dipper.sources.SGD module

class dipper.sources.SGD.SGD(graph_type, are_bnodes_skolemized, data_release_version=None)

Bases: dipper.sources.Source.Source

Ingest of Saccharomyces Genome Database (SGD) phenotype associations

SGD_BASE = 'https://downloads.yeastgenome.org/curation/literature/'

fetch(is_dl_forced=False)

Override Source.fetch() Fetches resources from yeast_genome_database using the yeast_genome_doenload site.

Args:

param is_dl_forced (bool):  Force download

Returns:

:return None

files = {'sgd_phenotype': {'columns': ['Feature Name', 'Feature Type', 'Gene Name', 'SGDID', 'Reference', 'Experiment Type', 'Mutant Type', 'Allele', 'Strain Background', 'Phenotype', 'Chemical', 'Condition', 'Details', 'Reporter'], 'file': 'phenotype_data.tab', 'url': 'https://downloads.yeastgenome.org/curation/literature/phenotype_data.tab'}}

static make_apo_map()

make_association(record)

contstruct the association :param record: :return: modeled association of genotype to mammalian??? phenotype

parse(limit=None)

Override Source.parse() Args:

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

Returns:

:return None