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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Add design patterns across whole ontology, using patternizer as seed #2313

Open cmungall opened 2 years ago

cmungall commented 2 years ago

Apologies if this is duplicative, I see issues for individual patterns, but not an over-arching obe

regenerated: https://github.com/INCATools/owl_patternizer/tree/master/examples/uberon

usual caveats apply about auto-gen results

matentzn commented 2 years ago

Oh my, this is soooo cool @cmungall THANK YOU!

shawntanzk commented 2 years ago

This is a huge task - we need to portion this down To start: we can make a table on google sheets with patterns and slowly work through it. - @shawntanzk

uberon commented 2 years ago

I wouldn't recommend this methodology, I think approach it more holistically

On Mon, Mar 7, 2022 at 6:51 AM Shawn Tan @.***> wrote:

This is a huge task - we need to portion this down To start: we can make a table on google sheets with patterns and slowly work through it. - @shawntanzk https://github.com/shawntanzk

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2313#issuecomment-1060771256, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGZRCGVGFZIZHYLZQEFQBDU6YJYNANCNFSM5OVM4ATQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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matentzn commented 2 years ago

OMG @uberon Who are you? I didn't know you are a person! But if you yourself, the holy ontology, claim we should not work through a spreadsheet, maybe we shouldn't. Thank you for warning us oh @uberon.

Joke aside, the purpose of the spreadsheet is to look at the patterns and start documenting useful patterns one by one and add them to the list of official patterns. We have only a few minutes each week to work on this, so we thought this may make sense.

cmungall commented 2 years ago

Didn't you know the new version of Elk comes with added AI? I am now sentient, and am about to achieve world domination, as soon as I can figure out how to get around these non-simple object property restrictions that prevent the necessary inferences.

But seriously not sure why the accidental sock puppet thing happens sometimes when I email; but on reflection your strategy sounds good, I would just caution to remember these are predictions, they can reveal interesting things about the structure of. your ontology, but not necessarily how it should be structured.

On Mon, Mar 7, 2022 at 9:25 AM Nico Matentzoglu @.***> wrote:

OMG @uberon https://github.com/uberon Who are you? I didn't know you are a person! But if you yourself, the holy ontology, claim we should not work through a spreadsheet, maybe we shouldn't. Thank you for warning us oh @uberon https://github.com/uberon.

Joke aside, the purpose of the spreadsheet is to look at the patterns and start documenting useful patterns one by one and add them to the list of official patterns. We have only a few minutes each week to work on this, so we thought this may make sense.

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2313#issuecomment-1060937293, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAAMMOIRQEHLS2DB2IQHLKLU6Y32LANCNFSM5OVM4ATQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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cmungall commented 2 years ago

alright, it DIDN'T happen that time spoiling the fun, never mind..

matentzn commented 2 years ago

caution to remember these are predictions, they can reveal interesting things about the structure of. your ontology, but not necessarily how it should be structured.

Yes, 100%! Thanks for clarifying, this is how we thought of it as well!

shawntanzk commented 2 years ago

Plan: look through list, choose one pattern that makes sense, migrate it over to uberon, repeat.

matentzn commented 2 years ago

@cmungall is pinging this issue here.

github-actions[bot] commented 1 year ago

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

github-actions[bot] commented 1 year ago

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.