emma-wilson/syngap-sr
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# SYNGAP SR Code for my PhD thesis systematic review "Heterogeneity in Syngap1 rodent seizure phenotype: a systematic review and meta-analysis" registered on PROSPERO https://www.crd.york.ac.uk/PROSPERO/view/CRD42024596586 ## 2024-10-30 SEARCH Searches conducted of PubMed, Embase, Scopus and WOS on 30 October 2024. In total there were 811 searh results. Results were downloaded in formats compatible with EndNote 20 for Desktop. Results were imported into an EndNote library. A label column was created for each: - Pubmed: 'pubmed-' & Accession Number (e.g. pubmed-0000), matching SOLES format - Embase: 'embase-' & Accession Number (e.g. embase-0000), where no accession number was given, x1, x2, x3, etc. was used (e.g. embase-x1) - Scopus: the accession number for Scopus used in SOLES is not a field in the scopus EndNote export but it is part of the URL field. As EndNote does not allow advanced find and replace, formatting of Scopus labels will need to be done in R (e.g. scopus-0000) - WOS: 'wos-' & Accession Number (e.g. wos-0000), matching SOLES format Individual search result files and the combined Endnote file are in the '01_search' folder. Note that the WOS extended search was conducted after the first round of deduplication and these results were added in separately. ## 2024-10-30 DEDUPLICATION I read in the EndNote search file and formatted the label column. This was then transferred to the Record ID column so it could be used as an ID. I also made sure the source column contained each database name. NOTE: I did two rounds of deduplication because I had to add in WoS extended search. I dedplicated using ASySD. In total, 516 duplicates were removed. 512 duplicates were removed via automated dedup. 4 additional duplicates were removed via manual deduplication. 324 unique records remained. ## 2024-10-31 PDF RETRIEVAL Of the 324 unique records, 306 had a DOI. I used EndNote to retrieve PDFs. I was able to download 168 PDFs automatically. I had to hand search for 117. ## 2024-10-31 SCREENING I uploaded 324 records from the initial search/deduplcation to SyRF along with the PDF files. I wrote a screening guide to help with screening. ## 2025-01-08 SCREENING RECONCILIATION Reviewers disagreed on 53 publications, which had to be reconciled. In the end, 18 records met the inclusion criteria, however after removal of abstracts and preprint versions of published records, this was reduced to 13. ## 2025-01-08 RETRACTIONS I searched etraction watch and PubPeer and could not find any comments or retractions related to the included publications. ## 2025-03-10 DATA CLEANING AND ANALYSIS I cleaned and analysed my own data for my thesis.