Skip to content

Patch 1 #39

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ddeightmore wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Patch 1 #39

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
8d9c214
Update extract.py: add NCBI taxonomy RRIDs
ddeightmore Jul 17, 2025
be93cda
Update extract.py
ddeightmore Jul 17, 2025
57de8d9
Update extract.py
ddeightmore Jul 18, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions scibot/extract.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -340,6 +340,12 @@ def find_rrids(text):
for prefix, a, b, nums, suffix in matches4:
yield prefix, f'RRID:SAMN{nums.strip()}', f'{a}{b}{nums}', suffix

# fifth round for NCBI Taxonomy
regex5 = r'(.{0,32})(NCBI)(:?\s?)(taxid|Taxid|taxId|TaxId|taxID|TaxID|txid|txId|txID|Txid|TxId|TxID|Taxon|Taxonomy)(_|:)(\s?)([0-9]{3,8})([^\w].{0,31})'
matches5 = re.findall(regex5, text)
for prefix, ncbi, delim1, tax, delim2, delim3, nums, suffix in matches5:
yield prefix, f'RRID:NCBITaxon_{nums.strip()}', f'{ncbi}{tax}{nums}', suffix


# extract from post

Expand Down