Query Ensembl REST API for gene annotations, sequences, variants, and homology.
npx skills add https://github.com/Runchuan-BU/BioClaw --skill query-ensembl
Please help me install this Agent Skill. Skill: query-ensembl Source: https://github.com/Runchuan-BU/BioClaw/tree/main/.claude/skills/query-ensembl Command: npx skills add https://github.com/Runchuan-BU/BioClaw --skill query-ensembl
This Skill provides programmatic access to Ensembl data so users can quickly retrieve gene coordinates, sequences, variant annotations, and homology information without manual navigation of web pages.
Ask the skill to look up BRCA2 gene coordinates in homo_sapiens and return transcripts and the protein sequence.
High-intent search queries and answers about installing and using this skill.
To retrieve gene coordinates, you can query Ensembl using a gene symbol or Ensembl ID to resolve genomic locations, transcripts, and exon details. This Skill handles REST API lookups and returns JSON-formatted genomic annotations for common model organisms.
Yes, you can fetch genomic, cDNA, or protein sequences by querying Ensembl IDs or specific genomic regions. The Skill queries sequence endpoints and returns the requested sequence data formatted in JSON.
You can look up rsIDs to return variant annotations and overlapping genomic features by querying Ensembl variation and overlap endpoints. The Skill processes these REST API requests and retrieves the corresponding variant details.
Yes, cross-species homology is supported. You can retrieve orthologs and paralogs across supported species by querying Ensembl homology endpoints, which return the comparative genomic relationships in JSON format.
When querying large genomic regions from Ensembl, you must respect region size limits imposed by the REST API. The Skill processes overlap and sequence retrieval requests while adhering to these constraints to ensure successful JSON responses.
To find mouse orthologs, query the Ensembl homology endpoints with a human gene symbol or Ensembl ID. The Skill retrieves cross-species ortholog data, returning the corresponding mouse gene annotations and comparative details.
google-deepmindResolve gene symbols and Ensembl IDs, retrieve sequences, and predict variant effects via Ensembl REST APIs.
PKU-YuanGroupPredict RNA-seq, CAGE, DNase, and ChIP tracks from DNA sequences.
SologaQuery the Ensembl REST API for gene, sequence, and variant data.
IDEA-XLQueries Ensembl REST endpoints for genomic annotations, sequences, and variants.
