uniprot-database

Files (6)

• SKILL.md
• api_examples.md · references/
• api_fields.md · references/
• id_mapping_databases.md · references/
• query_syntax.md · references/
• uniprot_client.py · scripts/

SKILL.md (first lines)

# UniProt Database

## Overview

UniProt is the world's leading comprehensive protein sequence and functional information resource. Search proteins by name, gene, or accession, retrieve sequences in FASTA format, perform ID mapping across databases, access Swiss-Prot/TrEMBL annotations via REST API for protein analysis.

## When to Use This Skill

This skill should be used when:
- Searching for protein entries by name, gene symbol, accession, or organism
- Retrieving protein sequences in FASTA or other formats
- Mapping identifiers between UniProt and external databases (Ensembl, RefSeq, PDB, etc.)
- Accessing protein annotations including GO terms, domains, and functional descriptions
- Batch retrieving multiple protein entries efficiently
- Querying reviewed (Swiss-Prot) vs. unreviewed (TrEMBL) protein data
- Streaming large protein datasets
- Building custom queries with field-specific search syntax

## Core Capabilities

### 1. Searching for Proteins

Search UniProt using natural language queries or structured search syntax.

**Common search patterns:**
```python
# Search by protein name
query = "insulin AND organism_name:\"Homo sapiens\""

# Search by gene name
query = "gene:BRCA1 AND reviewed:true"

# Search by accession
query = "accession:P12345"

# Search by sequence length
query = "length:[100 TO 500]"

# Search by taxonomy
query = "taxonomy_id:9606"  # Human proteins

# Search by GO term
query = "go:0005515"  # Protein binding
```

Use the API search endpoint: `https://rest.uniprot.org/uniprotkb/search?query={query}&format={format}`

**Supported formats:** JSON, TSV, Excel, XML, FASTA, RDF, TXT

### 2. Retrieving Individual Protein Entries

Retrieve specific protein entries by accession number.

**Accession number formats:**
- Classic: P12345, Q1AAA9, O15530 (6 characters: letter + 5 alphanumeric)
- Extended: A0A022YWF9 (10 characters for newer entries)

**Retrieve endpoint:** `https://rest.uniprot.org/uniprotkb/{accession}.{format}`

Example: `https://rest.uniprot.org/uniprotkb/P12345.fasta`

### 3. Batch Retrieval and ID Mapping

Map protein identifiers between different database systems and retrieve multiple entries efficiently.

**ID Mapping workflow:**
1. Submit mapping job to: `https://rest.uniprot.org/idmapping/run`
2. Check job status: `https://rest.uniprot.org/idmapping/status/{jobId}`
3. Retrieve results: `https://rest.uniprot.org/idmapping/results/{jobId}`

**Supported databases for mapping:**
- UniProtKB AC/ID
- Gene names
- Ensembl, RefSeq, EMBL
- PDB, AlphaFoldDB
- KEGG, GO terms
- And many more (see `/references/id_mapping_databases.md`)

**Limitations:**
- Maximum 100,000 IDs per job
- Results stored for 7 days

### 4. Streaming Large Result Sets

For large queries that exceed pagination limits, use the stream endpoint:

`https://rest.uniprot.org/uniprotkb/stream?query={query}&format={format}`

The stream endpoint returns all results without pagination, suitable for downloading complete datasets.

### 5. Customizing Retrieved Fields

Specify exactly which fields to retrieve for efficient data transfer.

**Common fields:**
- `accession` - UniProt accession number
- `id` - Entry name
- `gene_names` - Gene name(s)
- `organism_name` - Organism
- `protein_name` - Protein names
- `sequence` - Amino acid sequence
- `length` - Sequence length
- `go_*` - Gene Ontology annotations
- `cc_*` - Comment fields (function, interaction, etc.)
- `ft_*` - Feature annotations (domains, sites, etc.)

**Example:** `https://rest.uniprot.org/uniprotkb/search?query=insulin&fields=accession,gene_names,organism_name,length,sequence&format=tsv`

See `/references/api_fields.md` for complete field list.

## Python Implementation

For programmatic access, use the provided helper script `scripts/uniprot_client.py` which implements:

- `search_proteins(query, format)` - Search UniProt with any query
- `get_protein(accession, format)` - Retrieve single protein entry
- `map_ids(ids, from_db, to_db)` - Map between identifier types
- `batch_retrieve(accessions, format)` - Retrieve multiple entries
- `stream_results(query, format)` - Stream large result sets

From foryourhealth111-pixel/Vibe-Skills, Apache-2.0.

More from foryourhealth111-pixel/Vibe-Skills