lifesciences-genomics

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

Task	API	Endpoint
Resolve gene symbol	HGNC	/search/{symbol}
Get gene metadata	Ensembl	/lookup/id/{ENSG}
Annotate variant	Ensembl VEP	/vep/:species/hgvs
Find orthologs	Ensembl	/homology/id/:species/:id
Cross-reference IDs	Ensembl	/xrefs/id/{ENSG}
Search NCBI Gene	E-utilities	/esearch.fcgi?db=gene
Link gene→PubMed	E-utilities	/elink.fcgi?dbfrom=gene&db=pubmed

Curl Examples

HGNC: Resolve Gene Symbol

# 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

# 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

# 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

# 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

# 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

# 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

# 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

API	Limit	Notes
HGNC	10 req/s	No auth required
Ensembl	15 req/s	No auth required
NCBI	3 req/s	10 req/s with NCBI_API_KEY

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