About Sco3P

Scop3P, developed at Ghent University and is online since June 2019, provides a unique and powerful resource to explore and understand the impact of phospho-sites on human protein structure and function, and can thus serve as a springboard for researchers seeking to analyse and interpret a given phosphosite or phosphoprotein in a structural, biophysical, and biological context.

The resource re-uses public domain data from a variety of leading international resources, including UniProtKB and PDB, but also uses reprocessed mass spectrometry-based phospho-proteomics data from PRIDE/ProteomExchange, which is in turn globally collected and thus wholly international-driven.

Scop3P is an ELIXIR Belgium Node Service since 2019.

About the Python client

The official Scop3P REST API Python client, developed and maintained by CompOmics and Bio2Byte, provides CLI and Python interfaces to retrieve phospho-site modifications, structures, and peptides with cache-aware requests, JSON/TSV exports, and FAIR provenance logging for reproducible analysis.

Changelog

v1.1.0:

• Supporting the "mutations" endpoint.

v1.0.1:

• Minor fixes related to project metadata (like links).

v1.0.0:

• First version including modifications, peptides and structures.

Features

• CLI built with argparse
• Python classes (Scop3pResult, Scop3pRestApi)
• HTTP request using requests library including local cache with TTL and cache-fallback behavior
• Multiple output formats (JSON and tabular variants such as TSV/CSV)
• FAIR-oriented provenance log written by default (output.log)

Quick start

Installation

Either, install from PyPI: pip install scop3p.

Or, Install from source (editable):

1. Clone the project to your working environment:

   git clone git@github.com:Bio2Byte/scop3p-api-client.git
   cd scop3p-api-client

    
2. Create the virtual environment:

   python -m venv .venv
   source .venv/bin/activate
   python -m pip install -U pip
   python -m pip install -e .
   

Usage

From a console session:

# Basic usage - fetch phospho modifications for a UniProt accession
scop3p --accession O95755

# With API version
scop3p --accession O95755 --api-version 1

# FAIR provenance log is always written by default
scop3p --accession O95755
# -> writes FAIR metadata log to ./output.log

# Customize FAIR log file path
scop3p --accession O95755 --log-file run-fair.log

# Customize JSON indentation
scop3p --accession O95755 --indent 4

# Output raw (compact) JSON
scop3p --accession O95755 --raw

# Bypass cache and force fresh API request
scop3p --accession O95755 --no-cache

# Set custom cache TTL (in seconds)
scop3p --accession O95755 --cache-ttl 600

# Include structures, peptides, and mutations in stdout JSON (no saved files)
scop3p --accession O95755 --include-structures --include-peptides --include-mutations

# Save multiple outputs in one invocation (TARGET:FORMAT:PATH)
scop3p --accession O95755 \
  --save modifications:tsv:modifications.tsv \
  --save structures:tsv:structures.tsv \
  --save peptides:json:peptides.json \
  --save mutations:tsv:mutations.tsv

# Save one output file (same --save syntax)
scop3p --accession O95755 --save modifications:json:results.json

# Export peptides as TSV without header
scop3p --accession O95755 --save peptides:tsv:peptides.tsv --no-header

# Run via module (without installing)
PYTHONPATH=./src python -m scop3p_api_client phospho --accession O95755

Links

Documentation is available at https://bio2byte.github.io/scop3p_api_client/.