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)¶
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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)¶
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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]
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