Add curations to semi-automated literature workflow

[nagutm]

This pull request updates the curated_papers.tsv file with all PubMed papers identified till 2024-10-01 in #1165.

Here are some statistics about the classification of each paper based on relevancy_type so far:

Relevant (1) classifications: 14

• new_prefix: 3
• new_provider: 4
• new_publication: 2
• unclear: 2**
• existing: 3

Irrelevant (0) classifications: 40

• irrelevant_other: 31
• no_website: 2
• not_identifiers_resource: 7

** 1. 39104285 is a provider for UniProt IDs but was not curated due to the variable nature of the uri_format. 2. 38991851 was curated as a prefix but there was some discussion about whether it should be a provider instead. See #1194. Regardless, both of these were curated as relevant (1) which seems to be the more important classification.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 43.49%. Comparing base (8950e70) to head (91c6dd8).
Report is 112 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1223      +/-   ##
==========================================
+ Coverage   42.51%   43.49%   +0.97%     
==========================================
  Files         117      118       +1     
  Lines        8327     8190     -137     
  Branches     1963     1346     -617     
==========================================
+ Hits         3540     3562      +22     
+ Misses       4582     4464     -118     
+ Partials      205      164      -41     

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[cthoyt]

Hi @nagutm, please do a bit of reading on writing good pull requests before making your next issue/pull request. It's difficult to keep up with so many that are not descriptive, full of typos, etc.

Some suggested resources:

1. https://github.blog/developer-skills/github/how-to-write-the-perfect-pull-request/
2. https://devdocs.prestashop-project.org/8/contribute/contribution-guidelines/pull-requests/
3. https://www.ssw.com.au/rules/write-a-good-pull-request/

[nagutm]

Per #1227 (comment), I have updated the value of the pr_added field to reflect what pull request # the row in curated_papers.tsv was added.