This is a reusable UI that accesses and creates speadsheets of unique papers found from a searchterm in Pubmed and Embase.
This was built so that you can enter a single search query in PubMed syntax and search both Embase and Pubmed. This allows us to easily make searches, once we are certain that these are the searches we want to complete, and remove duplciates.
Currently this is a simple program that provides a UI to interface with the APIs for searching across these two medical databases: Embase and PubMed. It checks that your search string is properly formatted in PubMed syntax then converts it to Embase format to search there. Once the search is completed, the results of the search are added to a dataframe, duplicate entries are removed, and a CSV of results is produced.
The results saved to a csv file contain columns for:
- Source
- Author
- Title
- Abstract
- ID
- Link
- Query
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Clone this repository locally
git clone https://github.com/Pituitary-Neurochemistry-Heatmap/database-searcher -
Ensure you have pip and python 3 installed.
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Download our package manager poetry (if you have not downloaded it already)
pip install poetry
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I have created the pyproject.toml files so you don't have to worry about any of that. Just do the below.
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Add configuration to have venv in project directory
poetry config virtualenvs.in-project true -
Set up virtual environment using poetry
poetry install --no-root
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Now you should have a created venv that you can switch into with the following command
poetry shell
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Run the program with this command
python main.py
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If you chose to change the source code--as you develop you can add packages with the following command
poetry add <package-name>