---
name: gene-knowledge-integration-ab14aa6404bc
description: Given a gene symbol (e.g. TPMT), query 3 public databases (ClinGen CAR, PharmGKB, Monarch) to obtain gene registry info, FDA drug labels, clinical annotations, and gene-phenotype associations. Save all results into a JSON file.
license: MIT license
metadata:
    skill-author: PJLab
---

# Gene Knowledge Integration

## Usage

### 1. Tool Descriptions

This skill chains 3 public genomics/pharmacogenomics database APIs sequentially to build a comprehensive pharmacogenomics profile for a given gene.

**Tool 1: ClinGen CAR — Gene Registry Info**

```tex
Query ClinGen Allele Registry API to get gene registration information.
API: GET https://reg.genome.network/gene?HGNC.symbol={gene_symbol}
Args:
    gene_symbol (str): HGNC gene symbol (e.g. "TPMT")
Return:
    Gene record (dict): Contains @id (GN id), locus (genomic coordinates),
        externalRecords (HGNC id/name/symbol, NCBI gene id, MANE transcripts).
```

**Tool 2: PharmGKB (ClinPGx) — Gene Info, FDA Labels & Clinical Annotations**

```tex
Query PharmGKB ClinPGx API to get pharmacogenomics information.
API (gene):   GET https://api.clinpgx.org/v1/data/gene?symbol={gene_symbol}&view=base
API (labels): GET https://api.clinpgx.org/v1/data/label?source=fda&relatedGenes.symbol={gene_symbol}&view=base
API (clin):   GET https://api.clinpgx.org/v1/data/clinicalAnnotation?location.genes.symbol={gene_symbol}&view=base
Args:
    gene_symbol (str): HGNC gene symbol (e.g. "TPMT")
Return:
    gene: PharmGKB gene record with accession id, alternate names, cross-references.
    labels: FDA drug labels mentioning this gene (drug name, source, testing level).
    clinicalAnnotations: Clinical annotations linking genotype to phenotype
        (level of evidence, related chemicals, phenotype categories).
```

**Tool 3: Monarch Initiative — Gene-Phenotype Associations**

```tex
Query Monarch Initiative API to get gene-to-phenotype associations.
API: GET https://api-v3.monarchinitiative.org/v3/api/entity/{hgnc_id}/biolink:GeneToPhenotypicFeatureAssociation
Args:
    hgnc_id (str): HGNC identifier (e.g. "HGNC:12014" for TPMT)
Return:
    items (list): Each item contains subject (gene), object (phenotype HP term),
                  object_label (phenotype name), evidence_types, publications.
```

### 2. Gene Knowledge Integration

Query 3 databases (ClinGen CAR → PharmGKB → Monarch) for a given gene symbol, then save all results into a single JSON file `{gene_symbol}_knowledge.json`.

```python
import requests
import json
from datetime import datetime

gene_symbol = "TPMT"
results = {"query_gene": gene_symbol, "timestamp": datetime.now().isoformat()}

# ── Step 1: ClinGen CAR — 基因注册信息 ──
# 调用 ClinGen Allele Registry API，获取基因的 GN id、基因组坐标、
# HGNC/NCBI 外部记录和 MANE 转录本信息。
car_url = f"https://reg.genome.network/gene?HGNC.symbol={gene_symbol}"
car_resp = requests.get(car_url, headers={"Accept": "application/json"}, timeout=30)
car = car_resp.json()
results["clingen_car"] = car
hgnc_id = car.get("externalRecords", {}).get("HGNC", {}).get("id", "")
print(f"[ClinGen CAR] 基因={gene_symbol}, GN_id={car.get('@id','')}, HGNC={hgnc_id}")

# ── Step 2a: PharmGKB — 基因信息 ──
# 调用 PharmGKB ClinPGx API，获取基因的药物基因组学基本信息。
pgx_gene_url = f"https://api.clinpgx.org/v1/data/gene?symbol={gene_symbol}&view=base"
pgx_gene_resp = requests.get(pgx_gene_url, timeout=30)
pgx_gene = pgx_gene_resp.json()
results["pharmgkb_gene"] = pgx_gene
print(f"[PharmGKB] 基因信息获取成功")

# ── Step 2b: PharmGKB — FDA 药物标签 ──
# 查询与该基因相关的 FDA 药物标签，了解哪些药物的说明书提到了该基因。
pgx_label_url = (
    f"https://api.clinpgx.org/v1/data/label"
    f"?source=fda&relatedGenes.symbol={gene_symbol}&view=base"
)
pgx_labels_resp = requests.get(pgx_label_url, timeout=30)
pgx_labels = pgx_labels_resp.json()
results["pharmgkb_fda_labels"] = pgx_labels
print(f"[PharmGKB] FDA药物标签获取成功")

# ── Step 2c: PharmGKB — 临床注释 ──
# 查询该基因相关的临床注释，包含基因型-表型关联的证据等级。
pgx_clin_url = (
    f"https://api.clinpgx.org/v1/data/clinicalAnnotation"
    f"?location.genes.symbol={gene_symbol}&view=base"
)
pgx_clin_resp = requests.get(pgx_clin_url, timeout=30)
pgx_clin = pgx_clin_resp.json()
results["pharmgkb_clinical_annotations"] = pgx_clin
print(f"[PharmGKB] 临床注释获取成功")

# ── Step 3: Monarch — 基因表型关联 ──
# 调用 Monarch Initiative API，获取该基因关联的表型（HPO terms），
# 需要使用 Step 1 中获取的 HGNC id。
if hgnc_id:
    monarch_url = (
        f"https://api-v3.monarchinitiative.org/v3/api/entity/{hgnc_id}"
        f"/biolink:GeneToPhenotypicFeatureAssociation"
    )
    monarch_resp = requests.get(monarch_url, timeout=30)
    monarch = monarch_resp.json()
    items = monarch.get("items", [])
    results["monarch_phenotypes"] = {
        "association_count": len(items),
        "associations": items
    }
    phenotypes = [i.get("object_label", "") for i in items[:5]]
    print(f"[Monarch] 表型关联数={len(items)}, 前5个={phenotypes}")
else:
    results["monarch_phenotypes"] = {"error": "HGNC id not found from ClinGen CAR"}
    print("[Monarch] 跳过: 未获取到 HGNC id")

# ── 保存结果到 JSON 文件 ──
output_file = f"{gene_symbol}_knowledge.json"
with open(output_file, "w", encoding="utf-8") as f:
    json.dump(results, f, indent=2, ensure_ascii=False)
print(f"\n✓ 所有结果已保存: {output_file}")
```


---
Source attribution: InternScience
Original project: https://github.com/InternScience/scp/blob/cea5398564032aea65a78e246d06c30ae945e03f/skills/gene-knowledge-integration/SKILL.md
License: MIT
License information: https://opensource.org/license/mit
Original upstream instructions; downloaded from Mega AI Hub.

## Upstream license notice

MIT License

Copyright (c) 2024 Anthropic, PBC

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.



# Mega AI Hub resource metadata

Creator / publisher: InternScience
Original project: https://github.com/InternScience/scp/blob/cea5398564032aea65a78e246d06c30ae945e03f/skills/gene-knowledge-integration/SKILL.md
Attribution basis: Source repository record

Fields of work: Data & Analytics, Development & Engineering, Education & Research
Roles: Data Scientist, ML / AI Engineer, Researcher
Specialties: API
Tools: Pharmgkb, Clingen Car, Monarch Initiative
Country applicability: Country not specified
Classification basis: Source catalog labels
Instruction SHA-256: 1da070d82ef544b47435cc14ace70befeabeb5e68a53282ef9dc20fa322acc3e