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wiki:autolit:search:exploration [2023/04/08 21:18] jthurnham [3. Edit PICO Details] |
wiki:autolit:search:exploration [2024/09/20 16:10] (current) jthurnham |
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====== Search Exploration ====== | ====== Search Exploration ====== | ||
- | The Search Exploration page allows you to generate search | + | The Search Exploration page allows you to input concepts, explore the literature and generate |
===== How to Begin Search Exploring ===== | ===== How to Begin Search Exploring ===== | ||
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==== 1. Navigate to Search Exploration ==== | ==== 1. Navigate to Search Exploration ==== | ||
- | {{ :undefined:lise2.png?nolink |}} | + | {{ :undefined:screenshot-2024-09-05-at-17.20.30-2048x356.png?nolink |}} |
- | ==== 2. Enter PICO of Interest: ==== | + | |
- | When you create a nest, you will have the option to add details about the Population, Interventions (and comparators), | + | ==== 2. Enter concepts of Interest: ==== |
- | **Imagine you are asking | + | You may add in any concepts of interest, but it can often be helpful to add and group specific PICOs. Add individual terms into the concept box (red) and then hit Enter on your keyboard. This will add the terms into the central concept box. |
- | - First, enter the Population | + | As terms are added they are automatically building a search query whose Preview is shown on the right hand side (blue). Per a typical Boolean Query, you’ll notice they are “AND”ed together. To expand/ |
- | - Enter each concept, then hit the Enter button, this will move them under Concepts. | + | |
- | - Continue adding terms until you have enough terms to identify your specific topic area (**Recommended**: | + | |
- | {{ :undefined:se.png?nolink |}} | + | {{ :undefined:screenshot-2024-09-05-at-17.25.16-2048x1004.png?nolink |}} |
- | <WRAP center round help 90%> What is a **Comparator? | + | You can group like concepts to “OR” them together instead by dragging in the Group box icon (red), then dragging each relevant concept into a group (blue) |
+ | {{ : | ||
- | ==== 3. Edit Concepts ==== | + | **Negation: |
- | When you have completed the tasks above, you will have unstructured concepts of interest, but no grouping of terms and no information yet populated to the Abstracts, RoboPICO, Topic Modeling, and Keywords. | + | {{ : |
- | To proceed, click on the down arrow under Concepts to view, add, and group together PICO elements. Alternatively, | ||
- | {{ : | + | ==== 3. Refresh Exploration ==== |
- | ---- | + | Now you’ve added, grouped, and negated a few concepts of interest, minimise the concept box and select “Refresh Exploration.” This action searches PubMed and populates the following tabs from a subset of 250 studies: Abstracts, PICOs, Study Types, Location, Size, Topics, Acronyms and Keywords. |
+ | {{ : | ||
- | ==== 4. Group together PICO elements ==== | + | A modal will appear while Search Exploration refreshes. This may take a minute, since this will run a pre-search of PubMed. |
- | - Drag and drop the Group box from the right-side panel to the respective PICO section.{{:wiki:autolit: | + | {{ :undefined:screenshot-2024-09-05-at-17.38.18-2048x644.png? |
- | - Group together sets of populations, | + | |
- | {{: | + | When you update |
- | <WRAP center round info 90%> Negation: Check the negate box to exclude | + | Feel free to click out of this modal and it will continue to run in the background. You can check in on its progress via the background jobs icon (three horizontal progress lines in the top right). |
+ | ==== How to Interpret Search Exploration Findings ==== | ||
- | ==== 5. Run or Update Search Exploration ==== | + | There are several ways to explore the references pulled by your exploratory search. The goal of this process should be to expand |
- | To populate Abstracts, RoboPICO, Topic Modeling, and Keywords: | + | Iterative Refinement: As you use the tools outlined below to add, remove, or restructure your terms, you should periodically re-run “Update Search Exploration”, |
- | - In the PICO Detail, select " | + | === 1. Abstracts === |
- | - Review the query string to ensure that it is structured as intended. | + | |
- | - Run the exploratory search. This may take a minute, since this will run a pre-search of PubMed. | + | |
- | {{: | + | Skim through abstracts retrieved through your search |
- | When you update search exploration, | + | {{ : |
+ | The purpose of reviewing Abstracts should be to: | ||
- | ===== How to Interpret Search Exploration Findings ===== | + | - Confirm that your search is returning relevant records, and |
+ | - Identify the key terms found in relevant records and adding them to your PICO terms. | ||
- | There are several ways to explore the references pulled by your exploratory search. The goal of this process should be to **expand or refine your search terms** | + | === 2. PICOs === |
- | Iterative Refinement: As you use the tools outlined below to add, remove, or restructure your terms, you should periodically re-run " | + | Powered by RoboPICO, browse commonly-mentioned Populations, Interventions, and Outcomes from abstracts and titles. |
- | ==== 1. Abstracts ==== | + | {{ : |
- | Skim through abstracts retrieved through your search exploration terms. | + | The purpose of RoboPICO should be to: |
- | {{: | + | - Identify the most common topics of underlying abstracts, and |
+ | - Identify terms that you should add to your query (select term, view definition, and select enter in concept box to add) | ||
- | The purpose | + | Clicking a row in the chart also initiates a strict MeSH lookup on the PICO element; not all extracted PICOs will correspond to MeSHs, but expect approximately half of lookups |
- | - Confirm that your search is returning relevant records, and | + | What are MeSH? Medical Subject Headings (MeSH) are terms defined by the National Library of Medicine as a way to organize |
- | - Identify the key terms found in relevant records | + | |
+ | ==== 3. Study Type ==== | ||
- | ==== 2. RoboPICO ==== | + | Powered by [[https:// |
- | Browse commonly-mentioned Populations, | + | {{ :undefined:screenshot-2024-09-05-at-17.43.09-2048x1048.png?nolink |}} |
- | {{: | + | ==== 4. Location ==== |
- | The purpose | + | Powered by [[https:// |
- | | + | {{ : |
- | | + | |
- | ---- | + | ==== 5. Study Size ==== |
- | Clicking a row in the chart also initiates a strict MeSH lookup on the PICO element; not all extracted PICOs will correspond to MeSHs, but expect approximately half of lookups to succeed. In the event of a failed lookup, MeSH and Google search linkouts | + | Powered by [[https:// |
- | {{:wiki:autolit: | + | {{ :undefined:screenshot-2024-09-05-at-17.49.05-2048x1015.png? |
- | <WRAP center round help 90%> What are MeSH? Medical Subject Headings (MeSH) are terms defined by the National Library of Medicine as a way to organize and search the content of medical literature. In some ways, MeSH are similar to Nested Knowledge tags, but unlike tags, MeSH are standardized. </ | + | ==== 6. Topics ==== |
- | + | ||
- | + | ||
- | ==== 3. Topics ==== | + | |
Explore topics that appear most frequently among the references. References may belong to one or more topics, or none. Clicking a topic shows references belonging to the topic. | Explore topics that appear most frequently among the references. References may belong to one or more topics, or none. Clicking a topic shows references belonging to the topic. | ||
- | {{:wiki:autolit: | + | {{ :undefined:screenshot-2024-09-05-at-17.50.10-2048x1019.png? |
These topics are derived from a [[https:// | These topics are derived from a [[https:// | ||
- | ---- | + | ==== 7. Acronyms ==== |
+ | Powered by [[https:// | ||
- | ==== 4. Keywords and N-Grams ==== | + | {{ : |
+ | |||
+ | ==== 8. Keywords and N-Grams ==== | ||
Explore the frequency of word combinations (n-grams) from abstracts or indexed descriptors (MeSH and/or journal keywords). While n-grams are presented in order of occurence in abstract text, descriptors are inherently unordered. Clicking a row shows unique references containing the combination. | Explore the frequency of word combinations (n-grams) from abstracts or indexed descriptors (MeSH and/or journal keywords). While n-grams are presented in order of occurence in abstract text, descriptors are inherently unordered. Clicking a row shows unique references containing the combination. | ||
- | {{:wiki:autolit: | + | {{ :undefined:seabs4.png? |
- | + | ||
- | {{: | + | |
+ | Note: Study Type/ | ||
===== Next Steps ===== | ===== Next Steps ===== | ||
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==== When is Search Exploration finished? ==== | ==== When is Search Exploration finished? ==== | ||
- | You should continue iteratively refining your query until your Abstract, RoboPICO, Topics, and/or Keywords | + | You should continue iteratively refining your query until the Exploration tabs contain mostly relevant content and minimal extraneous records or concepts. |
- | It is useful to **check the total number of records** | + | It is useful to check the total number of records returned from your query. To do so, view the number of records in the top right of the Preview screen |
- | {{:wiki: | + | There is no ‘right’ number of records, but a good rule of thumb is to return: |
- | There is no ' | + | * A maximum of 200-300 records, with |
- | + | | |
- | - A maximum of **200-300 records**, with | + | |
- | | + | |
The reasoning behind this recommendation is that you want to capture relevant records while minimizing extra work during Screening (remember, your team will need to manually Screen all results from your Search!). You can always add new/ | The reasoning behind this recommendation is that you want to capture relevant records while minimizing extra work during Screening (remember, your team will need to manually Screen all results from your Search!). You can always add new/ | ||
- | ==== What comes after Search | + | {{ : |
+ | |||
+ | ==== Finalize your Search | ||
- | When you are finished with Search Exploration, | + | To finalize your query and make edits select “Finalize” |
+ | {{ : | ||
+ | Now you have added a search query, the next stage is [[wiki: |