Proteomics API Skills

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

Quick Reference

Curl Examples

UniProt: Protein Search & Retrieval

# Search for protein by gene name
curl -s "https://rest.uniprot.org/uniprotkb/search?query=gene:TP53+AND+organism_id:9606&format=json&size=3" \
  | jq '.results[:1][] | {accession: .primaryAccession, name: .proteinDescription.recommendedName.fullName.value}'

# Get protein by accession
curl -s "https://rest.uniprot.org/uniprotkb/P04637.json" \
  | jq '{accession: .primaryAccession, gene: .genes[0].geneName.value, function: .comments[] | select(.commentType=="FUNCTION") | .texts[0].value}'

# Get protein sequence (FASTA)
curl -s "https://rest.uniprot.org/uniprotkb/P04637.fasta"

# Search with field queries
curl -s "https://rest.uniprot.org/uniprotkb/search?query=reviewed:true+AND+organism_id:9606+AND+keyword:Apoptosis&format=json&size=5" \
  | jq '.results[] | {accession: .primaryAccession, gene: .genes[0].geneName.value}'

UniProt: Batch ID Mapping (Async)

# Submit ID mapping job
JOB_ID=$(curl -s "https://rest.uniprot.org/idmapping/run" \
  --form 'ids=P04637,P38398,P51587' \
  --form 'from=UniProtKB_AC-ID' \
  --form 'to=Ensembl' | jq -r '.jobId')

# Check job status
curl -s "https://rest.uniprot.org/idmapping/status/$JOB_ID"

# Get results (when complete)
curl -s "https://rest.uniprot.org/idmapping/results/$JOB_ID" | jq '.results'

STRING: Protein-Protein Interactions

# Get interaction network for proteins
curl -s "https://string-db.org/api/json/network?identifiers=TP53&species=9606&required_score=700&limit=10" \
  | jq '.[] | {proteinA: .preferredName_A, proteinB: .preferredName_B, score}'

# Network for multiple proteins
curl -s "https://string-db.org/api/json/network?identifiers=TP53%0dMDM2%0dATM&species=9606" \
  | jq '.[] | {A: .preferredName_A, B: .preferredName_B, score}'

# Get evidence scores breakdown
curl -s "https://string-db.org/api/json/network?identifiers=TP53&species=9606&required_score=900&limit=5" \
  | jq '.[] | {A: .preferredName_A, B: .preferredName_B, experimental: .escore, database: .dscore, textmining: .tscore}'

STRING: Functional Enrichment

# GO/KEGG/Reactome enrichment for protein set
curl -s "https://string-db.org/api/json/enrichment?identifiers=9606.ENSP00000269305%0d9606.ENSP00000258149%0d9606.ENSP00000278616&species=9606" \
  | jq '.[:5][] | {category, term, description, fdr}'

# Enrichment with gene symbols (need to resolve first)
curl -s "https://string-db.org/api/json/get_string_ids?identifiers=TP53%0dMDM2%0dATM&species=9606" \
  | jq '.[].stringId' # Use these IDs for enrichment

STRING: Network Visualization

# Get network image URL
echo "https://string-db.org/api/highres_image/network?identifiers=TP53%0dMDM2%0dATM&species=9606&network_flavor=confidence"

# Get SVG
curl -s "https://string-db.org/api/svg/network?identifiers=TP53&species=9606&add_nodes=5" > network.svg

BioGRID: Genetic & Physical Interactions

# Get interactions for gene (requires API key)
curl -s "https://webservice.thebiogrid.org/interactions?geneList=TP53&taxId=9606&format=json&accesskey=${BIOGRID_API_KEY}" \
  | jq 'to_entries[:5][] | .value | {geneA: .OFFICIAL_SYMBOL_A, geneB: .OFFICIAL_SYMBOL_B, system: .EXPERIMENTAL_SYSTEM}'

# Filter by experimental method
curl -s "https://webservice.thebiogrid.org/interactions?geneList=TP53&taxId=9606&evidenceList=Two-hybrid&format=json&accesskey=${BIOGRID_API_KEY}"

# Low-throughput only (higher confidence)
curl -s "https://webservice.thebiogrid.org/interactions?geneList=TP53&taxId=9606&throughputTag=low&format=json&accesskey=${BIOGRID_API_KEY}"

ID Resolution Patterns

# Gene symbol → STRING ID
curl -s "https://string-db.org/api/json/get_string_ids?identifiers=TP53&species=9606" \
  | jq '.[0].stringId'
# Output: "9606.ENSP00000269305"

# STRING ID → UniProt
curl -s "https://rest.ensembl.org/xrefs/id/ENSP00000269305?content-type=application/json" \
  | jq '.[] | select(.dbname=="Uniprot/SWISSPROT") | .primary_id'

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