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wiki:autolit:search:exploration [2023/04/08 21:19]
jthurnham [4. Group together PICO elements] 		wiki:autolit:search:exploration [2023/06/06 22:01] (current)
jthurnham [When is Search Exploration finished?]
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 <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>
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 +{{ :undefined:se4.png?nolink |}}
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 +<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>
  
  
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 ==== 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.
  
 {{ :undefined:se3.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> 
  
  
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 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 =====
  
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 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:
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 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:
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   - 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>
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 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.
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 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&  }}+
  
  
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 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. To do so, view the number of records in the bottom 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, where you can also click to view the query on PubMed:
  
-{{:wiki:autolit:search:screenshot_2023-01-05_105115.png?400|}}+{{ :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: There is no 'right' number of records, but a good rule of thumb is to return:
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 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? ====
wiki/autolit/search/exploration.1680988772.txt.gz · Last modified: 2023/04/08 21:19 by jthurnham

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