ontorunner.converters package

Submodules

ontorunner.converters.biohub_converter module

Biohub convertor.

ontorunner.converters.biohub_converter.parse(input_filename, output_filename) → None

Parse the typical KGX tsv nodes into Bio Term Hub format for compatibility with OGER.

Mapping of columns from KGX format to Bio Term Hub format, - [0] ‘CUI-less’ -> UMLS CUI - [1] ‘N/A’ -> resource from which it comes - [2] CURIE -> native ID - [3] name -> term (this is the field that is tokenized) - [4] name -> preferred form - [5] category -> type

Parameters

  • input_filename – (str) Input file path.

  • output_filename – (str) Output file path.

Returns

None.

ontorunner.converters.biohub_converter.parse_header(elements) → dict

Parse headers from nodes TSV.

:param elements:The header record. :type elements:List :return:A dictionary of node header names to index. :rtype:Dict

ontorunner.converters.biohub_converter.write_line(elements, outstream) → None

Write line to OUTSTREAM.

Parameters

  • elements – list - The record to write.

  • OUTSTREAM – File handle to the output file.

Returns

None.

Module contents

__init__.