https://github.com/grll/pubmedclient
A simple python SDK around PubMed API.
https://github.com/grll/pubmedclient
Last synced: 10 months ago
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A simple python SDK around PubMed API.
- Host: GitHub
- URL: https://github.com/grll/pubmedclient
- Owner: grll
- License: mit
- Created: 2025-01-01T13:39:03.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-01-01T14:16:01.000Z (over 1 year ago)
- Last Synced: 2025-05-04T09:04:43.985Z (about 1 year ago)
- Language: Python
- Homepage:
- Size: 124 KB
- Stars: 7
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# PubMed Client
[PubMed](https://pubmed.ncbi.nlm.nih.gov/) is a database of over 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.
PubMed Client is a simple open-source Python client for calling the NCBI PubMed API.
At the moment, the SDK mostly wraps around Entrez 'E-Utilities' API.
See for more details on the E-Utilities API from PubMed:
* [A General Introduction to the E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25497/)
* [The E-utilities In-Depth: Parameters, Syntax and More](https://www.ncbi.nlm.nih.gov/books/NBK25499/)
## Installation
```bash
# recommended uv, will add pubmesdk to your uv project
uv add pubmedclient
# or pip
pip install pubmedclient
```
## Usage
warning: without api key, you can only make 3 requests per second per IP.
```python
from pubmedclient import pubmedclient_client
# this is a thin wrapper around httpx
# with a few headers set for Entrez API
async with pubmedclient_client() as client:
# get the name of all available databases via EInfo
params = EInfoRequest()
response = await einfo(client, params)
print(response)
# get info about pubmed database
params = EInfoRequest(db="pubmed")
response = await einfo(client, params)
print(response)
# search for articles about asthma in the pubmed database
params = ESearchRequest(db="pubmed", term="asthma")
response = await esearch(client, params)
print(response)
# fetch the abstract for one of the returned id
params = EFetchRequest(db="pubmed", id="39737528", rettype="abstract", retmode="text")
response = await efetch(client, params)
print(response)
```
## Development
During development, setup the pip package in editable mode to resolve imports from the local package.
```bash
uv pip install -e .
# or pip
pip install -e .
```
## Contributing
The API coverage is far from complete.
We welcome contributions. Please feel free to open an issue or a PR.