pub_worm

Wormbase

http://rest.wormbase.org/index.html

API integration of Wormbase and NCBI Utils

Call from the commandline
$PYTHONPATH="./src" python -m pub_worm.wormbase.WormbaseREST

Helpful Sites

https://researchguides.library.wisc.edu/c.php?g=1144260&p=8349872

ncbi_utils

eInfo

eSearch

Search nlmcatalog only get pubmed journals

eSummary

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=37144896

eFetch

Pull Article

        efetch_params = {
            "db": "pubmed",
            "id": ",".join(papers),  # Join IDs with comma
            "retmode": "json",
            "rettype": "abstract"
        }

Pytest

Run a specific test from the command line

cd /Users/dan/Code/Python/pub_worm/tests
export PYTHONPATH=..;python -m pytest ncbi/test_entreze_api.py::test_entreze_esearch

Release files for pub-worm 0.3.18

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pub-worm 0.3.18
File	Size	Uploaded
pub_worm-0.3.18.tar.gz	3.0 MB	Sep 2, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for pub-worm 0.3.18
File	Interpreter	ABI	Platform	Reset
pub_worm-0.3.18-py3-none-any.whl 400.1 kB Sep 2, 2026	Python 3	none	any	Details

Total release size: 3.4 MB

Release files / pub_worm-0.3.18.tar.gz

Download URL	pub_worm-0.3.18.tar.gz
Size	3.0 MB
Tags	Source
SHA-256 checksum How to use checksums	`8cee435eee6f3cf1cc5b0f752b7d808bc3ea3cb8edf71730171eeb6cba1a50d5`
BLAKE2b-256 checksum How to use checksums	`a69b113afccf74a4f6cb33a46a37ed9e0bbbb73842c1fc9f30cb709fe8933989`
Upload date	Sep 2, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`uv/0.9.17 {"installer":{"name":"uv","version":"0.9.17","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"macOS","version":null,"id":null,"libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}`

Release files / pub_worm-0.3.18-py3-none-any.whl

Download URL	pub_worm-0.3.18-py3-none-any.whl
Size	400.1 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`902a99e70df38328d0bb44e225a7dcf4c932de556cc2841e291b07fe79f58ee7`
BLAKE2b-256 checksum How to use checksums	`44bab5dc06ded793b9138174752752ecb7d43dd94efe0910c15f05c5736ef48a`
Upload date	Sep 2, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`uv/0.9.17 {"installer":{"name":"uv","version":"0.9.17","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"macOS","version":null,"id":null,"libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}`