dipper.sources.Monarch module

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

Bases: dipper.sources.Source.Source

This is the parser for data curated by the [Monarch Initiative](https://monarchinitiative.org). Data is currently maintained in a private repository, soon to be released.

fetch(is_dl_forced=False)

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

files = {'omia_d2p': {'columns': ['Disease ID', 'Species ID', 'Breed Name', 'Variant', 'Inheritance', 'Phenotype ID', 'Phenotype Name', 'Entity ID', 'Entity Name', 'Quality ID', 'Quality Name', 'Related Entity ID', 'Related Entity Name', 'Abnormal ID', 'Abnormal Name', 'Phenotype Desc', 'Assay', 'Frequency', 'Pubmed ID', 'Pub Desc', 'Curator Notes', 'Date Created'], 'file': '[0-9]{6}.txt'}}

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

process_omia_phenotypes(limit)