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EnvironmentOntology / envo

A community-driven ontology for the representation of environments
http://www.environmentontology.org
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new dust terms #583

Closed cmungall closed 5 years ago

cmungall commented 6 years ago

For MONDO environmental diseases

nicolevasilevsky commented 6 years ago

would like to create term: Aluminum lung (MONDO_0022428) from aluminum dust

pbuttigieg commented 6 years ago

All classes created and queued for release. I've axiomatised and added missing definitions to classes added by @cmungall. More axioms will follow more imports from CHEBI. Provisional PURLs are as follows:

class purl
kaolin dust http://purl.obolibrary.org/obo/ENVO_01001288
slate dust http://purl.obolibrary.org/obo/ENVO_01001286
talc dust http://purl.obolibrary.org/obo/ENVO_01001285
barium dust http://purl.obolibrary.org/obo/ENVO_01001284
aluminium dust http://purl.obolibrary.org/obo/ENVO_01001283
silica dust http://purl.obolibrary.org/obo/ENVO_01001282
coal dust http://purl.obolibrary.org/obo/ENVO_02000099
cmungall commented 6 years ago

Thanks! @nicolevasilevsky can you axiomatize all of the remaining forms of dust-caused diseases in MONDO? Thanks!

nicolevasilevsky commented 6 years ago

I need to MIREOT in the ENVO terms into MONDO, right? I know you showed me before, but could confirm the workflow? (Sorry, I don't think I wrote this down before)

This is what I remember:

  1. I should find ENVO branch in MONDO (eg, 'kaolin dust' is a subclass of 'dust' in ENVO)
  2. I'd add that the purl for 'kaolin dust' as a subclass of 'dust' in the ENVO branch in MONDO (I just did this so I could capture a screenshot, but won't save it) image
  3. Then I can use the new class in the logical def. In this case it would used for 'kaolin pneumoconiosis' (see screenshot below)

image

  1. Then I need to run the make file (or I could run the make file after step 2?) But I don't remember exactly what commands I should use in the terminal Based on some old notes, would I do this:
    • navigate to the ontology subfolder in the terminal
    • make imports/envo_import.owl ?

Thank you!

cmungall commented 6 years ago

that works. But if it's easier you can simply axiomatize the MONDO class directly using the ENVO URI. I will take care of the imports.

nicolevasilevsky commented 6 years ago

these have all been addressed in https://github.com/monarch-initiative/mondo/pull/144

pbuttigieg commented 6 years ago

FYI: CHEBI added kaolin a while back, adding the axioms to the kaolin dust class now.