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wiki:autolit:extraction:export

Exporting Tables

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 Exporting all Data.

Risk of Bias is exported separately from Tagging and Extraction.

Custom Table Export

Custom tables enable you to choose which bibliographic data, tags, and data elements you would like to export. Use this option if:

  1. You want to choose the table type between tables of Study-level data, Study-Arm-level data, or Intervention-level data (i.e., in order to choose what the rows represent).
  2. You want to filter to only a subset of the studies in your nest.
  3. You are seeking to define exactly which columns should be presented.

Throughout the Custom Table build, the page presents a Preview; use this Preview to understand the structure that your exported table will have after you are finished!

On the Nest menu, click “Export”

It should already be opened to Custom Tables; if you navigate away, click the “Custom Tables” toggle to return to this page.

2. Choose Type of Table

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.

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.”

Table of Studies

Export a Table of Studies if you want one row per study, and only if you do not plan to export Data Elements. This is because the only Data Element that is scoped to the Study (rather than Study Arm) is total Study Size.

To choose a Table of Studies, select “Study” in the drop-down, and proceed to Filters and Adding Columns. You will be able to choose among Bibliographic data, Tag data, or Study Size. This will create a table where each row (red box) represents a single study and each header (red arrow) is either a bibliographic attribute or a tag:

Table of Study Arms

Export a Table of Study Arms if you want each arm in each study to have its own row. This is the most similar table type to the Export All Data option below.

This is the most common export type for completing statistical analysis, since it is the only table type that can list the exact data elements from the underlying studies. It will create a table where each row is an arm (so a study, as shown by the boxes, may be split into multiple rows), and can have bibliographic, tag, or data element columns (arrows):

Table of Interventions

Export a Table of Interventions if you want to summarize all data at the level of Interventions. This is the most similar table type to the initial Summary view of Quantitative Synthesis.

This table type will have each Intervention in a row, and the only options for rows will be summaries of the Data Elements for each Intervention:

Table of Tags

Selecting Table of Tags is a specialized option; instead of exporting underlying study information, this exports your tagging hierarchy with basic information about the use of each tag.

If you select this option, you will export a table where each row is a tag, and you will additionally be able to note:

  • The Tag Description
  • The “Depth” of that tag, representing where it is in the hierarchy (0 = Root Tag, 1 = right below Root Tag, etc.)
  • If that tag was configured as a Data Element
  • The frequency of the use of that Exact Tag
  • The Recursive Frequency of that tag, representing how commonly that tag OR any of its children were used

3. Filter (Optional)

If you want to export only the data from a subset of the studies in the nest, use the “Filter To” dropdown after selecting “Table of …”. This will work differently based on the Table Type you selected above:

  • In Tables of Studies, you can filter to studies that have a Tag at or below a certain level.
  • In Tables of Study Arms, you can filter to study arms that have a certain Intervention, a certain Data Element collected for them, or that have a specific Tag at or below a certain level on the corresponding study.
  • In Tables of Interventions, you can filter to studies that have a specific Intervention.
  • In Tables of Tags, you can filter to studies that have a Tag at or below a certain level.

4. Add Columns

Once you have selected the type of Table you are exporting and applied any relevant filters, you can customize what columns will be presented in your exported Table.

Depending on Table Type, you can select:

  • Bibliographic Data: Name, Author, Year, PubMed ID, and/or a Link to the article, among others.
    • 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.
  • Intervention: The Intervention applied to an entire cohort or to a Study Arm.
  • Study/Arm Size: The total number of patients in a Study or an Arm.
  • Data Element: The exact quantitative data associated with a given Study Arm or cohort. Note: Categorical Data Elements cannot be exported in this table structure due to their large column sizes.

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CER-specific Exports

Nested Knowledge offers export of certain data required by the EU MDR 2.7.1 Rev 4 as part of the Clinical Evaluation Report submission process.

Accessing the CER Export page

To access the CER Export page, select Export from the AutoLit menu, and then in the resulting page, toggle to “CER Builder.”

Exporting Documents and Data

In the CER Builder, you have the options of exporting your Literature Search or your Screening activities.

1. Literature Search Export

To export a record of the Search Engines you used, the number of total records, and the number included and excluded from each search (as well as all studies that were added individually), select “Literature Search” from the drop-down.

Then, choose whether to export as a .docx or a .csv, and select “Download.” This will create a document that contains records such as:

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.

Then, choose whether to export as a .docx or a .csv, and select “Download.” This will create a document that contains records such as:

Export All Data

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.

On the Nest menu, click “Export” (same page as Custom Tables above).


2. Toggle "Extracted Data"

At the top of the page, toggle to “Extracted Data”

Choose Included-Only?

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.

If you export Included Records Only (default), no Excluded or Unscreened record will be exported even if data were collected for that specific study.


3. Click "Download"

Click on the “Download” button to automatically save a CSV file (compatible with Excel or other spreadsheet software) to your local computer.

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 Risk of Bias interactive visuals), then do the following:

  1. Navigate to the Export page
  2. Toggle to “RoB” (see visual below)
  3. Choose whether to export Included-only (default) or all studies
  4. 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.
  5. When ready, select “Download.”

wiki/autolit/extraction/export.txt · Last modified: 2022/07/05 22:13 by kevinkallmes