TITLE: Bioinformatics in Sudan-Publications
AUTHORS: Sabah  Ibrahim, Sofia  Ali, Sumaya  Kambal

[DESCRIPTION]
This protocol shows in details how to extract Bioinformatics-related Publications from Sudan. It consists of six sections: PubMed Database Advance Search Bulider, Science Direct Database Advance Search Builder, Citation Manager, Exporting to Excel, Inclusion and exclusion Criteria and Data analysis. 

[STEPS]
SECTION: PubMed Database Advance Search Bulider
2. Start buliding your search by adding Sudan (the country under subject) to the query box under the "Affilation field", then use the Boolean Operators (Add with AND).
SECTION: PubMed Database Advance Search Bulider
1. Open PubMed Advance search bulider (https://pubmed.ncbi.nlm.nih.gov/advanced/)
SECTION: PubMed Database Advance Search Bulider
3. To include papers from 2003 to 2020, under the Date publication field write "2003/01/01" to "present" (at the time writing this paper 2020 was not ended yet). Then use the Boolean operater (Add with AND) and click "add to histroy". 
The outcome will be the following search query:

 ((Sudan[Affiliation]) AND (("2003/01/01"[Date - Publication] : "3000"[Date - Publication]))
SECTION: Science Direct Database Advance Search Builder
7. Go to the Sience direct advance search (https://www.sciencedirect.com/search).
SECTION: Citation Manager
10. Choose your favourite Citation Manager (we used EndNote x9.3.3"Bld 13966") and upload all the resulted files from steps 5 and 8 to EndNote library  "Bioinfromatics_in_Sudan_All_Search_terms.enl"
SECTION: Inclusion and exclusion Criteria
13. Open each article alone and apply the following inclusion and exclusion criteria, you need to focus in each article to extract the required information. These are listed below:

SECTION: Exporting to Excel
12. To export the results to an excel sheet Change the Output style of the artilcles according to the following Sub-steps:

SECTION: Exporting to Excel
12.1. Move to the following path: Edit/Output styles/New style/Bibliography/Templates
SECTION: Exporting to Excel
12.2. Open "Reference types" and choose "Journal Article"
SECTION: Exporting to Excel
12.3. Click on "Insert field" and choose the following in order: 

Year+Tab+Title+Tab+Author+Tab+Journal+ Tab+Volume+ Tab+Issue+ Tab+ DOI.
SECTION: Exporting to Excel
12.4. Exit the window and Save the new style as (Bioinfromatics_in_Sudan_All_Search_terms_excel).
SECTION: Exporting to Excel
12.6. Make a copy from the Orginal file "Bioinfromatics_in_Sudan_All_Search_terms" and then click on "export references" and save the file as a text file (*.txt), then under "Output style" choose the style you created in the above step.
SECTION: Exporting to Excel
12.7. Open a Blank workbook Excel spreedsheet and click on File/Open and then choose the text file you genarated in the above step, a "Text import wizard" window will apear, choose the file type as delimited and then leave every option as default, click next and finish. All results will appear in excel.
SECTION: Exporting to Excel
12.5. Open "Edit/ Find and replace" ,  a window will appear click on "any field" then click on "search" and "enter special carriage return". Add a "semicolon plus a space" to the "change text" tool and just click ok.
SECTION: Citation Manager
11. Remove all the duplicated articles (there is an option in EndNote that can "find duplication", then you can compare all duplicated and remove the similar ones). 

Notice that: some articles have different versions and it can include Journals as full names or as abbreviation and EndNote may fail to discard these duplicated articles, thus you need to complete the rest manually.
SECTION: Inclusion and exclusion Criteria
14. Save the final output of the articles and start the data analysis
SECTION: Inclusion and exclusion Criteria
13.1. Choose articles that are applied to all the below:
 Written in English
Authored by at least one scientist affiliated with a Sudanese institution (Be aware that "Sudan" is mentioned as affilation because some authors are named "Sudan")
Incorporating bioinformatics techniques according to the definition by authors [Luscombe et al. 2001]. 

Luscombe NM, Greenbaum D, Gerstein M. What is bioinformatics? A proposed definition and overview of the field. Methods of information in medicine. 2001;40(04):346-58.
SECTION: Inclusion and exclusion Criteria
13.2. Discard any articles that consit at least one of the folllowings:
Affiliated with South Sudan (now a separate country from Sudan since 2011), 
Available only as abstracts and thus we were not able to confirm whether a Bioinformatics tool was used or not
Review papers (40 papers) due to the lack of a Bioinformatics tool application.
SECTION: Data Analysis
15. Order the articles by years and count the frequency of articles per year, list them in an excel sheet to create the figure.
SECTION: Data Analysis
16. Categorize each article to a research area using the article title, keywords and the Journal scope, then count the frequency of each research area, list them in an excel sheet to create the figure.
SECTION: PubMed Database Advance Search Bulider
4. Add the query search you created in step  3 to the query box by clicking the "Action button" then choose "add query". 
SECTION: PubMed Database Advance Search Bulider
5. Add the query terms ("Next generation sequencing", "Genomics", "Bioinformatics", "Sequencing", "Computational Biology" and "in silico" ) under "All fields" each one at a time (separted from the other) to the query box, then click "add to history" (or search if you want to move directly to the search results). This will result in the following  search querys:

((Sudan[Affiliation]) AND (("2003/01/01"[Date - Publication] : "3000"[Date - Publication]))) AND (Next generation Sequencing)
((Sudan[Affiliation]) AND (("2003/01/01"[Date - Publication] : "3000"[Date - Publication]))) AND (Genomics)
((Sudan[Affiliation]) AND (("2003/01/01"[Date - Publication] : "3000"[Date - Publication]))) AND (Bioinfromatics)
((Sudan[Affiliation]) AND (("2003/01/01"[Date - Publication] : "3000"[Date - Publication]))) AND (Sequencing)
((Sudan[Affiliation]) AND (("2003/01/01"[Date - Publication] : "3000"[Date - Publication]))) AND (Computational Biology)
((Sudan[Affiliation]) AND (("2003/01/01"[Date - Publication] : "3000"[Date - Publication]))) AND (In Silico)
SECTION: PubMed Database Advance Search Bulider
6. Go to the search page of each "query seach", choose sorted by "Best match" and then click "send to citation Manager" , select "All results" and then "create file". Save all the files to a proper repository.
SECTION: Science Direct Database Advance Search Builder
8. Start Buliding your seach according to the below sub-steps
SECTION: Science Direct Database Advance Search Builder
8.1. Add the query terms (mentioned in step 4) each one at a time to the "Find articles with these terms" Field.
SECTION: Science Direct Database Advance Search Builder
8.2. Then under the Year field write "2003-2020"
SECTION: Science Direct Database Advance Search Builder
8.3. Write Sudan under the "Author Affilation" Field. Finallyt, click on "search".
SECTION: Science Direct Database Advance Search Builder
9. In the search results page, select ALL RESULTS and then click on export "export citation to RIS" (or any other choice you prefer). Save the results to a proper repository.