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Synthesis Video Tutorials

The following are video tutorials for how to work with Synthesis.
synthesis_v2.3_summary_sheet.pdf
File Size: 371 kb
File Type: pdf
Download File

synthesis_flowchart_-_march_2014.pdf
File Size: 52 kb
File Type: pdf
Download File

Linux or Java Version usage: java -jar -Xmx1g Synthesis.jar)

A Synthesis Project in Ten Steps

Step 1 - Registration

  • Starting Synthesis for the first time
  • Creating a Project 
  • Registration of Synthesis









Step 2 and 3 - Importing References and de-Duplication

  • Importing References from PubMed
  • De-Duplication
  • hint: when de-duplicating keep a list of unique concepts from the abstract you may want to collate later (i.e. simulation, six sigma, etc)






Step 4 and 5 - Configure Settings and Inclusion/Exclusions

  • Configure Project Setting (Project Title and Description)
  • Highlight Keywords
  • Add Exclusion Reasons
  • Ctrl-I (Include) or Ctrl-O (Exclude)
  • Search Feature (year:, title:, abstract:, author:, journal:, and mesh:)






Step 6 - Downloading Papers 

  • Automated Download of Included PDFs
  • Individual Download of PDF
  • Manually Importing PDF into Synthesis








Step 7 and 8 - Custom Columns and Exporting CSV

  • Create Custom Data Collection Columns
  • Automate Data Collection
  • Exporting to CSV file (Excel, R, Stata)
  • Search Custom Column (custom_<columnname>:<value>)



Step 9 is Export to RIS format for Cite and Write (RefWorks, EndNote)
Step 10 is cite Synthesis in your Paper



Synthesis Info - Dual Reviewers 

  • Primary and Secondary Reviewers
  • Export Project
  • Import Project








Step 10 - Cite Synthesis

Yergens D, Ray J, Doig CJ: KSv2: Application for Enhancing Scoping and
Systematic Reviews, American Medical Informatics Association (AMIA) 2012 Annual Symposium; 2012. November 2012. (poster)


Methods Write up Example from: 

Yergens DW, Dutton DJ, Patten SB: An overview of the statistical methods reported by studies using the Canadian community health survey. BMC Medical Research Methodology 2014, 14:15  

Data management and custom software
Once references were identified for inclusion by our literature search strategy, they were imported into a custom Java-based program that was used to facilitate the management of references and PDF documents. This software was created by DWY [9] and utilized for this project, hereafter “ Synthesis ” (www.synthesis.info). Synthesis uses the open-source Apache Lucene [10] database, which is a searchable database designed for the management and retrieval of textual information.
Lucene has been applied to medical and biology Information Retrieval projects in the past [11,12]. Synthesis uses Lucene's text search abilities to find key words or phrases in an article, similar to what can be done in most commercially available word processors by using the "find" com-
mand. Lucene is also able to search information within tables, as long as the table has not been embedded in the PDF as an image. The software then summarized, counted, and organized the identified keywords. These organized results included bibliographic information for each document, the electronic copy of that document with keywords identified in the document, and identified keyword variables that can later be filtered or otherwise manipulated (similar to values stored in a spreadsheet  program). Using this software greatly increased the speed with which this literature search and analysis could be completed, thereby increasing the volume of articles that could be feasibly searched.

[9] Yergens D, Ray J, Doig CJ: KSv2: Application for Enhancing Scoping and Systematic Reviews, American Medical Informatics Association (AMIA) 2012 Annual Symposium; 2012. November 2012. (poster)
[10] McCandless M, Hatcher E, Gospodnetic O: Lucene in action. 2nd
editionStanford, CT USA: Manning Publications Co; 2010.
[11] Spat S, Cadonna B, Rakovac I, Gutl C, Leitner H, Stark G, Beck P: Enhanced information retrieval from narrative German-language clinical text documents using automated document classification. Stud Health TechnolInform 2008, 136:473 – 478.




Additional Synthesis Video Features:

Synthesis Info - Hints and Tips 

  • Change Synthesis Project Directory (i.e. dropbox)
  • Highlight Keywords (Abstract and Full-Text)
  • Crl-I and Ctrl-O Hotkeys for Include (In) and Exclude (Out)
  • Projects saved under <user home directory>/Synthesis
  • Backups and/or Cloning a Synthesis Project
  • Change Projects






Synthesis Info - Tabs 

  • Paper
  • Stats
  • Bibliography
  • BibTex
  • Duplicates
  • Wordcloud





Synthesis Info - Grey Literature

  • Grey Literature
  • BibTex Paste into Grey Literature









Synthesis Info - Sample Columns and Kappa 

  • Creation of Sample Columns (i.e. 10% sampling)
  • Kappa Score of Custom Columns 
  • (note: automated kappa score for inclusion/exclusion occurs under Stats tab)








Synthesis Info - Scan PDFs and Extract Images 

  • Scan other Synthesis Projects for common PDFs
  • Extract images and figures from PDFs (saves them in <user home directory>/Synthesis/<project directory>/images









Synthesis Info - Directories and Backups

  • Synthesis Projects in <user home directory>/Synthesis/<Project>
  • PDFs saved in <Project> directory using format year_author_title.pdf
  • <Project>/images directory contains figures and images from PDF (when menu Tools>Extract PDF Images is used)
  • <Project>/import directory saves all imported reference files
  • Backups and/or Cloning a Synthesis Project