uniprot-lookup

name	uniprot_lookup
description	Query UniProt database for protein information including function, organism, sequence, and structure. Use this skill when: (1) User provides a UniProt accession (e.g., P38398, Q9H3P7), (2) User asks about a protein by name (e.g., "BRCA1", "hemoglobin"), (3) User wants protein function, organism, or sequence information, (4) User needs to find similar proteins by sequence search.
license	MIT
category	protein-annotation
tags	["uniprot","protein","annotation","sequence-search"]

UniProt Lookup

Query UniProt database for protein annotation and homology search.

When to Use

• User provides a UniProt accession (P38398, Q9H3P7)
• User asks about a protein by name ("BRCA1", "p53")
• User wants protein function, organism, or sequence
• User needs to find similar proteins

Workflow

Step 1: Determine Query Type

If user provides accession (e.g., "P38398"):

• Use uniprot.fetch to get full entry

If user provides protein name (e.g., "BRCA1"):

• Use uniprot.search with name as query
• Extract top hit accession
• Fetch full entry

Step 2: Fetch UniProt Entry

from open_rosalind.skills_v2.uniprot import tools

# Fetch by accession
entry = tools.fetch(accession="P38398")
# Returns: {id, accession, name, organism, function, sequence, ...}

Step 3: Optional Homology Search

If user asks "find similar proteins":

# Search by sequence fragment
results = tools.search(query="MVKVGVNGFGRIGRLVTRA")
# Returns: {hits: [{accession, name, organism, score}, ...]}

Step 4: Return Evidence-Grounded Result

return {
    "annotation": {
        "kind": "protein",
        "accession": entry["accession"],
        "name": entry["name"],
        "organism": entry["organism"]
    },
    "confidence": 0.9,
    "notes": [],
    "entry": entry  # Full UniProt entry (evidence)
}

Expected Outputs

Fetch Result

Field	Description
id	UniProt ID (e.g., BRCA1_HUMAN)
accession	Primary accession (P38398)
name	Protein name
organism	Source organism
function	Protein function description
sequence	Amino acid sequence
length	Sequence length

Search Result

Field	Description
hits	List of matching proteins
accession	UniProt accession
name	Protein name
organism	Source organism
score	Match score (0-1)

Design Principles

Following Open-Rosalind core principles:

1. Tool-first: All data from uniprot.fetch and uniprot.search tools
2. Evidence-grounded: Return full entry object (raw API response)
3. Traceable: Every API call logged to trace
4. Fail-safe: API errors logged to notes, don't crash skill

Fallback Strategy

If direct accession fetch fails:

1. Try token-based search (extract protein name from query)
2. Use top hit from search results
3. Log fallback to notes

Examples

See examples/ directory for:

• fetch_by_accession.json — Direct accession lookup
• search_by_name.json — Protein name search
• homology_search.json — Sequence-based search