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An ontology for MIDAS data types
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Diagnosis/COVID-19 #33

Closed LucieContamin closed 1 year ago

LucieContamin commented 2 years ago

In the ontology, COVID-19 is a subclass of Diagnosis. In the data catalog entry form, COVID-19 is a subclass of "Disease(s)" (issue #9 ) Should we remove/deprecate Diagnosis and add Disease(s)?

For the Disease(s) subclasses, we currently have:

For the Pathogen Species subclasses, we currently have:

For the Host subclass, we currently have:

Should we use the NCBI and SNOMED terms for Disease/Pathogen/Host subclasses??

hoganwr commented 2 years ago

When you say "we currently have", what does that mean? Who is "we"? And "where" do you have it? What is the point of reference?

On Thu, Jul 28, 2022 at 5:38 PM Lucie Contamin @.***> wrote:

In the ontology, COVID-19 is a subclass of Diagnosis. In the data catalog entry form, COVID-19 is a subclass of "Disease(s)" (issue #9 https://github.com/midas-network/midas-data/issues/9 ) Should we remove/deprecate Diagnosis and add Disease(s)?

For the Disease(s) subclasses, we currently have:

For the Pathogen Species subclasses, we currently have:

For the Host subclass, we currently have:

  • Humans

Should we use the NCBI and SNOMED terms for Disease/Pathogen/Host subclasses??

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LucieContamin commented 2 years ago

Sorry for the confusion, I mean in the MIDAS data catalog entry form.

hoganwr commented 2 years ago

Thanks! I see references to that form in other issues you've logged. Where can I find that form? We can obviously discuss more in project meetings. For now, it would be extremely helpful if there is a "source of truth" for that form that is accessible online.

On Fri, Jul 29, 2022 at 12:59 PM Lucie Contamin @.***> wrote:

Sorry for the confusion, I mean in the data catalog entry form.

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harryhoch commented 2 years ago

Follow suggestions as per @LucieContamin, using the OBO version of NCBI Taxon.

LucieContamin commented 1 year ago

thanks for the update, I just have a small questions. Disease, Pathogen and the different subclass has been added in the Ontology. However, "diagnosis" (midas0) is still present and active (without any active subclass), would it be possible to "deprecated" diagnosis as it's not use in the MIDAS catalog and is now redundant with Disease and Pathogen?

LucieContamin commented 1 year ago

Also would it be possible to have the terms: Pathogen, Host and Disease without being the subclass of Topic, please?

hoganwr commented 1 year ago

So you pathogen, host, and disease as subClassOf owl:Thing only?

And deprecate "Diagnosis"?

harryhoch commented 1 year ago

Suggest deprecating diagnosis and making pathogen, host, and disease subclasses of topic. Is that acceptable?

LucieContamin commented 1 year ago

For diagnosis, I agree.

For pathogen, host, and disease, currently in the MIDAS DB, they are independent to topic. So, they are not subclasses of anything. I wonder which make is the best: to move them to topic or keep them separate?

harryhoch commented 1 year ago

suggest we move them to topic. @hoganwr , what do you think?

hoganwr commented 1 year ago

They're already under topic. If that's ok, then we can close this issue.

On Wed, Oct 19, 2022 at 5:14 PM Harry Hochheiser @.***> wrote:

suggest we move them to topic. @hoganwr https://github.com/hoganwr , what do you think?

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harryhoch commented 1 year ago

ok thanks.