Control strategy#95
Conversation
- minor update
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is this a request for a review? |
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Sorry for the confusion, is just to go with the issue #94, I will keep it open until revision. It contains the same information. |
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ok |
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Can I keep it open as a draft maybe to avoid confusion but to have the branch open for update and revision? |
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that's fine. |
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Here a summary of all the updates in the current PR, the column "change" indicate any change in the control strategy topics (new, move to a new tier, deprecated (noted removed in the table)). I also have some open question in the Notes column: The issue #99 , is also still ongoing and I will update the PR once resolved.
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I will try to look at this tomorrow, but it looks very thorough and impressive - thanks! |
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@LucieContamin, this looks very good. One minor comment. Population treatment Census. You asked how it algns with individual treatment control strategy. I think the two things are quite different. For one, population treatment census is a count, while individual treatment control strategy is a concept. This gets back to the difference between "X" and "census of x". These should be distinct. The other issue is that individual treatment control strategy is designed to be aiming at individual persons. If you look at its parent - infectious disease control strategy , you'll sae lots of control strategies, many of which are population level, so this one stands out as being individual. I assume we'll keep open until #99 is addressed? |
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Thank you for the feedback, after discussion I updated the control strategy (census included) topic to fix the individual/population level issue and added the new classes to the MIDAS ontology for now (we can update it later if they got added to Apollo, so I don't think we need to wait). I also updated the "antibody administration census" to "monoclonal antibody administration census" to match the corresponding control strategy. May I please have a review of it before merging?
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this is from Claude, I take no credit: Category/type placement (real problems under is_a, cosmetic under SKOS): The control strategy census branch mixes information content entities with action specifications. vaccination administration capacity (APOLLO_SV_00000047) and laboratory testing capacity (APOLLO_SV_00000613) are both defined as "An action specification" but sit under a census. In APOLLO_SV neither is a census subclass; they don't belong in this branch. Procedures/processes, not plans: Therapeutic Procedure (NCIT_C49236), Screening Test (NCIT_C181548), vaccination (APOLLO_SV_00000142). event cancellations (midas45) is defined as "Events that were cancelled" (occurrents) but placed as a control strategy (plan). Redefine as a strategy to cancel events, or move it. Definition / label problems: census of vaccination supplies (APOLLO_SV_00000609) opens "A control strategy inventory census..." but there's no control strategy inventory census node in the file. Add that intermediate class or reword. Typos: travel restriction control strategy (APOLLO_SV_00000231): "organims" → "organisms." |
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Thanks, to reply to your comments:
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Thanks for the good discussion. I will try to give some thoughts/responses here. Interleaving comments from John's review via Claude and Lucie's responses: Category/type placement (real problems under is_a, cosmetic under SKOS):CLAUDE: The control strategy census branch mixes information content entities with action specifications. vaccination administration capacity (APOLLO_SV_00000047) and laboratory testing capacity (APOLLO_SV_00000613) are both defined as "An action specification" but sit under a census. In APOLLO_SV neither is a census subclass; they don't belong in this branch. Lucie: First I don't know what "(real problems under is_a, cosmetic under SKOS):" means so not sure what to reply about that. However for the vaccination administration capacity and laboratory testing capacity that where they were before. These 2 have not changed. For me. as I understand, the definition its about a "giving number" of possible tests or vaccination that can be run (for example, number of tests available, number of doses available, etc.), so I understand it as a census. I am not sure what the "action specification" adds here. Harry's response: Response- things like vaccination control strategy and infectious disease control strategy show up in APOLLOl-SV as descendants of action specification, while others like laboratory testing capcity are instances of plan specification. By moving these things over, we are “breaking” what goes on in apollo. What do we lose if we keep them where they are in apollo? Processes vs. plansCLAUDE: Procedures/processes, not plans: Therapeutic Procedure (NCIT_C49236), Screening Test (NCIT_C181548), vaccination (APOLLO_SV_00000142). Therapeutic procedure is a procedure. It is listed under infectious disease control strategy, which in Event cancellationsCLAUDE: event_ cancellations (midas45) is defined as "Events that were cancelled" (occurrents) but placed as a control strategy (plan). Redefine as a strategy to cancel events, or move it. LUCIE I don't understand the issue with event cancellations Event cancellations shows up as a plan under infectious disease control strategy. Maybe we should just call it event cancellation strategy? Definition / label problems:CLAUDE: census of vaccination supplies (APOLLO_SV_00000609) opens "A control strategy inventory census..." but there's no control strategy inventory census node in the file. Add that intermediate class or reword. LUCIE: census of vaccination supplies is a child of "census" and "control strategy inventory census" in Apollo, NOT a child of control strategy census. So I will need to create another level under topic to have "control strategy census", "infectious disease control strategy", "control strategy inventory census" which might be more confusing if we split terms in more categories, but I can do it if we want to do it. I moved other Apollo term to different parent/location to simplify our ontology, but we can discuss changing it if necessary. I think the issue is that control strategy inventory census should be imported from apollo as well… to Other definitionsI think we should just revisit the definitions of social media, media, and wildlife health interventions. Typos:@LucieContamin , please fix the identified typos in midas-data BreadthLucie: For the infectious disease control strategy containing "broad" topic that are not define directly as a "control strategy". I understand the issue. However, I cannot find the equivalent control strategy in an ontology already existing. For example, if we want to replace face mask with masking policy or something like this. I cannot find a good term in any ontologies, maybe I am missing something. So either we use these "broad" terms or we need to create a new term in the midas ontology for it. I don't really understand the conern here. LinkageThere are several apollo terms that are imported without being clearly imported/attributed. We should verify that we're doing this right. @LucieContamin , @JohnLevander , would it help to set aside a separate meeting to discuss? |
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Thank you for the review, I think a meeting will be very useful for me. |
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How's 1pm on Monday? |
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I have a meeting on Monday 1pm, but I can reschedule it without too much issue. So it should be ok |
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10, 11, or 12 would work also |
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10 will be perfect, thank you very much |
3 participants
fixes #92 , #93 , #91 , #94