SEMI-AUTOMATED ONLINE ABSTRACT SCREENING USING ABSRACKR Technical Report
In this report, we are using a semi-automated, online, free software called Abstrackr developed by the Center of Evidence Based Medicine. The present methods were explained and discussed by members of Medical Research Group of Egypt during a systematic review workshop in October, 2015.
Semi-automated Online Abstract Screening Using Absrackr - Technical Report Mohammed Yasser Elsherbeny1,2, Ahmed Negida1,3*
ABSTRACT Systematic reviews are defined as a summarized scientific approach, with predetermined methods that collect, appraise, and communicate the results of multiple primary research. Systematic reviews start with a specific research question supported by obvious eligibility criteria and detailed description of methods of evidence synthesis. The process includes a rigorous search of the literature including multiple relevant electronic databases then screening the retrieved citations for relevant records. In our previous record, we showed how to export citations from multiple databases and manage them using EndNote. Herby, we present an approach for abstract screening easier than manual screening. In this report, we are using a semi-automated, online, free software called Abstrackr developed by the Center of Evidence Based Medicine. The present methods were explained and discussed by members of Medical Research Group of Egypt during a systematic review workshop in October, 2015.
1Medical
Research Group of Egypt
2Faculty
of medicine, Mansoura University, Egypt
3Faculty
of medicine, Zagazig University, Egypt
Correspondence to Ahmed Negida; Faculty of Medicine, Zagazig University, Zagazig, El-Sharkia, Egypt. Tel: +201125549087 and +201150333699; Email:
[email protected]
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Open an internet browser and type (http://abstrackr.cebm.brown.edu) at the URL box, the home page will be appear as shown in the (figure 1).
(Figure 1): Home page of abstracher.cebm.brown.edu
If you already have an account, type the username and the password and press (Submit), if not you will have to create a new account by pressing (register here) as shown in (figure 2).
(Figure 2): Login fields and register here option to create a new account.
Create your account by filling the information need (first name, last name, number of systematic reviews you participated at, e-mail, username and password) then press (sign me up) as shown in (figure 3) then log in.
(Figure 3): sign up page to create a new account.
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After logging in the workspace page will appear, to create a new systematic review project press (Start a new project/review) as shown in (figure 4).
(Figure 4): the workspace page and how to create a new project/review.
You will be asked to submit few details about the review you are conducting (Project name, project description, upload the file that contains the results of the systematic search of the databases, screening mode, the order of the abstracts, pilot round size and tag visibility) then press (Create new review) as shown in (figure 5). You can import a few different file types/formats into Abstracker. The easiest (and suggested) file format is a list of PubMed IDs, one-per line. Such a list can be exported directly from the PubMed search results page as follows. Click Send to, then select PMID List as the Format. Abstrackr will fetch the corresponding titles and abstracts for each id as shown in (figure 6,7).
(Figure 5): submission of the details required for the systematic review, import a file to Abstracker and how to create new review.
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(Figure 6): How to export a PMID list file form pubmed.
(Figure 7): How to export a PMID list file form pubmed.
After creating your review project, you will be able to share this project with other participants through a direct link. Press (Ok, go to my home screen) as shown in (figure 8).
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(Figure 8): Successfully creation of a new review project.
At the homepage you can find the details of the new review project (name, number to screen, screened so far, assigned, due and actions) from (Actions) section press (Screen) as shown in (figure 9).
(Figure 9): the details of the review project and (screen) button.
At the screening page you can find the available details of the article (Title, authors abstract, and journal). Also you can find at the bottom of the page three buttons, green one to include this article according to the predetermined inclusion criteria, red button to exclude the article and a white button in between that indicates you cannot appraise this article from the title and abstract, as shown in (figure 10). You can press (review This work is protected by MRGE; Publishing, reusing or printing this file is strictly prohibited.
labels) to see your progress. Abstracker use number (1) for the included articles, number (-1) for the excluded articles and number (0) for the articles that you are not sure about as shown in (figure 11).
(Figure 10): the screening page shows the available details of the article, the selection buttons and (review labels) button.
(Figure 11): review labels showing the progress and results of the screening.
During screening process you can add few terms/words to help you either include or exclude this article. After adding theses terms/words Abstracker will highlight the matched terms/words by blue, green, burble or red color according to how these terms/words will help in
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include or exclude this article, as shown in (figure 12).
(Figure 12): using highlighted terms/words to help in including or excluding the article.
After finishing your screening process the page shown in (figure 13) will appear, then press (my projects).
(Figure 13): After finishing the screening process, return to the projects page.
At my projects page you will find the review project, press (Export) to save the results of the screening to your device. Choose the export labels you want at the export file then press (export). A direct link for the exporting file will appear, press the link and an excel file will be saved to your device, as shown in (Figures 14-16).
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(Figure 14): the projects page and export button.
(Figure 15): selecting the export labels needed for the export file.
(Figure 16): the direct link for the exported file. This work is protected by MRGE; Publishing, reusing or printing this file is strictly prohibited.
After download the exporting excel file, you can see the labels you have chosen and the results of your screening process as shown in (Figure 17).
REFERENCES 1- Abstrackr: Software for Semi-Automatic Citation Screening - Abstract - Final | AHRQ Effective Health Care Program. http://effectivehealthcare.ahrq.gov/index.cfm/search-forguides-reviews-and-reports/?productid=985&pageaction=displayproduct Accessed December 26, 2015. 2- Rathbone J, Hoffmann T, Glasziou P. Faster title and abstract screening? Evaluating Abstrackr, a semi-automated online screening program for systematic reviewers. Syst Rev. 2015;4(1):80. doi:10.1186/s13643-015-0067-6. 3- Negida A. MRGE REPORT 1 : How to Export Citations from Multiple Databases and Check Duplications during Systematic Review.; 2015. doi:10.13140/RG.2.1.1067.7844.
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