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musen-lab / hgnc2owl

A Python tool to convert HGNC database (https://www.genenames.org/) to OWL format
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HGNC-to-OWL

A Python tool to convert HGNC dataset to OWL format.

Installation

$ git clone https://github.com/musen-lab/hgnc2owl.git
$ cd hgnc2owl
$ pip install .

Running command

$ hgnc2owl http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/hgnc_complete_set.json \
           http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/json/withdrawn.json \
           -o hgnc.owl

Alternatively, you can shorten the command using the Makefile

$ make EXTRAS=false hgnc

Enabling the EXTRAS parameter will require the installation of the ROBOT tool. This option will add the extra synonyms from the PRO ontology.

$ make hgnc