dipper.sources.RGD module¶

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

Ingest of Rat Genome Database gene to mammalian phenotype gaf file

RGD_BASE = 'ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/'¶

fetch(is_dl_forced=False)¶

Override Source.fetch() Fetches resources from rat_genome_database via the rat_genome_database ftp site Args:

param is_dl_forced (bool):

Force download

files = {'rat_gene2mammalian_phenotype': {'columns': ['DB', 'DB Object ID', 'DB Object Symbol', 'Qualifier', 'GO ID', 'DB:Reference (|DB:Reference)', 'Evidence Code', 'With (or) From', 'Aspect', 'DB Object Name', 'DB Object Synonym (|Synonym)', 'DB Object Type', 'Taxon(|taxon)', 'Date', 'Assigned By', 'Annotation Extension', 'Gene Product Form ID'], 'file': 'rattus_genes_mp', 'url': 'ftp://ftp.rgd.mcw.edu/pub/data_release/annotated_rgd_objects_by_ontology/rattus_genes_mp'}}¶

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