Datasets

[El-psy-k-congroo]

Hello, how do you map proteins into ids? Do you have the name of the protein?Can you share your mapping file?Thank you

[emreg00]

Hi,

Within the context of this package/repo, the following scripts are used for mapping

• parse_ncbi.py gene ids to gene symbols using the files provided by NCBI. Note that the code expects a specific formatted file generated using
  wget ftp://ftp.ncbi.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
zcat Homo_sapiens.gene_info.gz | cut -f 2,3,5 > geneid_to_symbol.txt
• parse_uniprot.py uniprot ids to gene ids using the files provided by Uniprot. Note that the code expects specific formatted files generated using
  wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/HUMAN_9606_idmapping.dat.gz
zgrep Gene_Name HUMAN_9606_idmapping.dat.gz | cut -f 1,3 > uniprot_to_symbol.txt
zgrep GeneID HUMAN_9606_idmapping.dat.gz | cut -f 1,3 > idmapping.tab

Alternatively, you might want to check ID Mapping services from Uniprot. Keep in mind that if you want to keep control on the timestamp/version of the mappings you would need to do it with the local files (using the code above).

Hope this answers your question.

Best,

Emre

[El-psy-k-congroo]

I am very grateful that you can answer me, your reply is very useful to me