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--- wiki:autolit:search:exploration [2023/06/06 22:00]
jthurnham
+++ wiki:autolit:search:exploration [2024/09/20 16:10] (current)
jthurnham
@@ Line 1: / Line 1: @@
 ====== Search Exploration ======
-The Search Exploration page allows you to generate search terms based on central concepts of your nest. Enter your Population, Interventions (and Comparators), and Outcomes (PICO) to generate a Boolean query that can be used on PubMed, and explore potential search results' abstracts, key terminology, and topics of interest to help construct your final search strategy. When complete, proceed to [[:wiki:autolit:search|Lit Search]] and [[:wiki:autolit:search:execute|Run your Search]].
+The Search Exploration page allows you to input concepts, explore the literature and generate a search query to finalize in your nest. Enter your Population, Interventions (and Comparators), and Outcomes (PICO) to generate a Boolean query that can be used on PubMed, and explore potential search results’ abstracts, key terminology, and topics of interest to help construct your final search strategy. When complete, proceed to [[:wiki:autolit:search|Lit Search]] and [[:wiki:autolit:search:execute|Run your Search]].
 ===== How to Begin Search Exploring =====
@@ Line 7: / Line 7: @@
 ==== 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), and Outcomes (PICO).
+==== 2. Enter concepts of Interest: ====
-**Imagine you are asking the Research Question**: How do __atypical antipsychotics (I)__ impact the __quality of life and disability (O)__ in__ adults with schizophrenia (P)__//?//
+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 (patients with schizophrenia), Interventions (atypical antipsychotics), and Outcomes (disability and quality of life) in the Concept bar under Create.
+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/minimise the page select the up arrow at the bottom of the concepts box (orange).
-  - 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**: 2 to 5 terms per category).
-{{ :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?**  A comparator is the drug, device, or intervention that the main intervention is tested against. Typical comparator arms include placebo and standard of care (SOC). In the framework shown here, comparators can be included under interventions. </WRAP>
+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) and naming each group if you wish (orange). You’ll notice the right-hand query preview has now “OR”ed the grouped concepts.
-{{ :undefined:se4.png?nolink |}}
+{{ :undefined:screenshot-2024-09-05-at-17.27.15-2048x993.png?nolink |}}
-<WRAP center round info 90%> Negation: Check the negate box to exclude the specific PICO elements from your search. For example, you can add the population "Pediatric" and negate it if you would like to exclude pediatric populations from your research question. </WRAP>
+**Negation:** Check the negate box to exclude an entire group, or the circle to the left of a concept to negate the specific concept.
+{{ :undefined:screenshot-2024-09-05-at-17.33.12-2048x995.png?nolink |}}
-==== 3. Edit Concepts ====
-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.
+==== 3. Refresh Exploration ====
-To proceed, click on the down arrow under Concepts to view, add, and group together PICO elements. Alternatively, you can drag and drop a group into the concepts box to expand.
+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.
-{{ :undefined:se2.png?nolink |}}
+{{ :undefined:screenshot-2024-09-05-at-17.37.43-2048x1023.png?nolink |}}
-----
+A modal will appear while Search Exploration refreshes. This may take a minute, since this will run a pre-search of PubMed.
+{{ :undefined:screenshot-2024-09-05-at-17.38.18-2048x644.png?nolink |}}
-==== 4. Group together PICO elements ====
+When you update search exploration, the references in your nest **will not change.** The records and data returned from this step will only be used for Search Exploration.
-  - Drag and drop the Group box into the concepts box.
+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).
-  - Group together sets of populations, interventions, or outcomes. This group will function like the OR operator in search strings. In this example, specific types of antipsychotic medications are grouped together.
-  - You can also negate whole groups by checking the box next to Negate.
-{{ :undefined:se3.png?nolink |}}
+==== How to Interpret Search Exploration Findings ====
+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 so that they return as many records of interest while limiting irrelevant results.
-==== 5. Run or Update Search Exploration ====
+Iterative Refinement: As you use the tools outlined below to add, remove, or restructure your terms, you should periodically re-run “Update Search Exploration”, as this is only run manually, and not automatically updated.
-To populate Abstracts, RoboPICO, Topic Modeling, and Keywords:
+=== 1. Abstracts ===
-  * Select the "Refresh Exploration" button
+Skim through abstracts retrieved through your search exploration terms.
-{{ :undefined:se5.png?nolink |}}
+{{ :undefined:screenshot-2024-09-05-at-17.40.13-2048x974.png?nolink |}}
-  * A modal will appear while Search Exploration refreshes. This may take a minute, since this will run a pre-search of PubMed.
+The purpose of reviewing Abstracts should be to:
-{{ :undefined:refresh.png?nolink |}}
+  - Confirm that your search is returning relevant records, and
+  - Identify the key terms found in relevant records and adding them to your PICO terms.
-When you update search exploration, the references in your nest **will not change.**  The records and data returned from this step will only be used for Search Exploration.
+=== 2. PICOs ===
-===== How to Interpret Search Exploration Findings =====
-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**  so that they return as many records of interest while limiting irrelevant results.
+Powered by RoboPICO, browse commonly-mentioned Populations, Interventions, and Outcomes from abstracts and titles.
-Iterative Refinement: As you use the tools outlined below to add, remove, or restructure your terms, you should periodically re-run "Update Search Exploration", as this is **only run manually**, and not automatically updated.
+{{ :undefined:screenshot-2024-09-05-at-17.41.29-2048x1026.png?nolink |}}
-==== 1. Abstracts ====
+The purpose of RoboPICO should be to:
-Skim through abstracts retrieved through your search exploration terms.
+  - 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)
-{{ :undefined:seabs.png?nolink |}}
+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 are offered.
-The purpose of reviewing Abstracts should be to:
+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.
-  - Confirm that your search is returning relevant records, and
+==== 3. Study Type ====
-  - Identify the key terms found in relevant records and adding them to your PICO terms.
+Powered by [[https://about.nested-knowledge.com/docs/core-smart-tags/| Core Smart Tags]], explore a representation of reported Study Types based on your concepts via our sunburst diagram. Select different parts of the diagram to view associated references, for example, when the “RCT” tag is selected, 14 associated records are reported, which may be viewed further.
-==== 2. RoboPICO ====
+{{ :undefined:screenshot-2024-09-05-at-17.43.09-2048x1048.png?nolink |}}
-Browse commonly-mentioned Populations, Interventions, and Outcomes from abstracts and titles. PICO elements are identified by [[https://github.com/holub008/robopico|RoboPICO]], which is an open source fork of the models offered in [[https://www.robotreviewer.net/|RobotReviewer]].
+==== 4. Location ====
-{{ :undefined:seabs2.png?nolink |}}
+Powered by [[https://about.nested-knowledge.com/docs/core-smart-tags/| Core Smart Tags]], view a choropleth/map of the location of reported studies. The darker the blue, the greater the number of studies reported in this region. We can see below that studies are mostly reported in China and, when selected, 107 associated records can be explored.
-The purpose of RoboPICO should be to:
+{{ :undefined:screenshot-2024-09-05-at-17.47.28-2048x1048.png?nolink |}}
-  - Identify the most common topics of underlying abstracts, and
+==== 5. Study Size ====
-  - Identify terms that you should add to your PICO (which you can populate to "Add a PICO Element" by clicking on the relevant row).
-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 are offered.
-<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. </WRAP>
+Powered by [[https://about.nested-knowledge.com/docs/core-smart-tags/| Core Smart Tags]], view a histogram displaying sets of records of increasing study size ranges. We can see when Study Size 7-20 is selected, only 3 records are shown.
+{{ :undefined:screenshot-2024-09-05-at-17.49.05-2048x1015.png?nolink |}}
-==== 3. Topics ====
+==== 6. 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.
-{{ :undefined:seabs3.png?nolink |}}
+{{ :undefined:screenshot-2024-09-05-at-17.50.10-2048x1019.png?nolink |}}
 These topics are derived from a [[https://en.wikipedia.org/wiki/Carrot2|Carrot2]] clustering of abstract text to identify semantically similar concepts and group them.
-----
+==== 7. Acronyms ====
+Powered by [[https://about.nested-knowledge.com/docs/core-smart-tags/| Core Smart Tags]], explore commonly reported acronyms and associated references.
-==== 4. Keywords and N-Grams ====
+{{ :undefined:screenshot-2024-09-05-at-17.52.24-2048x1048.png?nolink |}}
+==== 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.
@@ Line 111: / Line 110: @@
 {{ :undefined:seabs4.png?nolink |}}
+Note: Study Type/Location/Size cannot be incorporated into the search strategy e.g. Study Type: RCT or Study Location: Germany. You must finalize the search and then a filter can be applied to view and/or bulk include!
 ===== Next Steps =====
@@ Line 116: / Line 116: @@
 ==== When is Search Exploration finished? ====
-You should continue iteratively refining your query until your Abstract, RoboPICO, Topics, and/or Keywords contain mostly relevant content and minimal extraneous records or concepts.
+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**  returned from your query. To do so, view the number of records in the top right of the Preview screen, where you can also click to view the query on PubMed:
-{{ :undefined:pre.png?nolink |}}
-To view the full query, expand using the dropdown arrow. You can view the results returned in PubMed by clicking on #### results. You can finalize the query (input it into your nest) by selecting Finalize and following the steps.
-{{ :undefined:pre1.png?nolink |}}
+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 (red), where you can also click to view the query on PubMed. To view the full query, expand using the dropdown arrow.
-There is no 'right' number of records, but a good rule of thumb is to return:
+There is no ‘right’ number of records, but a good rule of thumb is to return:
-  - A maximum of **200-300 records**, with
+  * A maximum of 200-300 records, with
-  - An anticipated inclusion rate **at or above 20%.**
+  * An anticipated inclusion rate at or above 20%.
 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/expanded Searches as you proceed, so achieving a high rate of inclusion should be prioritized over comprehensiveness.
-After hitting Finalize, you will be taken to the Add Search modal, but pre-populated with the query you have built. Here you can edit the query, the search engine, and notes before hitting Add. This adds the search just like a regular one!
+{{ :undefined:screenshot-2024-09-05-at-17.54.08-2048x1025.png?nolink |}}
-==== What comes after Search Exploration? ====
+==== Finalize your Search Query ====
-When you are finished with Search Exploration, proceed to review, test, and finalize your search string in [[:wiki:autolit:search|Lit Search]]!
+To finalize your query and make edits select “Finalize” in the top right (blue). This takes you to the main [[https://wiki.nested-knowledge.com/doku.php?id=wiki:autolit:search| Literature Search]] page to add an Automatic Search but is pre-populated with the query you have built. Here you can edit the query, the search engine, and notes before hitting Add. This adds the search just like a regular one.
+{{ :undefined:screenshot-2024-09-05-at-17.58.22-2048x1037.png?nolink |}}
+Now you have added a search query, the next stage is [[wiki:autolit:screening|Screening.]]

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