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lasigeBioTM / DiShIn

Semantic Similarity Measures using Disjunctive Shared Information
http://labs.fc.ul.pt/dishin/
Apache License 2.0
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create HPO database #2

Closed dridk closed 4 years ago

dridk commented 4 years ago

Hi,

Did success to create a database with HPO : (https://hpo.jax.org/app/download/ontology ) It seems empty : 

ssmpy.create_semantic_base("hp.owl", "hp3.db", "http://purl.obolibrary.org/obo/", "http://www.w3.org/2000/01/rdf-schema#subClassOf", "list.txt")
ssmpy.semantic_base("hp3.db")
ssmpy.get_id("HP:0006855") # => -1

Could you tell where I am wrong ? It may come from the prefix ? the relation ?

AndreLamurias commented 4 years ago

The ":" characters of the ontology ID are replaced with a "_", so if you try with HP_0006855 it should work. This was done for compatibility reasons.

dridk commented 4 years ago

Hi, thx . I will try but I am not sure. The database looks empty

Le jeu. 7 mai 2020 à 15:23, André Lamúrias notifications@github.com a écrit :

The ":" characters of the ontology ID are replaced with a "_", so if you try with HP_0006855 it should work. This was done for compatibility reasons.

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AndreLamurias commented 4 years ago

if it's really empty let me know, could be some issue with the HPO file you're using. I just tried that example with the latest version and it worked for me.

dridk commented 4 years ago

It works ! tx!