dipper.sources.ZFINSlim module¶

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

zfin mgi model only containing Gene to phenotype associations Using the file here: https://zfin.org/downloads/phenoGeneCleanData_fish.txt

fetch(is_dl_forced=False)¶: abstract method to fetch all data from an external resource. this should be overridden by subclasses :return: None

files = {'g2p_clean': {'columns': ['ID', 'Gene Symbol', 'Gene ID', 'Affected Structure or Process 1 subterm ID', 'Affected Structure or Process 1 subterm Name', 'Post-composed Relationship ID', 'Post-composed Relationship Name', 'Affected Structure or Process 1 superterm ID', 'Affected Structure or Process 1 superterm Name', 'Phenotype Keyword ID', 'Phenotype Keyword Name', 'Phenotype Tag', 'Affected Structure or Process 2 subterm ID', 'Affected Structure or Process 2 subterm name', 'Post-composed Relationship (rel) ID', 'Post-composed Relationship (rel) Name', 'Affected Structure or Process 2 superterm ID', 'Affected Structure or Process 2 superterm name', 'Fish ID', 'Fish Display Name', 'Start Stage ID', 'End Stage ID', 'Fish Environment ID', 'Publication ID', 'Figure ID'], 'file': 'phenoGeneCleanData_fish.txt', 'url': 'https://zfin.org/downloads/phenoGeneCleanData_fish.txt'}, 'zpmap': {'columns': ['iri', 'id'], 'file': 'id_map_zfin.tsv', 'url': 'http://purl.obolibrary.org/obo/zp//id_map_zfin.tsv'}}¶

parse(limit=None)¶: abstract method to parse all data from an external resource, that was fetched in fetch() this should be overridden by subclasses :return: None