How to get a list of all human protein targets and their target class? UniProt or ChEMBL?

Question

[Leanna]

Dear all,

I would like to gain (a) an up-to-date number for all human proteins, (b) the list of all human proteins (and their target classes). My thoughts after googling, searching forum (e.g.https://www.biostars.org/p/2619/) and reading literature are as follows:

I could use ChEMBL to get both a number and a list of all human targets (which have been explored), together with their target classes.

But what happens, when a human protein target has not been explored? I could parse UniProt for more human protein targets, but then I would probably get the different protein modifications of one human protein target, and also, I don't think that I can extract target classes from UniProt.

What would you suggest?

Many thanks for any suggestion! Leanna

[Pierre Lindenbaum]

(a) a number for all human proteins

42

[Leanna]

If only it were that easy ....

Answer 1

[GenoMax]

You can get all human proteins (currently manually validated) from UniProt. There are 20258 as of this writing.

What exactly do you mean by target? You can explore that using OpenTargets or LINK, both from EMBL. There is an API available for OpenTargets to get information programmatically.

Answer 2

[Leanna]

Dear Genomax,

Many thanks & sorry for the late reply! Your links seem to be what I was looking for!

To clarify a few points:

• I was looking for a list of all human proteins, which is what you have given me in the first link

• I was looking for a list of target classes for all proteins, e.g. like the target classes in ChEMBL (https://www.ebi.ac.uk/chembl/target/browser) I have found the following example : https://www.proteinatlas.org/humanproteome/proteinclasses (e.g. http://www.uniprot.org/docs/7tmrlist) and will search further.

Again, many thanks!

with best wishes, Leanna