dipper.sources.Xenbase module

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

Bases: dipper.sources.Source.Source

Xenbase is a web-accessible resource that integrates all the diverse biological, genomic, genotype and phenotype data available from Xenopus research.

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_assertions': {'columns': ['SUBJECT', 'SUBJECT_LABEL', 'SUBJECT_TAXON', 'SUBJECT_TAXON_LABEL', 'OBJECT', 'OBJECT_LABEL', 'RELATION', 'RELATION_LABEL', 'EVIDENCE', 'EVIDENCE_LABEL', 'SOURCE', 'IS_DEFINED_BY', 'QUALIFIER'], 'file': 'xb_xpo_spo_v_v1.tab', 'url': 'https://archive.monarchinitiative.org/DipperCache/xenbase/xb_xpo_spo_v_v1.tab'}, 'gene_literature': {'columns': ['xb_article', 'pmid', 'gene_pages'], 'file': 'LiteratureMatchedGenesByPaper.txt', 'url': 'http://ftp.xenbase.org//pub/GenePageReports/LiteratureMatchedGenesByPaper.txt'}, 'genepage2gene': {'columns': ['gene_page_id', 'gene_page_label', 'tropicalis_id', 'tropicalis_label', 'laevis_l_id', 'laevis_l_label', 'laevis_s_id', 'laevis_s_label'], 'file': 'XenbaseGenepageToGeneIdMapping.txt', 'url': 'http://ftp.xenbase.org//pub/GenePageReports/XenbaseGenepageToGeneIdMapping.txt'}, 'orthologs': {'columns': ['SUBJECT', 'SUBJECT_LABEL', 'SUBJECT_TAXON', 'SUBJECT_TAXON_LABEL', 'OBJECT', 'OBJECT_LABEL', 'RELATION', 'RELATION_LABEL', 'EVIDENCE', 'EVIDENCE_LABEL', 'SOURCE', 'IS_DEFINED_BY', 'QUALIFIER'], 'file': 'xb_ortho_spo_v_v20210318a.csv', 'url': 'https://archive.monarchinitiative.org/DipperCache/xenbase/xb_ortho_spo_v_v20210318a.csv'}}

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