dipper.sources.StringDB module

class dipper.sources.StringDB.StringDB(graph_type, are_bnodes_skolemized, data_release_version=None, tax_ids=None, version=None)

Bases: dipper.sources.Source.Source

STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases. From: http://string-db.org/cgi/about.pl?footer_active_subpage=content

STRING uses one protein per gene. If there is more than one isoform per gene, we usually select the longest isoform, unless we have information that suggest that other isoform regarded as cannonical (e.g., proteins in the CCDS database). From: http://string-db.org/cgi/help.pl

fetch(is_dl_forced=False)

Override Source.fetch() Fetches resources from String

We also fetch ensembl to determine if protein pairs are from the same species Args:

param is_dl_forced (bool):  Force download

Returns:

:return None

parse(limit=None)

Override Source.parse() Args:

:param limit (int, optional) limit the number of rows processed

Returns:

:return None