dipper.sources.EOM module

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

Bases: dipper.sources.PostgreSQLSource.PostgreSQLSource

Elements of Morphology is a resource from NHGRI that has definitions of morphological abnormalities, together with image depictions. We pull those relationships, as well as our local mapping of equivalences between EOM and HP terminologies.

The website is crawled monthly by NIF’s DISCO crawler system, which we utilize here. Be sure to have pg user/password connection details in your conf.yaml file, like: dbauth : {‘disco’ : {‘user’ : ‘<username>’, ‘password’ : ‘<password>’}}

Monarch-curated data for the HP to EOM mapping is stored at https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/src/mappings/hp-to-eom-mapping.tsv

Since this resource is so small, the entirety of it is the “test” set.

GHRAW = 'https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology'

fetch(is_dl_forced=False)

connection details for DISCO

files = {'map': {'columns': ['morphology_term_id', 'morphology_term_label', 'HP ID', 'HP Label', 'Notes'], 'file': 'hp-to-eom-mapping.tsv', 'url': 'https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/src/mappings/hp-to-eom-mapping.tsv'}}

getTestSuite()

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

parse(limit=None)

Over ride Source.parse inherited via PostgreSQLSource

resources = {'tables': {'columns': ['morphology_term_id', 'morphology_term_num', 'morphology_term_label', 'morphology_term_url', 'terminology_category_label', 'terminology_category_url', 'subcategory', 'objective_definition', 'subjective_definition', 'comments', 'synonyms', 'replaces', 'small_figure_url', 'large_figure_url', 'e_uid', 'v_uid', 'v_uuid', 'v_lastmodified', 'v_status', 'v_lastmodified_epoch'], 'file': 'dvp.pr_nlx_157874_1', 'url': 'nif-db.crbs.ucsd.edu:5432'}}

tables = ['dvp.pr_nlx_157874_1']