Uniprot different names / aliases

Question

[danielfortin86]

Does anyone know how to get a list of all protein aliases for human proteins from Uniprot? The aliases are described here: https://www.uniprot.org/help/different_protein_gene_names

These can be found individually for each protein but I wanted a table / list for all of them

[Ram]

I think you may have to download the entire UniProtKB and run a custom query.

[danielfortin86]

I was hoping that wasn't going to be necessary....

[GenoMax]

Not from UniProt (from NCBI) see my answer here : A: Easiest way to homogenize gene aliases across datasets?

[Ram]

I don't think these line up, GenoMax. The UniProt aliases are full descriptions where NCBI has symbol aliases.

[GenoMax]

Following should produce descriptions as well:

$ esearch -db gene -query "human [orgn]" | efetch | grep -A 2 "Official" | head -11
Official Symbol: TP53 and Name: tumor protein p53 [Homo sapiens (human)]
Other Aliases: BCC7, BMFS5, LFS1, P53, TRP53
Other Designations: cellular tumor antigen p53; antigen NY-CO-13; mutant tumor protein 53; p53 tumor suppressor; phosphoprotein p53; transformation-related protein 53; tumor protein 53; tumor supressor p53
--
Official Symbol: EGFR and Name: epidermal growth factor receptor [Homo sapiens (human)]
Other Aliases: ERBB, ERBB1, HER1, NISBD2, PIG61, mENA
Other Designations: epidermal growth factor receptor; avian erythroblastic leukemia viral (v-erb-b) oncogene homolog; cell growth inhibiting protein 40; cell proliferation-inducing protein 61; epidermal growth factor receptor tyrosine kinase domain; erb-b2 receptor tyrosine kinase 1; proto-oncogene c-ErbB-1; receptor tyrosine-protein kinase erbB-1
--
Official Symbol: TNF and Name: tumor necrosis factor [Homo sapiens (human)]
Other Aliases: DIF-alpha, TNFA, TNFSF2, TNLG1F, TNF
Other Designations: tumor necrosis factor; APC1 protein; TNF, macrophage-derived; TNF, monocyte-derived; TNF-a; tumor necrosis factor ligand 1F; tumor necrosis factor ligand superfamily member 2; tumor necrosis factor-alpha

Answer 1

[GenoMax]

You could also download them from UniProt as a table using: https://www.uniprot.org/uniprot/?query=proteome:UP000005640+AND+proteomecomponent:%22Chromosome+1%22&sort=score

Actual query uses:proteomecomponent:"chromosome 1" AND organism:"Homo sapiens (Human) [9606]" AND proteome:up000005640 (change chromosome number to get tables for all chromosomes).

Configure columns as needed.

Answer 2

[Elisabeth Gasteiger]

You can configure the output format of your search result table to include the columns you want, and then download the results in tab- delimited format. This can be done for any query, including the wildcard query "*" which allows you to retrieve all entries.

See https://www.uniprot.org/help/customize, (video, at about 1min25) or https://insideuniprot.blogspot.com/2015/03) and follow these instructions to include a column for the protein name (or gene names), and remove all columns that you do not wish to see or download.

For example for all reviewed entries, reviewed:yes

default columns, or the columns you had previously selected: https://www.uniprot.org/uniprot/?query=reviewed%3Ayes&sort=score

most columns removed: https://www.uniprot.org/uniprot/?query=reviewed%3Ayes&columns=id%2Centry%20name%2Creviewed%2Cprotein%20names&sort=score

tab-delimited, first 1000 entries: https://www.uniprot.org/uniprot/?query=reviewed:yes&format=tab&limit=1000&columns=id,entry%20name,reviewed,protein%20names&sort=score

(remove "&limit=1000" to get all). This URL can of course be used programmatically (see https://www.uniprot.org/help/api).

BTW we also provide this precomputed file, for all reviewed (i.e. UniProtKB/Swiss-Prot) entries https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/shortdes.txt