Medcat refresh

[eroell]

PR Checklist

• This comment contains a description of changes (with reason)
• Referenced issue is linked
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

Can I look at examples of how to use this version?
Yes, in the parallel PR for the ehrapy tutorial here(to be inserted).

Description of changes
Resolves #503.

The goal is to simplify the use of medcat. In #503, the following TODOs have been outlined.

• Look at how MedCAT currently works outside of ehrapy
• Look at how we implemented it in ehrapy
• Remove the custom class MedCATsomething object in ehrapy
• ehrapy should just have as few functions as possible that take an AnnData object and maybe a MedCAT object that then annotate the text and store something in an AnnData slot. Maybe we have our own object but nothing that builds on top of the AnnData object like it does now. This first draft works without a MedCAT object. Something like this might be reintroduced if it enhances user experience and/or maintenance.
• Then plot the stuff in the AnnData slot with ehrapy functions This first draft works by requiring to use add_medcat_annotation_to_obs before plotting, simplifying the overhead.
• Implement everything.
• Add tests
• Update the tutorials

This draft removes the MedCAT and EhrapyMedcat classes and temporary moving-annotations-to-plotting.
Instead, it introduces scanpy-like methods

• ep.tl.annotate_text
• ep.tl.get_medcat_annotation_overview
• ep.tl.add_medcat_annotation_to_obs

Technical details

This does not move the CAT instance out of sight from the user: e.g. vanilla tutorials for MedCAT as well as sophisticated user adjustment can be done all on the CAT instance, nothing special here.

The desired CAT can then be passed to ep.tl.annotate_text, and ehrapy takes care of shaping the output into the right fields in the right format: such that ep.tl.add_medcat_annotation_to_obs can be used, followed by any plotting function which can use .obs entries.

Questions

• What do you think?
• Better suggestions for naming?
• Should the run_unsupervised_training convenience method be re-enabled?
• Should temporary move-to-obs be re-enabled?

Todos if path is outlined

• Add tests
• Add examples into docstrings

[Zethson]

I think that this looks much better. It's going back to a design that we once had but then killed in favor of what we currently have.

1. I saw your PR on the tutorials repository. I assume that you ran it?
2. Cannot access medcat model #591 - are we resolving this issue with this? Basically, can we make it easier for people to download the models? Or is that MedCat's problem?
3. Are there any new MedCat features that we could make use of? It's under active development and I only looked at it one year ago.
4. Related to 3 - can we get hierarchies somehow?
5. Is there a reasonable way for us to offer transferring the annotations into some kind of word2vec that people can append to a layer? Overkill?

Thank you so much!

[eroell]

1. I saw your PR on the tutorials repository. I assume that you ran it?

Yes, I ran it, using this branch of ehrapy: it used a stored medmen_wstatus_2021_oct.zip though, which is why it worked with an outdated link. This link has now been fixed there.

2. Cannot access medcat model #591 - are we resolving this issue with this? Basically, can we make it easier for people to download the models? Or is that MedCat's problem?

Yes, we are resolving it. This was an outdated link, which has been updated in the tutorial now.

3. Are there any new MedCat features that we could make use of? It's under active development and I only looked at it one year ago.

Did not check this in more detail yet.

4. Related to 3 - can we get hierarchies somehow?

Did not check this in more detail yet.

5. Is there a reasonable way for us to offer transferring the annotations into some kind of word2vec that people can append to a layer? Overkill?

Did not check this in more detail yet. Think this would be a very nice future addition, probably not doable in a clean way for the next release though?

[Zethson]

Did not check this in more detail yet. Think this would be a very nice future addition, probably not doable in a clean way for the next release though?

Yeah, something for later