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HumanBrainProject / openMINDS_instances

The openMINDS_instances repository contains well defined metadata representations (JSON-LDs) that are most likely to be reused across different research products.
MIT License
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ExpApproach updates #27

Closed UlrikeS91 closed 3 years ago

UlrikeS91 commented 3 years ago

All approaches have an InterLex ID now. A few comments/questions for @lzehl and @tgbugs:

1) I couldn't find "chemogenetics". Does this exist yet?

2) "genetics" and "informatics" are listed under "scientific discipline" in InterLex. Will those get a new/updated entry or is this was we should use here?

3) "optogenetics" exists twice (http://uri.interlex.org/ilx_0108079 & http://uri.interlex.org/ilx_0737732). Definitions were rather similar, so I just picked one. Any objections?

4) The "preferred ID" was the InterLex ID. So I copied the same one in for the "interlexID" as well. In almost all cases this was the preferred ID according to the InterLex entry. @lzehl if you don't want this repetition, we can remove them from the preferred ID again.

tgbugs commented 3 years ago

There are a number of issues here that I need to work through here related to the identifiers. I'm not sure whether you should use the existing terms for genetics and optogenetics because their modelling is different and we will need to figure out how to deal with merging them.

I would suggest using the mod: as the preferred ids since they are what is used in the ontology and they now resolve! (yay! http://uri.interlex.org/tgbugs/uris/readable/modality/Anatomy). https://github.com/SciCrunch/NIF-Ontology/blob/methods/ttl/approach.ttl I have created mod:Genetics and friends but we need to get them interlex ids (@tmsincomb) so that they will resolve. We will update the InterLex records to reflect this now that they resolve correctly.

For reference, check the children tab here for the list of the actual approach terms that is currently in InterLex.

UlrikeS91 commented 3 years ago

Thanks, @tgbugs. I've made some adjustments according to your feedback.

  1. I removed interlex ID, preferred ID and synonyms from "chemogenetics", "genetics", "informatics" and "optogenetics". These are the only four that aren't part of the experimental modalities (https://scicrunch.org/scicrunch/interlex/view/ilx_0770148) yet. As soon as they are added and/or get interlex IDs, we can update those again.
  2. For the rest, I changed the preferred ID to "http://uri.interlex.org/tgbugs/uris/readable/modality/<>".

@lzehl, this PR should be ok to merge now (but decide for yourself :P).

lzehl commented 3 years ago

@UlrikeS91 also here: could you transfer this please also to the controlledTerms repo? The openMINDS_instances repo will be deprecated. Instances are version dependent and are therefore now stored on the respective version branch of the openMINDS metadata model repo.

UlrikeS91 commented 3 years ago

@UlrikeS91 also here: could you transfer this please also to the controlledTerms repo? The openMINDS_instances repo will be deprecated. Instances are version dependent and are therefore now stored on the respective version branch of the openMINDS metadata model repo.

Done :)