Differences

This shows you the differences between two versions of the page.

--- wiki:autolit:search:exploration [2024/09/20 15:54]
jthurnham
+++ wiki:autolit:search:exploration [2024/09/20 16:10] (current)
jthurnham
@@ Line 54: / Line 54: @@
 The purpose of reviewing Abstracts should be to:
-Confirm that your search is returning relevant records, and
+  - Confirm that your search is returning relevant records, and
-Identify the key terms found in relevant records and adding them to your PICO terms.
+  - Identify the key terms found in relevant records and adding them to your PICO terms.
-  - Drag and drop the Group box into the concepts box.
+=== 2. PICOs ===
-  - 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 |}}
+Powered by RoboPICO, browse commonly-mentioned Populations, Interventions, and Outcomes from abstracts and titles.
+{{ :undefined:screenshot-2024-09-05-at-17.41.29-2048x1026.png?nolink |}}
-==== 5. Run or Update Search Exploration ====
+The purpose of RoboPICO should be to:
-To populate Abstracts, RoboPICO, Topic Modeling, and Keywords:
+  - 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)
-  * Select the "Refresh Exploration" button
+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.
-{{ :undefined:se5.png?nolink |}}
+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.
-  * A modal will appear while Search Exploration refreshes. This may take a minute, since this will run a pre-search of PubMed.
+==== 3. Study Type ====
-{{ :undefined:refresh.png?nolink |}}
+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.
-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.
+{{ :undefined:screenshot-2024-09-05-at-17.43.09-2048x1048.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.
+==== 4. Location ====
-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.
+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.
-==== 1. Abstracts ====
+{{ :undefined:screenshot-2024-09-05-at-17.47.28-2048x1048.png?nolink |}}
-Skim through abstracts retrieved through your search exploration terms.
+==== 5. Study Size ====
-{{ :undefined:seabs.png?nolink |}}
+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.
-The purpose of reviewing Abstracts should be to:
+{{ :undefined:screenshot-2024-09-05-at-17.49.05-2048x1015.png?nolink |}}
-  - Confirm that your search is returning relevant records, and
+==== 6. Topics ====
-  - Identify the key terms found in relevant records and adding them to your PICO terms.
-==== 2. RoboPICO ====
-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]].
-{{ :undefined:seabs2.png?nolink |}}
-The purpose of RoboPICO should be to:
-  - Identify the most common topics of underlying abstracts, and
-  - 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>
-==== 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.
-{{ :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 128: / 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 133: / 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:
+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.
-{{ :undefined:pre.png?nolink |}}
+There is no ‘right’ number of records, but a good rule of thumb is to return:
-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.
+  * A maximum of 200-300 records, with
+  * An anticipated inclusion rate at or above 20%.
-{{ :undefined:pre1.png?nolink |}}
-There is no 'right' number of records, but a good rule of thumb is to return:
-  - A maximum of **200-300 records**, with
-  - 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 |}}
-{{ :undefined:searchexplorfinalize.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.]]

Nested Knowledge

User Tools

Site Tools

Differences

Page Tools