Phospho.ELM (indra.sources.phosphoelm)

This module provides an interface to the Phospho.ELM database and extracts phosphorylation relationships as INDRA Statements. Phospho.ELM is available at http://phospho.elm.eu.org/, see also https://academic.oup.com/nar/article/39/suppl_1/D261/2506728

Phospho.ELM API (indra.sources.phosphoelm.api)

indra.sources.phosphoelm.api.process_from_dump(fname, delimiter='\t')[source]

Process a Phospho.ELM file dump

The dump can be obtained at http://phospho.elm.eu.org/dataset.html.

Parameters:
  • fname (str) – File path to the phospho.ELM file dump.
  • delimiter (str) – The delimiter to use for csv.reader
Returns:

An instance of a PhosphoElmProcessor containing the statements generated from the file dump

Return type:

indra.sources.phosphoelm.PhosphoElmProcessor

Phospho.ELM Processor (indra.sources.phosphoelm.processor)

class indra.sources.phosphoelm.processor.PhosphoElmProcessor(phosphoelm_data)[source]

Processes data dumps from the phospho.ELM database.

See http://phospho.elm.eu.org/dataset.html

Parameters:phosphoelm_data (list[dict]) – JSON compatible list of entries from a phospho.ELM data dump
statements

A list of the phosphorylation statements produced by the entries in phosphoelm_data

Type:list[indra.statements.Phosphorylation]
process_phosphorylations(skip_empty=True)[source]

Create Phosphorylation statements from phosphoelm_data

Parameters:skip_empty (bool) – Default: True. If False, also create statements when upstream kinases in entry[‘kinases’] are not known.