ToxProt25

Analysis of ToxProt — UniProt's curated collection of animal toxin proteins — across 21 years of Swiss-Prot releases (2005-2025).

This project provides a reproducible pipeline that downloads historical Swiss-Prot releases, extracts toxin proteins, and produces per-year datasets (CSV + FASTA) enriched with taxonomy and habitat data. It enables decade-based comparisons (2005 → 2015 → 2025) and full timeline trend analysis.

Data Flow

UniProt FTP ──download──▶ XML ──parse──▶ TSV ──clean──▶ CSV + FASTA
                                                              │
                                                              ▼
                                                    toxprot analysis
                                                              │
                                                              ▼
                                                          Figures

Quick Start

git clone https://github.com/tsenoner/toxprot25.git
cd toxprot25
uv sync

toxprot data pipeline           # Download and process data (2005-2025)
toxprot analysis pipeline       # Generate all figures

Output: data/processed/toxprot/ (CSV + FASTA per year), figures/ (all analysis plots).

CLI Overview

Data Processing (toxprot data)

Process UniProt Swiss-Prot releases to extract toxin proteins.

Command	Description
pipeline	Full workflow (download → parse → clean)
download	Fetch releases from UniProt FTP
parse	Extract toxin proteins from XML
clean	Add taxonomy, habitat, create CSV/FASTA

Common options: -y years (e.g., 2020-2025), -f force reprocess, --keep-raw retain XML files, -v verbose.

See the Data Processing Guide for detailed command options and output descriptions.

Analysis (toxprot analysis)

Generate figures and statistics from processed data.

Command	Description
pipeline	Run all analyses with defaults
summary	Dataset statistics (entries, species)
taxa	Taxonomic distribution trends
families	Protein family distributions
length	Sequence length distributions
habitat	Terrestrial vs. marine distribution
source-tissue	Source tissue annotations
ptm	Post-translational modification trends
go	GO term distributions
protein-evidence	Protein existence level evolution
definitions	Compare selection criteria (2025 only)
protspace	Protein embedding analysis (subcommand)

Default filter: --definition venom_tissue. Use --definition all for all entries.

See the Analysis Guide for detailed command options and output descriptions.

ToxProt Selection Criteria

The parser replicates UniProt's ToxProt query, extracting reviewed Metazoa proteins matching either criterion:

(taxonomy_id:33208) AND (cc_tissue_specificity:venom OR keyword:KW-0800) AND (reviewed:true)

Criterion	UniProt Field	Match Type
Venom tissue	cc_tissue_specificity:venom	Free-text: "venom" in CC_TISSUE_SPECIFICITY
Toxin keyword	keyword:KW-0800	Exact match on keyword element

The --definition flag filters outputs: all, venom_tissue (default), kw_toxin, both_only.

Documentation

• Data Processing Guide — Download, parse, and clean pipeline
• Analysis Guide — Figure generation commands
• UniProt Release History — Swiss-Prot release versions (2005-2025)
• ProtSpace Guide — Protein embedding analysis

Data Sources

• ToxProt — UniProt animal toxin annotation program
• Habitat classification — manual taxonomic curation