orphacodes

Generate ORPHAcodes.

This plugin is able to generate a multilingual version of the ORPHAcodes nomenclature, and can infer parent-child relationships from the aggregation level. For more information on the aggregation level, please see this document from ORPHAnet.

Command line usage

/*^babelfsh
orphacodes
   --input INPUT [--dont-rewrite-aggregation-level] [--help]
   [--primary-language PRIMARY_LANGUAGE]
^babelfsh*/

Command line argument reference

Argument name	Description
--input INPUT -i INPUT Required	ORPHAcodes input files from the nomenclature packs. By repeating this argument, you can provide translations. JSON Format: [{"path": "./input-file_EN.xml", "language": "EN"}]
--dont-rewrite-aggregation-level --rewrite-aggregation-level	If provided, the system will infer parent relationships from the aggregation level property that is always generated. This serves to create multiple small trees for each disorder with their subtypes. Default: false
--help -h	show this help message and exit
--primary-language PRIMARY_LANGUAGE -l PRIMARY_LANGUAGE	Primary language to convert. Default: English