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wiki:autolit:extraction:export [2023/03/22 23:17]
kevinkallmes [Exporting Tables] 		wiki:autolit:extraction:export [2023/12/12 13:25] (current)
kevinkallmes [4. Add Columns]
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-====== Exporting Tables ======+====== Exporting Custom Tables and CER Materials ======
  
-If you'd like to export your collected data into an Excel spreadsheet (CSV file), you can do so by either Custom Table creation or [[wiki:autolit:utilities:inspector:download|Downloading from Inspector]].+If you'd like to export contents from your nest, you can use the Export page or [[wiki:autolit:utilities:inspector:download|Downloading from Inspector]].
  
 <WRAP center round important 60%> <WRAP center round important 60%>
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 Specifically, **all functions** except (1) the Custom Table Builder and (2) the CER Builder are now available under the "Download" button on Inspector. Specifically, **all functions** except (1) the Custom Table Builder and (2) the CER Builder are now available under the "Download" button on Inspector.
 </WRAP> </WRAP>
 +
 +**Use this Export page for:**
 +  * Custom Table Export and
 +  * CER Builder.
 +
 +**Use [[wiki:autolit:utilities:inspector:download|Download from Inspector]] for:**
 +  * Study metadata (CSV or RIS Files)
 +  * Screening decisions
 +  * Tags & Tag Contents
 +  * Extracted Data
 +  * Critical Appraisal
 +  * All Full Text PDFs
  
  
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 Under Synthesis, click "Export" Under Synthesis, click "Export"
  
-{{:wiki:autolit:extraction:img38.png?nolink&  }}+{{ :undefined:customcer.png?nolink |}}
  
 It should already be opened to Custom Tables; if you navigate away, click the "Custom Tables" toggle to return to this page. It should already be opened to Custom Tables; if you navigate away, click the "Custom Tables" toggle to return to this page.
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 Click on the drop-down menu under "Table of" in order to choose whether you would like a table showing elements from the study as a whole, the various study arms in each study (placebo, intervention groups, etc.), or across all interventions. Click on the drop-down menu under "Table of" in order to choose whether you would like a table showing elements from the study as a whole, the various study arms in each study (placebo, intervention groups, etc.), or across all interventions.
  
-{{:wiki:autolit:extraction:img39.png?nolink&  }}+{{ :undefined:studyarm.png?nolink |}}
  
 **Note** that if you want to be able to export/download any extracted data––to create tables for a manuscript, for example––you must select Table of "Study Arm." **Note** that if you want to be able to export/download any extracted data––to create tables for a manuscript, for example––you must select Table of "Study Arm."
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   * **Bibliographic Data:**  Name, Author, Year, PubMed ID, and/or a Link to the article, among others.   * **Bibliographic Data:**  Name, Author, Year, PubMed ID, and/or a Link to the article, among others.
 +      * Related Report Families can be identified as one of the pieces of Bibliographic data, with either the custom name or Author, Year of the Primary report.
       * To add all citation information in one cell, select "Citation" from the Attribute drop-down.       * To add all citation information in one cell, select "Citation" from the Attribute drop-down.
   * **Tag:**  The tag names and tag text excerpts at or below a given tag.   * **Tag:**  The tag names and tag text excerpts at or below a given tag.
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 {{  https://wiki.nested-knowledge.com//home/ubuntu/nkwiki/dokuwiki/lib/plugins/ckgedit/fckeditor/userfiles/image/wiki/autolit/screenshot2021-10-11at5.11.52pm.png?nolink&  }} {{  https://wiki.nested-knowledge.com//home/ubuntu/nkwiki/dokuwiki/lib/plugins/ckgedit/fckeditor/userfiles/image/wiki/autolit/screenshot2021-10-11at5.11.52pm.png?nolink&  }}
 +
 +=== Including Tag Tables ===
 +
 +If you have configured and extracted data in tag tables, you can add individual tags to your custom table or add all table contents. To do so, under the columns dropdown select "Exact Tag" and you will see both options. Tags with an associated table will have a table icon next to them allowing you to pick and choose:
 +
 +{{  :undefined:screenshot_2023-10-02_at_16.18.23.png?nolink&  }}
 +
 +Or select "All Table Contents" at the top.
 +
 +{{  :undefined:screenshot_2023-10-02_at_16.17.12.png?nolink&  }}
 +
 +When multiple tables are added, NK attempts to join columns that share similar names to reduce duplicate columns. In the below example, both the Age and Sex tables had a column for "Group" with rows for "Adult" and "Children" so they are joined for the purposes of exporting a custom table as you can see in the preview:
 +
 +{{  :undefined:screenshot_2023-10-02_at_16.20.53.png?nolink&  }}
 +
 +If this is incorrect, you can manually unjoin them by clicking the icon between tag tables listed (circled in red below) and clicking "X" on the incorrect joining (circled in blue below). Here you can also manually join other column names as appropriate (circled in green).
 +
 +{{  :undefined:screenshot_2023-10-02_at_16.28.38.png?nolink&  }}
 +
  
 ==== 5. Reorder Columns ==== ==== 5. Reorder Columns ====
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 {{ :wiki:autolit:extraction:doi2.png?nolink |}} {{ :wiki:autolit:extraction:doi2.png?nolink |}}
  
-===== CER-specific Exports =====+==== Advanced Settings ====
  
-Nested Knowledge offers export of certain data required by the [[https://ec.europa.eu/docsroom/documents/17522/attachments/1/translations/en/renditions/native|EU MDR 2.7.1 Rev 4]] as part of the [[https://eumdr.com/clinical-evaluation-process/|Clinical Evaluation Report]] submission process.+Once you start customizing your table, you can also toggle with the advanced setting. 
  
-==== Accessing the CER Export page ====+{{ :undefined:screenshot_2023-11-21_at_12.46.38.png?nolink |}}
  
-To access the CER Export page, select Export from the AutoLit menu, and then in the resulting page, toggle to "CER Builder."+By default, when you add multiple tag columns to your table that are organized under separate root tags in the hierarchy, they will be exported into separate sheets within your workbook. This can be helpful to organize large datasets. This can be turned off by unchecking the box, and all columns will be encompassed in a single sheet.
  
-{{:wiki:autolit:extraction:img41.png?nolink&  }}+{{ :undefined:screenshot_2023-11-30_at_15.27.38.png?nolink |}}
  
 +=== Multiple Tag Columns ===
  
-==== Exporting Documents and Data ====+See below for an example of tags organized under separate root tags. Specifically, the tags "Treatments" and "Clinical Effectiveness Evidence" (circled in red) belong to different root tags (circled in orange). 
  
-In the CER Builder, you have the options of exporting your Literature Search or your Screening activities.+{{ :undefined:screenshot_2023-11-30_at_14.52.18.png?nolink |}}
  
-=== 1. Literature Search Export ===+If you were to add both these tags as columns in your custom table...
  
-To export a record of the Search Engines you used, alongside specific queries used, the number of total records returned, duplicates found and the number included and excluded from each search (as well as all studies that were [[:wiki:autolit:search:manualaddition|added individually]]), select "Literature Search" from the drop-down.+{{ :undefined:screenshot_2023-11-30_at_15.04.12.png?nolink |}}
  
-Then, choose whether to export as a .docx or a .csv, and select "Download." See below for an example. Searches are listed in chronological order from top to bottom by when they were first ran in your nest. The duplicate column refers to the number of duplicates found in the corresponding search, compared to the studies already in the nest and therefore returned by previous searches.+...the export will separate their data into separate sheets within your workbook to mimic the structure of your hierarchy. Note: adding additional tag columns from under the same root tag will be encompassed in this same sheet and the initial bibliographic columns are maintained in each sheet.
  
-{{:wiki:autolit:admin:cer.png}}+Sheet 1:
  
-=== 2. Screening Export ===+{{ :undefined:screenshot_2023-11-30_at_15.23.28.png?nolink |}}
  
-To export a record of all studies Screened in your nest, with full citation information and links to full texts, as well as the Screening status and (if excluded) the Exclusion Reason, select "Screening" from the drop-down.+Sheet 2:
  
-{{:wiki:autolit:extraction:img42.png?nolink&  }}+{{ :undefined:screenshot_2023-11-30_at_15.24.52.png?nolink |}}
  
-Then, choose whether to export as a .docx or a .csv, and select "Download." This will create a document that contains records such as:+However, unchecking advanced settings ensures all data is encompassed within one sheet in your workbook: 
  
-{{:wiki:autolit:admin:cer2.png?nolink&}}+{{ :undefined:screenshot_2023-11-30_at_15.32.00.png?nolink |}}
  
 +**When your table is customized with the settings of your choice, click Download.**
 +===== CER-specific Exports =====
  
-===== Export All Data =====+Nested Knowledge offers export of certain data required by the [[https://ec.europa.eu/docsroom/documents/17522/attachments/1/translations/en/renditions/native|EU MDR 2.7.1 Rev 4]] as part of the [[https://eumdr.com/clinical-evaluation-process/|Clinical Evaluation Report]] submission process.
  
-Use Export All Data if you want to obtain a Study Arm-level spreadsheet containing the bibliographic data, Interventions, Arm Sizes, and all Data Elements for a nest.+==== Accessing the CER Export page ====
  
-==== 1. Navigate to Export ====+To access the CER Export page, select Export from the AutoLit menu, and then in the resulting page, toggle to "CER Builder."
  
-On the Nest menu, click "Export" (same page as Custom Tables above).+{{ :undefined:certabletype.png?nolink |}}
  
-----+==== Exporting Documents and Data ====
  
-==== 2. Toggle "Extracted Data" ====+In the CER Builder, you have the options of exporting your Literature Search or your Screening activities.
  
-At the top of the page, toggle to "Extracted Data"+=== 1. Literature Search Export ===
  
-{{:wiki:autolit:extraction:img43.png?nolink&  }}+To export a record of the Search Engines you used, alongside specific queries used, the number of total records returned, duplicates found and the number included and excluded from each search (as well as all studies that were [[:wiki:autolit:search:manualaddition|added individually]]), select "Literature Search" from the drop-down.
  
-=== Choose Included-Only? ===+Then, choose whether to export as a .docx or a .csv, and select "Download." See below for an example. Searches are listed in chronological order from top to bottom by when they were first ran in your nest. The duplicate column refers to the number of duplicates found in the corresponding search, compared to the studies already in the nest and therefore returned by previous searches.
  
-For this option, the only configuration choice you have is whether to restrict to Included Records Only; you can simply export all data at the Study Arm level.+{{:wiki:autolit:admin:cer.png}}
  
-If you export Included Records Only (default), no Excluded or Unscreened record will be exported **even if data were collected for that specific study.**+=== 2. Screening Export ===
  
-----+To export a record of all studies Screened in your nest, with full citation information and links to full texts, as well as the Screening status and (if excluded) the Exclusion Reason, select "Screening" from the drop-down.
  
 +{{:wiki:autolit:extraction:img42.png?nolink&  }}
  
-==== 3. Click "Download" ====+Then, choose whether to export as a .docx or a .csv, and select "Download." This will create a document that contains records such as:
  
-Click on the "Download" button to automatically save a CSV file (compatible with Excel or other spreadsheet software) to your local computer. +{{:wiki:autolit:admin:cer2.png?nolink&}}
- +
-Keep in mind that all data elements are broken out by their constituent parts (e.g. Mean, SD, N) into separate columns and are separated by timepoint. Rows in the spreadsheet will correspond to the various study arms. +
- +
- +
-===== Exporting Risk of Bias ===== +
- +
-Risk of Bias outputs are exported separately from all other study data. If you would prefer to export Risk of Bias (rather than using the Synthesis [[:wiki:synthesis:rob|Risk of Bias interactive visuals]]), then do the following:+
  
-  - Navigate to the Export page 
-  - Toggle to "RoB" (see visual below) 
-  - Choose whether to export Included-only (default) or all studies 
-  - If your Risk of Bias was assessed at the Data Element level, select which Data Element(s) to export. If your Risk of Bias was study-level (as in the visual below), this option will be greyed out. 
-  - When ready, select "Download." 
  
-{{:wiki:autolit:extraction:img44.png?nolink&  }}+===== Export All Data or Export RIS Files =====
  
 +These functions have been moved to [[wiki:autolit:utilities:inspector:download|Download from Inspector]].
  
wiki/autolit/extraction/export.1679527021.txt.gz · Last modified: 2023/03/22 23:17 by kevinkallmes

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