This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How do I retrieve withdrawn or replaced gene id for homosapiens from ncbi gene ?

I want to retrieve withdrawn or replaced gene id for homosapiens from ncbi gene. I accessed the ftp site using this link.

The file gene_history.gz for all the organisms. But the file does not give organism information.

ncbi eutils
• 1,195 views • link
updated by Ram Ram • written by DareDevil DareDevil

1 answer

Hi, The first column of the file is the taxid. For H. sapiens, the id is 9606. If you search for all the lines starting in 9606 and extract the values from the third column (Discontinued_GeneID), you should get a list of withdrawn taxids. Like this:

grep "^9606" gene_history | cut -f3 > Hsapiens_withdrawn-genes.txt

I hope it helps.

• 0 views • link
written by MirianT_NCBI • MirianT_NCBI

Log in to answer this question.

More posts like this