSNP rsID \| variant lookup \|
14	\| `CYP2D6` \| gene symbol (uppercase, 2-15 chars) \| gene detail + CPIC pairs \|
15	\| anything else \| drug / free text \| chemical detail + CPIC pairs \|
16
17	## API
18
19	\| Function \| Input \| Returns \|
20	\|---\|---\|---\|
21	\| `search(entity)` \| single entity string \| dict with `genes`, `chemicals`, `variants`, `cpic_pairs`, `related` \|
22	\| `search_batch(entities)` \| list of entity strings \| dict[str → search result] \|
23	\| `summarize(result, entity)` \| search result + label \| compact text (one line per hit) \|
24	\| `to_json(result)` \| search result \| indented JSON string \|
25	\| `search_gene(symbol)` \| gene symbol \| list of gene dicts (ClinPGx) \|
26	\| `search_drug(name)` \| drug name \| list of chemical dicts (ClinPGx) \|
27	\| `search_variant(rsid)` \| rsID string \| list of variant dicts (ClinPGx) \|
28	\| `get_cpic_pairs_by_gene(symbol)` \| gene symbol \| list of pair dicts (CPIC `pair_view`) \|
29	\| `get_cpic_pairs_by_drug(name)` \| drug name \| list of pair dicts (CPIC `pair_view`) \|
30
31	## Usage
32
33	See `if __name__ == "__main__"` block in `49_PHARMGKB_CLINPGX.py` for runnable
34	examples covering: gene symbol, drug name, rsID, ClinPGx accession, batch
35	search, and JSON output.
36
37	## Key Fields
38
39	Gene (ClinPGx): `id`, `symbol`, `name`, `hasCpicGuideline`
40
41	Chemical (ClinPGx): `id`, `name`, `types`
42
43	Variant (ClinPGx): `id`, `symbol`, `genes`, `location`
44
45	CPIC Pair (`pair_view`): `genesymbol`, `drugname`, `cpiclevel` (A/B/C/D),
46	`clinpgxlevel` (evidence), `pgxtesting`, `guidelinename`
47
48	## Data Sources
49
50	- ClinPGx (Stanford / NIH) — https://www.clinpgx.org/ — REST JSON, no key, ≤2 req/s, CC BY-SA 4.0
51	- CPIC API — https://api.cpicpgx.org/ — PostgREST, no key — gene-drug guideline pairs
52	- Note: PharmGKB was subsumed by ClinPGx (July 2025). CPIC API remains at `api.cpicpgx.org`.

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pharmgkb

132stars4forks

View on GitHub

How to install pharmgkb?

qsong-github/drugclaw/pharmgkb

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

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# PharmGKB / ClinPGx Query Skill
2
3	Queries two complementary APIs:
4
5	- ClinPGx API (`api.clinpgx.org/v1`) — gene, chemical, variant detail
6	- CPIC API (`api.cpicpgx.org/v1`) — gene-drug pairs, CPIC guideline levels (PostgREST)
7
8	Auto-detects input entity type by pattern:
9
10	\| Input Pattern \| Detected As \| Data Sources \|
11	\|---\|---\|---\|
12	\| `PA128` \| ClinPGx accession \| gene or chemical detail + CPIC pairs \|
13	\| `rs4244285` \| dbSNP rsID \| variant lookup \|
14	\| `CYP2D6` \| gene symbol (uppercase, 2-15 chars) \| gene detail + CPIC pairs \|
15	\| anything else \| drug / free text \| chemical detail + CPIC pairs \|
16
17	## API
18
19	\| Function \| Input \| Returns \|
20	\|---\|---\|---\|
21	\| `search(entity)` \| single entity string \| dict with `genes`, `chemicals`, `variants`, `cpic_pairs`, `related` \|
22	\| `search_batch(entities)` \| list of entity strings \| dict[str → search result] \|
23	\| `summarize(result, entity)` \| search result + label \| compact text (one line per hit) \|
24	\| `to_json(result)` \| search result \| indented JSON string \|
25	\| `search_gene(symbol)` \| gene symbol \| list of gene dicts (ClinPGx) \|
26	\| `search_drug(name)` \| drug name \| list of chemical dicts (ClinPGx) \|
27	\| `search_variant(rsid)` \| rsID string \| list of variant dicts (ClinPGx) \|
28	\| `get_cpic_pairs_by_gene(symbol)` \| gene symbol \| list of pair dicts (CPIC `pair_view`) \|
29	\| `get_cpic_pairs_by_drug(name)` \| drug name \| list of pair dicts (CPIC `pair_view`) \|
30
31	## Usage
32
33	See `if __name__ == "__main__"` block in `49_PHARMGKB_CLINPGX.py` for runnable
34	examples covering: gene symbol, drug name, rsID, ClinPGx accession, batch
35	search, and JSON output.
36
37	## Key Fields
38
39	Gene (ClinPGx): `id`, `symbol`, `name`, `hasCpicGuideline`
40
41	Chemical (ClinPGx): `id`, `name`, `types`
42
43	Variant (ClinPGx): `id`, `symbol`, `genes`, `location`
44
45	CPIC Pair (`pair_view`): `genesymbol`, `drugname`, `cpiclevel` (A/B/C/D),
46	`clinpgxlevel` (evidence), `pgxtesting`, `guidelinename`
47
48	## Data Sources
49
50	- ClinPGx (Stanford / NIH) — https://www.clinpgx.org/ — REST JSON, no key, ≤2 req/s, CC BY-SA 4.0
51	- CPIC API — https://api.cpicpgx.org/ — PostgREST, no key — gene-drug guideline pairs
52	- Note: PharmGKB was subsumed by ClinPGx (July 2025). CPIC API remains at `api.cpicpgx.org`.

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6 picks

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