---

name: lifesciences-proteomics description: "Queries protein databases (UniProt, STRING, BioGRID) via curl for protein lookups, protein-protein interactions, functional enrichment analysis, and cross-database ID mapping. This skill should be used when the user asks to "find protein interactions", "analyze interaction networks", "perform GO enrichment", "map protein IDs", or mentions PPI networks, UniProt accessions, STRING scores, BioGRID interactions, or protein ID conversion between databases."

Proteomics API Skills

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

Quick Reference

Curl Examples

UniProt: Protein Search & Retrieval

Copy# 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)

Copy# 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

Copy# 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

Copy# 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

Copy# 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

Copy# 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

Copy# 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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