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Update phenotypes after new HPO release (2020-06-08)

See original GitHub issue

https://github.com/obophenotype/human-phenotype-ontology/releases/tag/v2020-06-08

From today, check that phenotype parsing still works.

Checklist of commands to to be verified:

scout setup database --api-key working_api_key
scout update genes --api-key working_api_key
scout update diseases --api-key working_api_key
scout update omim --institute cust000 --api-key working_api_key
scout download everything --api-key working_api_key (should download hpo.obo, phenotype_to_genes.txt, genes_to_phenotype.txt + the other usual files)
scout download hpo should download hpo.obo, phenotype_to_genes.txt, genes_to_phenotype.txt
scout download omim --api-key working_api_key should download genemap2.txt, mim2genes.txt, phenotype_to_genes.txt

Issue Analytics

State:
Created 3 years ago
Comments:18 (14 by maintainers)

Top GitHub Comments

2reactions

northwestwitchcommented, Jul 8, 2020

Updating phenotypes and all today in the afternoon:

scout update genes --api-key working_api_key
scout update diseases --api-key working_api_key
scout update omim --institute cust000 --api-key working_api_key
scout update hpo

1reaction

northwestwitchcommented, Jun 9, 2020

I will be happy to test this in the servers PR. Hoping to manage that later this week (thursday/friday)

We have to ask production team when it’s a good time for them

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