Nested Knowledge

Bringing Systematic Review to Life

User Tools

Site Tools

Trace:
wiki:autolit:search:exploration

Differences

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

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
wiki:autolit:search:exploration [2023/01/05 16:49]
kevinkallmes 		wiki:autolit:search:exploration [2023/06/06 22:01] (current)
jthurnham [When is Search Exploration finished?]
Line 7: Line 7:
 ==== 1. Navigate to Search Exploration ==== ==== 1. Navigate to Search Exploration ====
  
-{{:wiki:autolit:search:img116.png?nolink&  }} +{{ :undefined:lise2.png?nolink |}}
 ==== 2. Enter PICO of Interest: ==== ==== 2. Enter PICO of Interest: ====
  
Line 15: Line 14:
 **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)__//?// **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)__//?//
  
-   - First, enter the Population (patients with schizophrenia), Interventions (atypical antipsychotics), and Outcomes (disability and quality of life). +   - First, enter the Population (patients with schizophrenia), Interventions (atypical antipsychotics), and Outcomes (disability and quality of life) in the Concept bar under Create. 
-  - Enter each element, identify whether it is a Population, Intervention, or Outcome, and then hit the Add button (upper right in the image below). +  - Enter each concept, then hit the Enter button, this will move them under Concepts.
-  - Optionally, leave a note.+
   - Continue adding terms until you have enough terms to identify your specific topic area (**Recommended**: 2 to 5 terms per category).   - Continue adding terms until you have enough terms to identify your specific topic area (**Recommended**: 2 to 5 terms per category).
  
-{{:wiki:autolit:search:img117.png?nolink&  }}+{{ :undefined:se.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> <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>
  
 +{{ :undefined:se4.png?nolink |}}
  
-==== 3. Edit PICO Details ====+<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>
  
-When you have completed the tasks above, you will have unstructured terms of interest, but no grouping of terms and no information yet populated to the Abstracts, RoboPICO, Topic Modeling, and Keywords. 
  
-To proceed, click on "PICO detail" in the right to view, add, and group together PICO elements.+==== 3. Edit Concepts ====
  
-{{:wiki:autolit:search:img118.png?nolink&  }}+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, you can drag and drop a group into the concepts box to expand. 
 + 
 +{{ :undefined:se2.png?nolink |}}
  
 ---- ----
Line 38: Line 40:
 ==== 4. Group together PICO elements ==== ==== 4. Group together PICO elements ====
  
-  - Drag and drop the Group box from the right-side panel to the respective PICO section.{{:wiki:autolit:search:img119.png?nolink&  }} +  - Drag and drop the Group box into the concepts box. 
-  - 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+  - 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.
  
-{{:wiki:autolit:search:img120.png?nolink&  }} +{{ :undefined:se3.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>+
  
  
Line 50: Line 51:
 To populate Abstracts, RoboPICO, Topic Modeling, and Keywords: To populate Abstracts, RoboPICO, Topic Modeling, and Keywords:
  
-  - In the PICO Detail, select "Update Exploration Records" in the bottom right hand corner. +  * Select the "Refresh Exploration" button
-  - 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.+
  
-{{:wiki:autolit:search:img121.png?nolink&  }}+{{ :undefined:se5.png?nolink |}}
  
-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.+  * A modal will appear while Search Exploration refreshes. This may take a minute, since this will run a pre-search of PubMed.
  
 +{{ :undefined:refresh.png?nolink |}}
  
 +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.
 ===== How to Interpret Search Exploration Findings ===== ===== How to Interpret Search Exploration Findings =====
  
Line 69: Line 70:
 Skim through abstracts retrieved through your search exploration terms. Skim through abstracts retrieved through your search exploration terms.
  
-{{:wiki:autolit:search:img122.png?nolink&  }}+{{ :undefined:seabs.png?nolink |}}
  
 The purpose of reviewing Abstracts should be to: The purpose of reviewing Abstracts should be to:
Line 81: Line 82:
 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]]. 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]].
  
-{{:wiki:autolit:search:img123.png?nolink&  }}+{{ :undefined:seabs2.png?nolink |}}
  
 The purpose of RoboPICO should be to: The purpose of RoboPICO should be to:
Line 87: Line 88:
   - Identify the most common topics of underlying abstracts, and   - 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).   - 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. 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.
- 
-{{:wiki:autolit:search:img124.png?nolink&  }} 
  
 <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> <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>
Line 101: Line 98:
 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:search:img126.png?nolink&  }}+{{ :undefined:seabs3.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. 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.
Line 112: Line 109:
 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:search:img127.png?nolink&  }} +{{ :undefined:seabs4.png?nolink |}}
- +
-{{:wiki:autolit:search:img128.png?nolink&  }}+
  
  
Line 123: Line 118:
 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 your Abstract, RoboPICO, Topics, and/or Keywords contain mostly relevant content and minimal extraneous records or concepts.
  
-It is useful to **check the total number of records**  returned from your query (see Test on PubMed in [[:wiki:autolit:search:query_builder|]]). There is no 'right' number of records, but a good rule of thumb is to return:+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 |}} 
 + 
 +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
Line 129: Line 132:
  
 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. 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:searchexplorfinalize.png?nolink |}}
  
 ==== What comes after Search Exploration? ==== ==== What comes after Search Exploration? ====
  
-When you are finished with Search Exploration, proceed to review, test, and finalize your search string in [[:wiki:autolit:search:query_builder|]]!+When you are finished with Search Exploration, proceed to review, test, and finalize your search string in [[:wiki:autolit:search|Lit Search]]!
  
  
wiki/autolit/search/exploration.1672937380.txt.gz · Last modified: 2023/01/05 16:49 by kevinkallmes

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
CC Attribution-Share Alike 4.0 International Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki