This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is there a way to convert GENE common name into IDs

I have a database of genes, and the only ID I have for the genes are the common name, i.e. COMT, ACE, NRF2, PON1. I need to find a way to get more universally accepted IDs to go with them, like Uniprot IDs. Also I need to find the name of the protein to go with it.

Do genes and proteins have universal IDs? Also I'm having this same issue with ligands, I have a database of common names like dopamine, sertraline, lamitrogine etc., if I'm going to feed these into APIs, I'm guessing I need a universal ID for them.

On this page: https://www.infino.me/gene/COMT/ they call the gene COMT and they call its protein 4xue. What is 4xue? Is that a universal ID for the protein? How would I go about finding these 4 letter codes for my genes? I have thousands of genes in the DB so I need a way to scrape this somehow

gene
• 1,852 views • link
written by entheologist33 • entheologist33

1 answer

Unfortunately genes and proteins do not have universal ID's. Different organisms may have different names for the genes. Situation in human/mouse is better since there are HUGO names that are standardized for most genes.

You could search UniProt, NCBI Gene or NCBI's homologene database with your gene names to see what you get. You can use programmatic means (API) to access NCBI data.

4xue is a protein data bank identifier (PDB ID). PDB is a database of protein structures. Information in PDB can also be access via an API.

For the ligands you can take a look at Open Target database, Drugbank and PharmGKB..

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this