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| 1 | + |
1 | 2 | .. _pubmed: |
2 | 3 |
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3 | 4 | PubMed |
4 | | -==================== |
| 5 | +====== |
| 6 | + |
| 7 | +PubMed is a free resource supporting the search and retrieval of biomedical and life sciences literature. |
| 8 | + |
| 9 | +Run a Query |
| 10 | +----------- |
| 11 | + |
| 12 | +Queries can be entered using either: |
| 13 | + |
| 14 | +- the `basic search box <https://pubmed.ncbi.nlm.nih.gov/>`_, or |
| 15 | +- the `advanced Query builder <https://pubmed.ncbi.nlm.nih.gov/advanced/>`_. |
| 16 | + |
| 17 | +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. |
5 | 18 |
|
6 | | -Run a query |
7 | | --------------- |
| 19 | +.. note:: |
8 | 20 |
|
9 | | -Queries can be executed in the [basic search box](https://pubmed.ncbi.nlm.nih.gov/) or the advanced [Query box](https://pubmed.ncbi.nlm.nih.gov/advanced/). |
| 21 | + 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. |
10 | 22 |
|
11 | | -Report a query |
12 | | ------------------ |
| 23 | + 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. |
13 | 24 |
|
14 | | -It is recommended to store the queries entered in the basic or advanced box as the *search_string* and leave the *general_search_field* empty. |
| 25 | +Store a Query |
| 26 | +------------- |
15 | 27 |
|
16 | | -TODO : interface illustration? |
| 28 | +When storing a PubMed query in a `.json` file or as a string: |
17 | 29 |
|
18 | | -The advanced search page also offers the option to "Add terms to the query box" (by selecting specific fields in the drop-down). |
19 | | -This box offers a convenient way to add queries and apply the same search field (from the drop-down menu) to the whole query. |
20 | | -Here, it is important to |
21 | | -- use search fields only in the *general_search_field* |
22 | | -- 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. |
| 30 | +- Use the content of the **Query box** or **Search details** section as the `search_string`. |
| 31 | +- Leave the `general_search_field` empty. |
23 | 32 |
|
24 | | -TODO : interface illustration (highlight "OR" button) |
25 | 33 |
|
26 | | -TODO : add a linter warning (convention) when multiple general_search_fields are given? (operator unclear) |
| 34 | +Best Practices and Recommendations |
| 35 | +---------------------------------- |
27 | 36 |
|
| 37 | +The advanced PubMed interface offers a dropdown for search fields such as `[Title/Abstract]`, `[Author]`, etc. When using this feature: |
28 | 38 |
|
29 | | -Note: We assume that the [basic search box](https://pubmed.ncbi.nlm.nih.gov/) and the advanced [Query box](https://pubmed.ncbi.nlm.nih.gov/advanced/) handle queries equivalently. |
| 39 | +- If you apply the **same field** to the entire query, it is safe to store this value in the `general_search_field`. |
| 40 | +- If the query contains **multiple search fields**, `search-query` will treat each term individually, and **leaving `general_search_field` empty is preferred**. |
30 | 41 |
|
31 | | -Resources: |
| 42 | +Resources |
| 43 | +--------- |
32 | 44 |
|
33 | 45 | - `PubMed User Guide <https://pubmed.ncbi.nlm.nih.gov/help/>`_ |
| 46 | +- `Search Builder Help <https://pubmed.ncbi.nlm.nih.gov/advanced/>`_ |
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