How to get articles that have used enrichment tools?

[markziemann]

The desired criteria are:

• used some sort of enrichment analysis
• high journal impact factor

It would be impractical to search full text or in all bibliographies.

[markziemann]

One strategy is to look at "cited by" articles for commonly used tools. For example, DAVID recommends users cite two articles:

• https://pubmed.ncbi.nlm.nih.gov/35325185/
• https://pubmed.ncbi.nlm.nih.gov/19131956/

We can look at the "cited by section". PMID: 19131956 has 18k results and PMID: 35325185 has just 391.

It can be downloaded in different forms, from normal citation, to csv, to medline formats.

[markziemann]

The next step is to figure out how to match up the journal to the impact factor. This could be a time sink if it needs to be done manually.

[markziemann]

JIF is paywalled, but SJR can be downloaded from here: https://www.scimagojr.com/journalrank.php?min=200&min_type=cd

As for setting a threshold, here are some interesting SJR scores:

• Nature communications is 5.1
• Genome research 4.9
• PNAS 4.0
• Gigascience 3.7

Based on this, <3 is low, >5 is high and 3-5 is middle. Will discuss with Team

JCR data can be read into R with the following:

sjr <- read.csv("scimagojr 2022.csv",header=TRUE,sep=";")

Then it can be filtered for high impact papers.

Then, using the ISSN as the key, the SJR score can be added to the citations.