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scientific-biothings-idmapping

Automate cross-database ID mapping and annotation for gene, variant, and chemical data.

3|1|Updated Feb 11, 2026
Search Tags:#genomics#batch-processing#data-integration#annotation#id-mapping#biothings
One-click install
npx skills add https://github.com/nahisaho/satori --skill scientific-biothings-idmapping
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: scientific-biothings-idmapping
Source: https://github.com/nahisaho/satori/tree/main/src/.github/skills/scientific-biothings-idmapping
Command: npx skills add https://github.com/nahisaho/satori --skill scientific-biothings-idmapping

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Automates cross-database ID mapping and unified annotation across BioThings MyGene.info, MyVariant.info, and MyChem.info for gene, variant, and chemical data.

Core Features & Use Cases

  • Cross-database ID mapping from Entrez to Ensembl, Symbol, UniProt, and more for genes.
  • Variant annotation retrieval (ClinVar, dbSNP, CADD) and chemical annotation aggregation.
  • Batch processing to consolidate multi-database metadata into unified results.

Quick Start

Run a batch mapping for a list of gene symbols to retrieve cross-database IDs and annotations.

Frequently Asked Questions about scientific-biothings-idmapping

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I map gene symbols to Ensembl and UniProt IDs in batch?▼

Batch ID mapping converts lists of gene symbols to cross-database identifiers like Ensembl and UniProt. It queries MyGene.info to consolidate multi-database metadata into unified JSON or CSV annotation outputs.

Can I retrieve ClinVar and dbSNP annotations for a list of genetic variants?▼

Yes, variant annotation retrieval pulls ClinVar, dbSNP, and CADD metadata for genetic variants. It queries MyVariant.info to aggregate cross-database variant annotations into a unified batch output.

What is the best way to integrate gene, variant, and chemical annotations together?▼

Unified annotation aggregation combines gene, variant, and chemical data into a single result set. It queries MyGene.info, MyVariant.info, and MyChem.info concurrently to consolidate multi-database metadata.

Does cross-database ID mapping support exporting results as CSV files?▼

Cross-database ID mapping supports exporting consolidated query results as both JSON and CSV files. This allows direct integration of unified gene, variant, and chemical annotations into downstream pipelines.

Can I use batch processing for chemical annotation retrieval from MyChem.info?▼

Batch processing supports chemical annotation retrieval by querying MyChem.info for lists of chemical identifiers. It aggregates the multi-database metadata into unified JSON or CSV output formats.

When do I need cross-database ID mapping for bio entities?▼

Cross-database ID mapping is needed when integrating genomic data across disparate databases. It maps Entrez to Ensembl, Symbol, and UniProt for genes, while aggregating variant and chemical annotations.

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