Add new provider for pdb: dionysus

[nagutm]

This pull request curates a new provider for PDB structure: dionysus.

PubMed: https://pubmed.ncbi.nlm.nih.gov/39436020/
Database: www.dsimb.inserm.fr/DIONYSUS/

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 44.48%. Comparing base (8950e70) to head (13b2ab0).
Report is 193 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1282      +/-   ##
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+ Coverage   42.51%   44.48%   +1.97%     
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  Files         117      118       +1     
  Lines        8327     8263      -64     
  Branches     1963     1357     -606     
==========================================
+ Hits         3540     3676     +136     
+ Misses       4582     4410     -172     
+ Partials      205      177      -28     

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[bgyori]

I just tried this and one problem here is that the example ID listed for pdb (2gc4) doesn't resolve in this resource, so the example link shown on the web would be broken.

[nagutm]

This resource only appears to import a filtered set of PDB IDs that are carbohydrate-containing structures and match specific keywords related to the classification tag used by PDB. This explains why 2gc4 cannot be resolved with this uri_format.

I'm not sure how much value there is to curating a provider that cannot resolve all IDs for its parent resource. I think we could consider marking this as not_notable instead.

[bgyori]

Yeah, I don't think in itself it's a problem that not every ID is resolved, but I think overall not sure if it's worth adding this given the anticipation of the broken example link.

[nagutm]

One other possible solution to this could be to curate this as its own prefix and use the "provides" key to signal that it is a PDB provider. That way we could use an example ID that would create a working example link.