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 0.3.17

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 0.3.17
File	Size	Uploaded
pub_worm-0.3.17.tar.gz	3.0 MB	Sep 1, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for pub-worm 0.3.17
File	Interpreter	ABI	Platform	Reset
pub_worm-0.3.17-py3-none-any.whl 400.1 kB Sep 1, 2026	Python 3	none	any	Details

Total release size: 3.4 MB

Release files / pub_worm-0.3.17.tar.gz

Download URL	pub_worm-0.3.17.tar.gz
Size	3.0 MB
Tags	Source
SHA-256 checksum How to use checksums	`4ac4ac8f537380a749edbf09a93b44c5f5f4978a169c31f8640edd36a0988fbd`
BLAKE2b-256 checksum How to use checksums	`c065439087c1fcfed0e2855848377dfdab23b528722d9f6d779c112dffa955a7`
Upload date	Sep 1, 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-0.3.17-py3-none-any.whl

Download URL	pub_worm-0.3.17-py3-none-any.whl
Size	400.1 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`c905f30a8db0bdee00662e11ecbf9ba87d3419e2568c08de6f0307a545a1ee5f`
BLAKE2b-256 checksum How to use checksums	`add2db98a949cc49780888b0bb6b62ac13a789aa532f30803b01b89873ed12a3`
Upload date	Sep 1, 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}`