Genomics API Skills

Name: lifesciences-genomics
Rating: 92
Author: donbr

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

bash

# 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

bash

# 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

bash

# 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

bash

# 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

bash

# 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

bash

# 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

bash

# 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

Genomics API Skills

Quick Reference

Curl Examples

HGNC: Resolve Gene Symbol

Ensembl: Gene Lookup & Metadata

Ensembl VEP: Variant Annotation

Ensembl: Orthology

Ensembl: Cross-References

Ensembl: Linkage Disequilibrium

NCBI E-utilities: Gene Search & Links

Rate Limits

Query Best Practices

Human-Centric Defaults

Efficient Querying

See Also