Improvements to EntitySetSlimmer #216
Conversation
deepakunni3
commented
Aug 27, 2018
deepakunni3
commented
- Use enum to specify available category
- Handle multiple subject IDs as input
Use enum to specify available category Handle multiple subject IDs as input
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@nathandunn FYI |
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Sure, we can add expression as needed to support the AGR use-case (or they can issue a PR) |
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Actually, I think that having them issue a PR is the better way to go here. |
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Yes, making a note to add additional categories to the enum when they are supported. |
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So it's unclear exactly how this changes the URL that is used for the query. Would you spell it out please. |
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@selewis I think the URL will be identical. I think this just enumerates the categories explicitly. |
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huh? |
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The API is
```
https://api.monarchinitiative.org/api/bioentityset/slimmer/{category}
https://api.monarchinitiative.org/api/bioentityset/slimmer/function
https://api.monarchinitiative.org/api/bioentityset/slimmer/phenotype
```
The mods requested that we enumerate the category, which seemed reasonable.
Nathan
… On Aug 28, 2018, at 1:20 PM, Suzanna Lewis ***@***.***> wrote:
huh?
They already look different.
https://api.monarchinitiative.org/api/bioentityset/slimmer/phenotype <https://api.monarchinitiative.org/api/bioentityset/slimmer/phenotype>?
vs.
https://api.monarchinitiative.org/api/bioentityset/slimmer/function <https://api.monarchinitiative.org/api/bioentityset/slimmer/function>?
vs.
whatever we need for some other ontology...
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Sorry, still isn't clear (and not sure why we'd let the MODs be the deciders, opinions sure). |
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Everything is pretty much the same. We were just specifying what we were providing AFAIK. But its a collaborative process and this is something we all agreed on in the API call. |
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Could you just answer the question please. "Pretty much the same" doesn't give me any information. What would each URLs be for GO, HPO, and UBERON exactly? |
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The URL has not changed at all AFAIK. They were just specified in the spec. So the GO slim, HPO slim, uberon slim, etc. should be what you had before and will not have changed AFAIK. Is this correct @deepakunni3 ? |
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@selewis @nathandunn The URLs haven't changed at all. This PR pretty much shows what values are possible for the URL parameter @selewis To answer your question, following are the URLs: GO - https://api.monarchinitiative.org/api/bioentityset/slimmer/function |
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Except there wasn't anything for UBERON, that's the one that was missing. Maybe it's there now, but we've lost some clarity here. If I look at the swagger page I can see "category * string", but nothing about what are the allowed values. And how does this change the URL? before the URL included "function" for GO or "phenotype" for HPO. Is that gone now? Is it now category="xxx" ? Someone please spell this out - and ah! Deepak just did... |
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Note that the swagger presentation doesn't list any of these. |
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Let me know please when expression is ready. |
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@selewis Since this PR was merged yesterday, the latest changes are accessible at: |
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Yes, saw that, but as I said this currently lacks any information on these options. |
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Oh, I see. Yes, I can describe the category parameter with more information |
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Thanks, that will help. @deepakunni3 - also question on "expression", to be comprehensive it would meed to have slim classes from both Uberon and GO cellular component. Could make two calls (one on 'function' and one on 'anatomy') or one call (with 'expression' looking over both ontologies). What do you prefer? |
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I think one call looking over both ontologies would be ideal |
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Certainly would be more convenient from the client side. |
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