[WikiPathways | BridgeDb] Uniprot-TrEMBL -> UniProtKB transition

[Egon Willighagen]

Hi everyone,

Tooba and I had a meeting this week about the UniProt datasource and the use in WikiPathways. Right now, BridgeDb and WikiPathways uses "Uniprot-TrEMBL" as full name of the datasource, noting that using two datasources (for TrEMBL and SwissProt) was not user-friendly enough, and we accepted the misnaming as downside.

Since then, and the above practice goes back at least 11 years, more and more people started using just "UniProtKB" and over the past months we discussed we basically wanted to migrate. This is going to be a big effort, not as big as the new WikiPathways website, but big nevertheless. And the impacts and risks are considerably, so we have to do this in a modern, branched way, until we are sure we can role it out without disrupting important data analysis in research.

To aid this transition, Tooba in I discussed in our meeting the steps, roughly. And I have just set up a "Project" on GitHub to support us. Tooba and I will coordinate this, but it's an open project, of course, and many people will have to give input and even do work. I am fairly sure, for example, that the current lists of tasks on the Project is incomplete. That is also the role of this list: to see what we are forgetting.

So, without further ado: https://github.com/orgs/bridgedb/projects/2/

Egon

[Alex Pico]

+1

Worth the effort to clear this up.  Just to make sure I’m clear on the high-level plan…

1. There will be one entry for UniProt called, “UniProtKB” with code “S”

2. It will handle IDs like “A4D1B5” and not like “GSAP_HUMAN” (e.g., in this case: https://www.uniprot.org/uniprotkb/A4D1B5/entry) 

 - Alex

[Egon Willighagen]

On Thu, 17 Aug 2023 at 20:28, 'Alex Pico' via bridgedb-discuss <bridgedb...@googlegroups.com> wrote:

+1

Okay, let's move ahead then. Further discussion will happen here: https://github.com/orgs/bridgedb/projects/2/

Worth the effort to clear this up.  Just to make sure I’m clear on the high-level plan…

1. There will be one entry for UniProt called, “UniProtKB” with code “S”

Yes, I think that's the best approach.

 

2. It will handle IDs like “A4D1B5” and not like “GSAP_HUMAN” (e.g., in this case: https://www.uniprot.org/uniprotkb/A4D1B5/entry) 

Correct too.

Out of curiosity, did we at any point in 2012 onwards support GSAP_HUMAN? I've seen these labels on UniProt but never in BridgeDb or WikiPathways/PathVisio.

Egon

--

Inherited disorders can be hard to interpret when multiple biomarkers are involved. A network approach can help bring insight:

https://doi.org/10.1186/s13023-023-02683-9 

--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Blog: https://chem-bla-ics.blogspot.com/
Mastodon: https://scholar.social/@egonw
PubList: https://orcid.org/0000-0001-7542-0286