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wiki:practice [2022/02/08 18:31]
nicole_hardy_alumni.brown.edu 		wiki:practice [2022/05/04 17:57]
katcow removed
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       - Focus on the PICO of the review. This stands for Population, Interventions, Comparisons and Outcomes. When it comes to looking through papers during screening, it will be important to look for all four factors in order to include a trial in your review. More about PICO in Step 1.       - Focus on the PICO of the review. This stands for Population, Interventions, Comparisons and Outcomes. When it comes to looking through papers during screening, it will be important to look for all four factors in order to include a trial in your review. More about PICO in Step 1.
   - Create a [[:wiki:autolit:admin:settings|new nest]] to get started on this research question.   - Create a [[:wiki:autolit:admin:settings|new nest]] to get started on this research question.
-  - Click skip when this pops up: (More on this later!) 
- 
-{{  :wiki:trainingpic1.png?nolink&  }} 
  
 **Add a nest description** **Add a nest description**
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   - View our page on [[:wiki:autolit:screening:configure|configuring exclusion reasons]].   - View our page on [[:wiki:autolit:screening:configure|configuring exclusion reasons]].
   - Once you are in your nest, go to the Configure Exclusion Reasons.   - Once you are in your nest, go to the Configure Exclusion Reasons.
-  - By clicking "Add Manual Exclusion," you can configure any reason to exclude a study. These options will be offered in the drop-down of exclusion reasons during screening. <font 11pt/Arial,Helvetica,sans-serif;;inherit;;inherit>**Note: **</font>  Some exclusion reasons can be automated such as publication date. This is done through using “Bulk Actions” and here is a [[https://www.loom.com/share/a792d8bafa6c4077b79533e2714f7804|loom video]] with instructions on how to exclude by publication date. Bulk Actions is a great tool but proceed with caution as it is the fast track to ruining a nest. Only exclude by publication date for now and we will discuss this in more depth later.+  - By clicking "Add Manual Exclusion," you can configure any reason to exclude a study. These options will be offered in the drop-down of exclusion reasons during screening. 
 + 
 +**Note: **Some exclusion reasons can be automated such as publication date. This is done through using “Bulk Actions” and here is a [[https://www.loom.com/share/a792d8bafa6c4077b79533e2714f7804|loom video]] with instructions on how to exclude by publication date. Bulk Actions is a great tool but proceed with caution as it is the fast track to ruining a nest. Only exclude by publication date for now and we will discuss this in more depth later.
  
 **Screen Sequentially** **Screen Sequentially**
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   - Click Screening in the panel on the left-hand side.   - Click Screening in the panel on the left-hand side.
   - Read the title and abstract of the study and include or exclude according to the criteria defined in the protocol.   - Read the title and abstract of the study and include or exclude according to the criteria defined in the protocol.
-  - <font 11.0pt/inherit;;inherit;;inherit>If the abstract contains insufficient information to decide, (sometimes the outcomes of interest are not obvious or included in the title/abstract so it’s best to check the full text when in doubt), select “View Study Source,” which links through to the PubMed site or the DOI of the article.</font>   - <font 11.0pt/inherit;;inherit;;inherit>If you don't have access to the full text, message us via email (include the PMID you're searching for) or try Sci-Hub. If you still cannot find it, after reaching out to us, add the exclusion reason “Full Text Unavailable”.</font>   - <font 11.0pt/inherit;;inherit;;inherit>After reviewing the article, if you determine it should be excluded, select an appropriate exclusion reason, then hit “exclude.”</font>   - <font 11.0pt/inherit;;inherit;;inherit>If you want to include the study, upload a full text PDF of the study to the nest, accessible either through PubMed or an online library subscription, check “Full text review” and hit “include.”</font>   - <font 11.0pt/inherit;;inherit;;inherit>Screen at least 30 studies. Don’t stop until you have at least 6 included studies. If you have screened 30 studies and haven’t yet included at least 6 studies, stop and check in with us. This may be because your literature search may have produced results that are too broad or too specific.</font>   - Once you have 6 included studies, click here: {{:wiki:trainingpic3.png?nolink&  }}{{  https://wiki.nested-knowledge.com//home/ubuntu/nkwiki/dokuwiki/lib/plugins/ckgedit/fckeditor/userfiles/image/wiki/trainingpic3.png?nolink&}} +  - If the abstract contains insufficient information to decide, (sometimes the outcomes of interest are not obvious or included in the title/abstract so it’s best to check the full text when in doubt), select “View Study Source,” which links through to the PubMed site or the DOI of the article. 
-  - Then, click here:+  - If you don't have access to the full text, message us via email (include the PMID you're searching for) or try Sci-Hub. If you still cannot find it, after reaching out to us, add the exclusion reason “Full Text Unavailable”. 
 +  - After reviewing the article, if you determine it should be excluded, select an appropriate exclusion reason, then hit “exclude.” 
 +  - If you want to include the study, upload a full text PDF of the study to the nest, accessible either through PubMed or an online library subscription, check “Full text review” and hit “include.” 
 +  - Screen at least 30 studies. Don’t stop until you have at least 6 included studies. If you have screened 30 studies and haven’t yet included at least 6 studies, stop and check in with us. This may be because your literature search may have produced results that are too broad or too specific. 
 +  - Once you have 6 included studies, click here:{{  :wiki:trainingpic3.png?nolink&  }}{{  https://wiki.nested-knowledge.com//home/ubuntu/nkwiki/dokuwiki/lib/plugins/ckgedit/fckeditor/userfiles/image/wiki/trainingpic3.png?nolink&}} 
 +  - Then, click here: {{  :wiki:trainingpic4.png?nolink&  }}
   - Once it's done loading, click done and refresh the page.   - Once it's done loading, click done and refresh the page.
   - You should now see a probability instead of "train inclusion model."   - You should now see a probability instead of "train inclusion model."
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 **Tasks:** **Tasks:**
   - Under the tagging menu, go to "Configure Tagging."   - Under the tagging menu, go to "Configure Tagging."
-  - Guidelines for creating tags can be found below , but you may modify the tagging hierarchy according to what topics are most relevant to your disease or intervention+  - Guidelines for creating tags can be found [[:wiki:autolit:tagging:configure|below]], but you may modify the tagging hierarchy according to what topics are most relevant to your disease or intervention 
 +  - The tagging hierarchy is essentially the break down of our PICO. From the broadest categories at the top that branch out to more specific categories as you go down.
   - Add Root Tags: A root tag is a tag that has no "parent". Root tags can be added by clicking "Create New Tag" and typing in the Tag name, without selecting a parent tag.   - Add Root Tags: A root tag is a tag that has no "parent". Root tags can be added by clicking "Create New Tag" and typing in the Tag name, without selecting a parent tag.
       - Add the following "baseline root tags" (in this order from left to right):       - Add the following "baseline root tags" (in this order from left to right):
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             - i. Cardiovascular death             - i. Cardiovascular death
  
-**Note:**  Here is a loom video that should help you create your hierarchy. +**Note:**  Here is a [[https://www.loom.com/share/411575c062f74d21928b3937efe5a024|loom video]] that should help you create your hierarchy.
- +
-**NICOLE INSERT LOOM VIDEO**+
  
 ==== Applying Tags ==== ==== Applying Tags ====
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   - Click on [[:wiki:autolit:tagging:tag|Tagging]] in the panel on the left-hand side.   - Click on [[:wiki:autolit:tagging:tag|Tagging]] in the panel on the left-hand side.
-  - Apply the tags to all studies.+  - Apply the tags to all 6 studies.
       - Keep in mind when you apply a tag you want to add relevant text that is the source of the tag. For example, if you tag NYHA class in the study, you will want to write the table you found it in or copy and paste the sentence where they talk about it.       - Keep in mind when you apply a tag you want to add relevant text that is the source of the tag. For example, if you tag NYHA class in the study, you will want to write the table you found it in or copy and paste the sentence where they talk about it.
       - Note: Aren't you glad you uploaded all the full texts in the screening stage? That's why we have you upload full texts while screening.       - Note: Aren't you glad you uploaded all the full texts in the screening stage? That's why we have you upload full texts while screening.
 +      - Be sure to check the supplements for reported data if they aren’t given in the main article. It is useful to do a CTRL + F to search for specific key words in large pdfs.
 +      - After tagging all 6 studies, go back and make sure you tagged the study titled “Effect of Sacubitril-Valsartan vs Enalapril on Aortic Stiffness in Patients With Heart Failure and Reduced Ejection Fraction: A Randomized Clinical Trial” by Desai et al., 2019. This is an important study and is required to be extracted after tagging.
  
 For a complete list of suggested tags, see [[:wiki:autolit:tagging:configure#useful_tags|useful tags]]. If you are still unsure what terms to use as tags: For a complete list of suggested tags, see [[:wiki:autolit:tagging:configure#useful_tags|useful tags]]. If you are still unsure what terms to use as tags:
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   * Consider the general categories of interest (patient characteristics, outcomes, etc)   * Consider the general categories of interest (patient characteristics, outcomes, etc)
  
-**Note:**  Here is a loom video that should help you apply tags. +**Note:**  Here is a [[https://www.loom.com/share/4ca3b6e0dbdc42b8b57e3502ba0054b6|loom video]] that should help you apply tags.
- +
-[[https://www.loom.com/share/4ca3b6e0dbdc42b8b57e3502ba0054b6|Loom Video on Applying Tags]]+
  
 ===== Step 5: Extract Data ===== ===== Step 5: Extract Data =====
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   - Configure interventions hierarchy as shown in Part A in the [[:wiki:autolit:extraction:configure|instructions]].   - Configure interventions hierarchy as shown in Part A in the [[:wiki:autolit:extraction:configure|instructions]].
  
-**Note:**  Here is a loom video you should check out. It should help you configure your hierarchy properly. +**Note:**  Here is a [[https://www.loom.com/share/a676d87ab5564a2788f156f599d3fd24|loom video]] you should check out. It should help you configure your hierarchy properly.
- +
-**NICOLE INSERT LOOM VIDEO**+
  
 **Extract Studies** **Extract Studies**
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   - Note: Median and mean are not interchangeable. IQR and range are not interchangeable. Standard deviation (SD) and standard error (SE) are not interchangeable!   - Note: Median and mean are not interchangeable. IQR and range are not interchangeable. Standard deviation (SD) and standard error (SE) are not interchangeable!
  
-**Note**** :**  Here is a loom video that should help you extract data. +**Note**** :**  Here is a [[https://www.loom.com/share/39cf79d246db48b9b1fdf811b303ca3c|loom video]] that should help you extract data.
- +
-[[https://www.loom.com/share/39cf79d246db48b9b1fdf811b303ca3c|{{:wiki:rackmultipart20220114-4-18mhxpr_html_f7ebd3a4fe982e71.gif?nolink&}}]]+
  
 ===== Step 6: Wrapping Up ===== ===== Step 6: Wrapping Up =====
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   * In our software you can also conduct ROBs. This one is a big one and we'll conduct separate trainings on this. For now, review this page in the [[:wiki:autolit:risk_of_bias|wiki]], and google SIGN ROB to familiarize yourself with it. Don't spend more than 30 minutes googling; we are going to train you on this later.   * In our software you can also conduct ROBs. This one is a big one and we'll conduct separate trainings on this. For now, review this page in the [[:wiki:autolit:risk_of_bias|wiki]], and google SIGN ROB to familiarize yourself with it. Don't spend more than 30 minutes googling; we are going to train you on this later.
  
-Download this file! {{:wiki:hf_practice_nest2.docx|hf_practice_nest2.docx}}+Download {{:wiki:new_hire_version_-_jt_edits.docx|this file!}}
  
  

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