lifesciences-research: Skill for Claude Code

Proteomics API Skills

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

Quick Reference

Task	API	Endpoint
Search proteins	UniProt	/uniprotkb/search
Get protein details	UniProt	/uniprotkb/{accession}
Batch ID mapping	UniProt	/idmapping/run
Protein interactions	STRING	/network
Functional enrichment	STRING	/enrichment
Genetic/physical interactions	BioGRID	/interactions

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}'