---

name: lifesciences-genomics description: "Queries genomic databases (Ensembl, NCBI, HGNC) via curl for gene lookup, variant annotation, orthology, and cross-database ID resolution. This skill should be used when the user asks to "annotate variants", "find orthologs", "map gene IDs", "analyze linkage disequilibrium", or mentions gene symbols, ENSG IDs, HGNC identifiers, VEP annotation, LD analysis, HGVS notation, or DNA sequences."

Genomics API Skills

Query genomic databases directly via curl. These endpoints complement the Life Sciences MCPs.

Quick Reference

Curl Examples

HGNC: Resolve Gene Symbol

Copy# Search for gene by symbol
curl -s "https://rest.genenames.org/search/symbol/TP53" \
  -H "Accept: application/json" | jq '.response.docs[0] | {hgnc_id, symbol, name}'

# Fetch by HGNC ID
curl -s "https://rest.genenames.org/fetch/hgnc_id/11998" \
  -H "Accept: application/json" | jq '.response.docs[0]'

Ensembl: Gene Lookup & Metadata

Copy# Lookup gene by Ensembl ID
curl -s "https://rest.ensembl.org/lookup/id/ENSG00000141510?expand=1&content-type=application/json" \
  | jq '{id, display_name, biotype, description, seq_region_name, start, end}'

# Resolve symbol to Ensembl ID
curl -s "https://rest.ensembl.org/lookup/symbol/homo_sapiens/TP53?content-type=application/json" \
  | jq '{id, display_name}'

# Get sequence
curl -s "https://rest.ensembl.org/sequence/id/ENSG00000141510?type=genomic&content-type=application/json" \
  | jq '.seq[:100]'

Ensembl VEP: Variant Annotation

Copy# Annotate variant by rsID
curl -s "https://rest.ensembl.org/vep/human/id/rs56116432?content-type=application/json" \
  | jq '.[0] | {most_severe_consequence, transcript_consequences: .transcript_consequences[:2]}'

# Annotate by HGVS notation (POST for batch)
curl -s -X POST "https://rest.ensembl.org/vep/human/hgvs" \
  -H "Content-Type: application/json" \
  -d '{"hgvs_notations": ["ENST00000366667:c.803C>T"]}' \
  | jq '.[0].transcript_consequences[0] | {consequence_terms, sift_prediction, polyphen_prediction}'

Ensembl: Orthology

Copy# Find orthologs for TP53
curl -s "https://rest.ensembl.org/homology/id/human/ENSG00000141510?type=orthologues&content-type=application/json" \
  | jq '.data[0].homologies[:5][] | {species: .target.species, gene_id: .target.id, perc_id: .target.perc_id}'

Ensembl: Cross-References

Copy# Get all cross-references for gene
curl -s "https://rest.ensembl.org/xrefs/id/ENSG00000141510?content-type=application/json" \
  | jq '.[] | select(.dbname | test("HGNC|UniProt|OMIM|RefSeq")) | {db: .dbname, id: .primary_id}'

Ensembl: Linkage Disequilibrium

Copy# LD between two variants
curl -s "https://rest.ensembl.org/ld/human/pairwise/rs56116432/rs1042522?population_name=1000GENOMES:phase_3:EUR&content-type=application/json" \
  | jq '.[0] | {r2, d_prime}'

# LD in genomic region
curl -s "https://rest.ensembl.org/ld/human/region/17:7668421..7687490/1000GENOMES:phase_3:EUR?content-type=application/json" \
  | jq '.[:3]'

NCBI E-utilities: Gene Search & Links

Copy# Search for gene
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=TP53[sym]+AND+human[orgn]&retmode=json" \
  | jq '.esearchresult | {count, idlist}'

# Get gene summary
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=7157&retmode=json" \
  | jq '.result["7157"] | {name: .name, description: .description, chromosome: .chromosome}'

# Link gene to PubMed articles
curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id=7157&retmode=json" \
  | jq '.linksets[0].linksetdbs[] | select(.dbto=="pubmed") | {db: .dbto, count: (.links | length)}'

Rate Limits

Query Best Practices

Human-Centric Defaults

• Filter to human by default unless performing comparative genomics
• Use human[orgn] in NCBI searches, homo_sapiens for Ensembl
• Only omit organism filter when explicitly comparing across species (e.g., ortholog analysis)

Efficient Querying

• Use page_size=10 for exploration
• Use cross-reference endpoints to resolve IDs rather than multiple searches
• Prefer Ensembl IDs (ENSG*) for programmatic access

See Also

• references/ensembl-endpoints.md - Full endpoint reference
• references/ncbi-eutils.md - E-utilities pipeline patterns