pubmed_parser

article doi medline-xml nlp parse parser pmid pubmed-central pubmed-parser python xml

Score: 19.909206884334907

Last synced: about 12 hours ago
JSON representation

Repository metadata:

:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

Host: GitHub
URL: https://github.com/titipata/pubmed_parser
Owner: titipata
License: mit
Created: 2015-03-05T05:13:57.000Z (over 11 years ago)
Default Branch: master
Last Pushed: 2025-07-31T15:29:44.000Z (11 months ago)
Last Synced: 2026-06-20T22:03:23.647Z (3 days ago)
Topics: article, doi, medline-xml, nlp, parse, parser, pmid, pubmed-central, pubmed-parser, python, xml
Language: Python
Homepage: http://titipata.github.io/pubmed_parser/
Size: 60.4 MB
Stars: 735
Watchers: 21
Forks: 180
Open Issues: 21
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff

Owner metadata:

Name: Titipat Achakulvisut
Login: titipata
Email:
Kind: user
Description: Applied ML & Science of Science @biodatlab Mahidol University | Former @KordingLab UPenn, intern @allenai, organizer/co-founder @neuromatch
Website: titipata.github.io
Location: Bangkok, Thailand
Twitter: titipat_a
Company: Mahidol University
Icon url: https://avatars.githubusercontent.com/u/8295838?u=899c9a74f288d297372303e5874d966feeebfbec&v=4
Repositories: 47
Last Synced at: 2024-10-31T07:04:20.293Z
Profile URL: https://github.com/titipata

GitHub Events

Total

Fork event: 10
Issue comment event: 23
Issues event: 10
Pull request event: 10
Pull request review comment event: 1
Pull request review event: 5
Push event: 19
Watch event: 112
Total: 190

Last Year

Fork event: 3
Issue comment event: 3
Issues event: 2
Watch event: 28
Total: 36

Committers metadata

Last synced: 3 days ago

Total Commits: 322
Total Committers: 39
Avg Commits per committer: 8.256
Development Distribution Score (DDS): 0.689

Commits in past year: 1
Committers in past year: 1
Avg Commits per committer in past year: 1.0
Development Distribution Score (DDS) in past year: 0.0

Name	Email	Commits
titipata	t**a@u**u	100
titipata	m**t@g**m	94
Nils Herrmann	n**8@l**x	24
Ray Pereda	r**a@g**m	11
Daniel Acuna	d**a@s**u	10
Michael E. Rose	M**e@g**m	9
tulakann	t**r@g**m	8
Daniel Acuna	d**a@n**u	7
titipata	t**a@a**g	7
Simon Wörpel	s**l@m**e	6
Ted Cybulski	t**i@g**m	6
Tommaso Leonardi	t**m@i**z	4
Kevin Henner	k****r	3
Daniel Mietchen	d**n@g**m	2
Julien Tourille	j**e@g**m	2
Mark A. Jensen	m**t@f**s	2
TariqAHassan	t**n@g**m	2
Tiansu	t**0@i**m	2
jim	z**3@s**u	2
patrusso2	p**2@g**m	2
yak1r	y**v@g**m	1
tanganyao	t**9@1**m	1
ianlongden	i**n@m**u	1
Ray Pereda	r**a@G**e	1
Ubuntu	u**u@i**l	1
titipata	t**a@u**u	1
iacopo	i****y	1
ZhangWoW123	1****3	1
Vincent Batts	v**s@h**m	1
Thomas Pan	t**n@g**m	1
and 9 more...

Issue and Pull Request metadata

Last synced: 13 days ago

Total issues: 89
Total pull requests: 76
Average time to close issues: 8 months
Average time to close pull requests: 12 days
Total issue authors: 55
Total pull request authors: 31
Average comments per issue: 2.82
Average comments per pull request: 0.86
Merged pull request: 60
Bot issues: 0
Bot pull requests: 0

Past year issues: 3
Past year pull requests: 2
Past year average time to close issues: N/A
Past year average time to close pull requests: N/A
Past year issue authors: 3
Past year pull request authors: 2
Past year average comments per issue: 0.33
Past year average comments per pull request: 1.0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/titipata/pubmed_parser

Top Issue Authors

titipata (14)
deakkon (6)
nils-herrmann (5)
tleonardi (5)
uludag (2)
ghost (2)
shrimonmuke0202 (2)
ZhangWoW123 (2)
Michael-E-Rose (2)
callebalik (2)
octotus (2)
qm-intel (2)
pidugusundeep (1)
soupstandstop (1)
schnobi1990 (1)

Top Pull Request Authors

nils-herrmann (31)
titipata (4)
kjhenner (3)
jtourille (2)
enjalot (2)
thomascpan (2)
tleonardi (2)
iacopy (2)
zyi103 (2)
Daniel-Mietchen (2)
ZhangWoW123 (2)
raypereda (2)
patrusso2 (2)
simonwoerpel (1)
soupstandstop (1)

Top Issue Labels

bug (23)
enhancement (11)
question (5)
help wanted (4)
invalid (2)
feature request (1)
duplicate (1)

Top Pull Request Labels

Package metadata

Total packages: 3
Total downloads:
- pypi: 9,237 last-month
Total docker downloads: 5,783
Total dependent packages: 1 (may contain duplicates)
Total dependent repositories: 4 (may contain duplicates)
Total versions: 8
Total maintainers: 1

pypi.org: pubmed-parser

A python parser for Pubmed Open-Access Subset and MEDLINE XML repository

Homepage:
Documentation: https://pubmed-parser.readthedocs.io/
Licenses: MIT (c) 2015 - 2024 Titipat Achakulvisut, Daniel E. Acuna
Latest release: 0.5.1 (published almost 2 years ago)
Last Synced: 2026-06-20T22:00:30.329Z (3 days ago)
Versions: 5
Dependent Packages: 1
Dependent Repositories: 4
Downloads: 9,237 Last month
Docker Downloads: 5,783
Rankings:
- Docker downloads count: 1.557%
- Stargazers count: 2.803%
- Forks count: 4.042%
- Average: 4.303%
- Dependent packages count: 4.733%
- Downloads: 5.162%
- Dependent repos count: 7.52%
Maintainers (1)
- titipata

proxy.golang.org: github.com/titipata/pubmed_parser

Homepage:
Documentation: https://pkg.go.dev/github.com/titipata/pubmed_parser#section-documentation
Licenses:
Latest release: v0.2.3 (published over 6 years ago)
Last Synced: 2026-06-20T22:00:33.158Z (3 days ago)
Versions: 2
Dependent Packages: 0
Dependent Repositories: 0
Rankings:
- Dependent packages count: 4.825%
- Average: 4.987%
- Dependent repos count: 5.149%

guix: python-pubmed-parser

Parser for Pubmed Open-Access Subset and MEDLINE XML repository

Homepage: https://titipata.github.io/pubmed_parser/
Documentation: https://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/python-xyz.scm#n15003
Licenses: expat
Latest release: 0.5.1 (published 4 months ago)
Last Synced: 2026-04-27T16:26:13.181Z (about 2 months ago)
Versions: 1
Dependent Packages: 0
Dependent Repositories: 0
Rankings:
- Dependent repos count: 0.0%
- Dependent packages count: 0.0%
- Average: 100%

Dependencies

docs/doc_requirements.txt pypi

sphinx *
sphinx-gallery *
sphinx_rtd_theme *

requirements.txt pypi

lxml *
numpy *
pytest *
pytest-cov *
requests *
six *
unidecode *

setup.py pypi

lxml *
numpy *
pytest *
pytest-cov *
requests *
six *
unidecode *

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