dipper.sources.MMRRC module

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

Bases: dipper.sources.Source.Source

Here we process the Mutant Mouse Resource and Research Center (https://www.mmrrc.org) strain data, which includes: * strains, their mutant alleles * phenotypes of the alleles * descriptions of the research uses of the strains

Note that some gene identifiers are not included (for many of the transgenics with human genes) in the raw data. We do our best to process the links between the variant and the affected gene, but sometimes the mapping is not clear, and we do not include it. Many of these details will be solved by merging this source with the MGI data source, who has the variant-to-gene designations.

Also note that even though the strain pages at the MMRRC site do list phenotypic differences in the context of the strain backgrounds, they do not provide that data to us, and thus we cannot supply that disambiguation here.

fetch(is_dl_forced=False)

abstract method to fetch all data from an external resource. this should be overridden by subclasses :return: None

files = {'catalog': {'columns': ['STRAIN/STOCK_ID', 'STRAIN/STOCK_DESIGNATION', 'STRAIN_TYPE', 'STATE', 'MGI_ALLELE_ACCESSION_ID', 'ALLELE_SYMBOL', 'ALLELE_NAME', 'MUTATION_TYPE', 'CHROMOSOME', 'MGI_GENE_ACCESSION_ID', 'GENE_SYMBOL', 'GENE_NAME', 'SDS_URL', 'ACCEPTED_DATE', 'MPT_IDS', 'PUBMED_IDS', 'RESEARCH_AREAS'], 'file': 'mmrrc_catalog_data.csv', 'url': 'https://www.mmrrc.org/about/mmrrc_catalog_data.csv'}}

getTestSuite()

An abstract method that should be overwritten with tests appropriate for the specific source. :return:

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

test_ids = ['MMRRC:037507-MU', 'MMRRC:041175-UCD', 'MMRRC:036933-UNC', 'MMRRC:037884-UCD', 'MMRRC:000255-MU', 'MMRRC:037372-UCD', 'MMRRC:000001-UNC']