Add prefix: eccDNA

[nalikapalayoor]

This pull request curates a new prefix eccDNA, which is a database based on single-cell whole genome sequencing data. This PR adds necessary metadata to bioregistry.json and adds the curated paper to currated_papers.tsv

https://pubmed.ncbi.nlm.nih.gov/39693568/

[cthoyt]

it's surprising that the resource is called eccdna but the identifier has ecDNA with one fewer c

[bgyori]

Actually, I realize now that it's even more complicated. The example ID is valid

but looking further, there are actually other ID's that use ecc as a prefix:

😮

So the regex pattern will need to be slightly adjusted and we can add an extra example.

[bgyori]

For future reference, there are two types of entries: ecDNA (extrachromosomal DNA) and eccDNA (extrachromosomal circular DNA) so the ID pattern makes sense. I added an extra example to show both types.

[bgyori]

There is a problem: for the eccDNA_* case:

            for example in entry.example_extras:
                with self.subTest(prefix=prefix, identifier=example):
>                   self.assertEqual(entry.standardize_identifier(example), example)
E                   AssertionError: 'hsa_35832' != 'eccDNA_hsa_35832'
E                   - hsa_35832
E                   + eccDNA_hsa_35832

This has to do with some core code in standardize_identifier that automatically strips off the prefix if followed by a _ at

bioregistry/src/bioregistry/schema/struct.py

Lines 1965 to 1966 in 36cad81

	elif icf.startswith(f"{self.prefix.casefold()}{peel}"):
	return identifier[len(self.prefix) + len(peel) :]

. This might have to be changed since in this case we wouldn't want to apply it.

[cthoyt]

Set "banana_peel": "", to get around this

[bgyori]

Unfortunately _ is hard-coded as an additional potential banana peel here:

bioregistry/src/bioregistry/schema/struct.py

Line 1960 in 36cad81

peels = [self.get_banana_peel(), "_"]

so that won't work by itself.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 46.27%. Comparing base (8950e70) to head (a60e5bc).
Report is 278 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1366      +/-   ##
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+ Coverage   42.51%   46.27%   +3.76%     
==========================================
  Files         117      118       +1     
  Lines        8327     8302      -25     
  Branches     1963     1357     -606     
==========================================
+ Hits         3540     3842     +302     
+ Misses       4582     4275     -307     
+ Partials      205      185      -20     

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[cthoyt]

please write out non-obvious acronyms like ECC in full in the title

[cthoyt]

what is an eccDNA? why do we care about them?