2.1. wc_onto package

2.1.2. Submodules

2.1.3. wc_onto.core module

wc_onto

Author:Jonathan Karr <karr@mssm.edu>
Date:2019-03-26
Copyright:2019, Karr Lab
License:MIT
wc_onto.core.get_dependent_ontologies(ontologies={'BFO': {'format': 'owl', 'url': 'https://raw.githubusercontent.com/BFO-ontology/BFO/master/releases/2.0/bfo.owl'}, 'BRO': {'format': 'owl', 'params': {'headers': {'Authorization': 'apikey token=d68d7174-a550-4845-b51b-8959c9bef365'}}, 'url': 'http://data.bioontology.org/ontologies/BRO/download'}, 'COMODI': {'format': 'owl', 'url': 'https://raw.githubusercontent.com/binfalse/COMODI/master/ontology/comodi.owl'}, 'FOAF': {'format': 'owl', 'url': 'http://xmlns.com/foaf/spec/index.rdf'}, 'IAO': {'format': 'owl', 'url': 'https://raw.githubusercontent.com/information-artifact-ontology/IAO/master/src/ontology/iao.owl'}, 'KISAO': {'format': 'owl', 'url': 'http://svn.code.sf.net/p/kisao/code/tags/kisao-owl-latest/kisao_full.owl'}, 'MATR': {'format': 'owl', 'params': {'headers': {'Authorization': 'apikey token=d68d7174-a550-4845-b51b-8959c9bef365'}}, 'url': 'http://data.bioontology.org/ontologies/MATR/download'}, 'SBO': {'format': 'obo', 'url': 'http://www.ebi.ac.uk/sbo/exports/Main/SBO_OBO.obo'}, 'SEPIO': {'format': 'owl', 'url': 'https://raw.githubusercontent.com/monarch-initiative/SEPIO-ontology/master/src/ontology/sepio.owl'}}, dir='/root/project/wc_onto/ontologies')[source]

Download dependent ontologies

Parameters:
  • ontologies (dict, optional) – dictionary that maps ids of ontologies to information about where to obtain them
  • dir (str, optional) – directory to save ontology
wc_onto.core.get_ontology(id, source, dir='/root/project/wc_onto/ontologies')[source]

Download ontology to disk

Parameters:
  • id (str) – id of ontology
  • source (dict) – information about source (URL, format) of ontology
  • dir (str, optional) – directory to save ontology

2.1.4. Module contents