R/python script to extract Subcellular locations (Compartments) from Genecards?

Question

[Shicheng Guo]

Dear All,

I'm writing to inquire if anyone has an R or Python script that can extract subcellular locations (compartments) from the GeneCards database. Ideally, the script should take a gene name as input and return a data frame or equivalent structure that displays the subcellular compartments and their corresponding confidence scores, just like the information presented on the GeneCards website. Having such a script would greatly facilitate the automation of retrieving and analyzing subcellular localization data for genes of interest, saving time and effort compared to manually browsing the website.

If anyone has developed or come across such a script, I would greatly appreciate if you could share it or provide guidance on where to find it. Thank you in advance for your assistance.

[Pierre Lindenbaum]

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• R/python script to extract Subcellular locations (Compartments) from Genecards?
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[GenoMax]

the automation of retrieving and analyzing subcellular localization data for genes of interest, saving time and effort compared to manually browsing the website.

Scraping of data from GeneCards site is explicitly not allowed (box in red): https://www.genecards.org/Guide/Datasets. Licensing for commercial use and free academic collaboration agreements are mentioned as options.

Answer 1

[Mensur Dlakic]

I think you have to be willing to work a little bit for your research. You certainly have the experience needed for such an endeavor. Here is what I find by doing a simple GeneCards search on GitHub:

https://github.com/search?q=GeneCards&type=repositories

Any of the top 10 hits seem like they could be useful to you, and at least this one seems very promising:

https://github.com/marswh12312313/GeneSumCrawler