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Data Sources

pynetworkin uses the following data sources for phosphosite and network data.

OmniPath (Primary)

OmniPath provides enzyme–substrate interactions via a public REST API with no authentication required.

  • Endpoint: https://omnipathdb.org/enzsub
  • Species: Homo sapiens (9606)
  • No registration required
  • Cached locally for 7 days (.cache/phosphosite.parquet)

PhosphoSitePlus (Optional Local)

PhosphoSitePlus requires a registered account. pynetworkin supports loading a locally downloaded export.

export NETWORKIN_PSP_LOCAL_FILE=/path/to/Phosphorylation_site_dataset.gz
pynetworkin predict input.fasta

Note: Phospho.ELM is no longer supported — the server is offline/unmaintained.

STRING v12.0

STRING provides functional protein association networks.

  • Flat file (preferred): data/string_data/9606.links.v12.0.tsv.gz
  • Override: NETWORKIN_STRING_FLAT_FILE=/path/to/file
  • REST API fallback: https://string-db.org/api/tsv/network
  • Cached locally for 7 days

pynetphorest Atlas (Bundled)

The NetPhoREST kinase motif atlas is bundled via the pynetphorest package. Over 500 kinase classifiers are loaded at import time.

Bundled Fallback Data

Offline fallback TSVs are provided in data/fallback/ for testing without network access:

  • phosphosites_sample.tsv
  • string_sample.tsv