.. _pubmed:

PubMed
======

PubMed is a free resource supporting the search and retrieval of biomedical and life sciences literature.

Run a Query
-----------

Queries can be entered using either:

- the `basic search box <https://pubmed.ncbi.nlm.nih.gov/>`_, or
- the `advanced Query builder <https://pubmed.ncbi.nlm.nih.gov/advanced/>`_.

These interfaces are functionally equivalent for the purposes of `search-query`. We recommend users always **copy and store the full query string** from either interface.

.. note::

   For parsing PubMed queries, we recommend using the queries entered in the basic or advanced box as the *search_string* and leave the *general_search_field* empty.

   When running the same query with different serach fields, as in this `example <https://www.cabidigitallibrary.org/doi/10.1079/SEARCHRXIV.2023.00236>`_, *search-query* will assume that the queries are added with an "OR" operator.

Store a Query
-------------

When storing a PubMed query in a `.json` file or as a string:

- Use the content of the **Query box** or **Search details** section as the `search_string`.
- Leave the `general_search_field` empty.


Best Practices and Recommendations
----------------------------------

The advanced PubMed interface offers a dropdown for search fields such as `[Title/Abstract]`, `[Author]`, etc. When using this feature:

- If you apply the **same field** to the entire query, it is safe to store this value in the `general_search_field`.
- If the query contains **multiple search fields**, `search-query` will treat each term individually, and **leaving `general_search_field` empty is preferred**.

TODO : explain list search: https://library.bath.ac.uk/pubmed/combine-searches
-> searches an be reused/combined with the "add" button (or with "#1" references)

Resources
---------

- `PubMed User Guide <https://pubmed.ncbi.nlm.nih.gov/help/>`_
- `Search Builder Help <https://pubmed.ncbi.nlm.nih.gov/advanced/>`_