PRIDE at EBI

The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data at EMBL-EBI @emblebi

[PRIDE at EBI @pride_ebi]

@pride_ebi team is working on a new API endpoint version v3 with multiple functionalities for streaming metadata. v2 of the API will be retired in January 2025. https://t.co/rTkJDRqRtO

[Yasset Perez-Riverol @ypriverol]

Multiple members of the team will be next week at #HUPO2024, that is the moment to ask about future features and bugs, and let us know in person what you think about PRIDE and how we can improve the infrastructure.

[Yasset Perez-Riverol @ypriverol]

You can use now pridepy to download this data:
- pridepy stream-projects-metadata -o all_pride_projects.json
- pridepy stream-files-metadata -o all_pride_files.json
Here is pridepy which also allows you to download files etc. https://t.co/lmLx6fkFrP

[Yasset Perez-Riverol @ypriverol]

#HUPO2024 is here. This week, we are releasing the v3 of @pride_ebi API https://t.co/RmttmByks5 . Apart from major upgrades of the existing endpoints, the killing feature is streaming. #reactiveprogramming #proteomics #opendata 🧵

[Yasset Perez-Riverol @ypriverol]

You can read about the project here: https://t.co/hAHuIuBQQq Feel free to add issues and give us feedback. We are focused on making @pride_ebi FAIR and accessible to everyone. Thanks to Sebastian, Jonas, and Enrique for helping us with the benchmark.

[Yasset Perez-Riverol @ypriverol]

I started today to curate some of the datasets the proteomics community has curated over the last 3 years in SDRF. More than 200 experiments are now annotated. No bad, Hope more people contribute in the future. https://t.co/oRcdhiGu1X

[PRIDE at EBI @pride_ebi]

We have just processed @proteomeXchange
dataset #PXD050000. #proteomics #opendata. Thanks to all submitters!
PXD000001- March 2012
PXD010000- Jun 2018
PXD020000- Jun 20
PXD025000- Mar 21
PXD030000- Nov 21
PXD040000- Feb 2023
PXD050000- Feb 2024!
Congrats to the team!

[Yasset Perez-Riverol @ypriverol]

During January, we worked on a new submission mechanism for @pride_ebi using the @globus protocol (https://t.co/BupVI5RCrl). In summary:

[Yasset Perez-Riverol @ypriverol]

@DeeptiJaiswal, the lead curator of @pride_ebi, has created a short video tutorial on how to transfer data to PRIDE using Globus. https://t.co/hxD2TPFgrm

[PRIDE at EBI @pride_ebi]

This is a great job opportunity to join our team!

[EMBL-EBI Jobs @EMBLEBIjobs]

NEW: Scientific Curator

Our goal is to help researchers to make the most of public #proteomics data! Join us, & you'll play a crucial role supporting @pride_ebi users through our helpdesk
#bioinformatics #lifesciencejobs @emblebi
Closing 1st Feb 2024

https://t.co/EY0RUomqcf

[PRIDE at EBI @pride_ebi]

@kkkkkkkkkkoli yes, it certainly is.

[PRIDE at EBI @pride_ebi]

Many congratulations Henning!

[Juan A. Vizcaino @juan_vizcaino]

#HUPO2023 Many congratulations to Henning Hermjakob (@HenningHermjak1) for the Distinguished Service Award @emblebi. I have really learnt a lot from him over the years!

[Tine Claeys @TineClaeys1]

Just had a great time presenting at #HUPO2023 about #lesSDRF! If you want to use it, add to it or have some feedback ➡️ https://t.co/agtCQFFbXH
@compomics @hupo_org @pride_ebi

[PRIDE at EBI @pride_ebi]

Last Thursday we processed @proteomeXchange dataset #PXD045000. #proteomics #opendata. Thanks to all submitters!
PXD000001- March 2012
PXD010000- Jun 2018
PXD020000- Jun 20
PXD025000- Mar 21
PXD030000- Nov 21
PXD040000- Feb 2023
PXD045000 - Aug 31st 2023
In 2024 #PXD050000

[PRIDE at EBI @pride_ebi]

Due to summer holidays and a long weekend here in the UK, our support related responses are slow at the moment. Apologies for this. Please be patient. Situation should get better from next Tuesday August 29th.

[Yasset Perez-Riverol @ypriverol]

The @pride_ebi submission system will experience disruptions from August 16th to 18th due to scheduled system maintenance. While validations and submissions may be delayed, data deposition will remain unaffected.

[Yasset Perez-Riverol @ypriverol]

Paper out: Tissue-based absolute quantification using large-scale TMT and LFQ experiments https://t.co/taOzPn8poY. Thanks, @OpenMS and #quantms teams.

[Juan A. Vizcaino @juan_vizcaino]

Attending #ISMB2023 in Lyon. My first ISMB meeting in many years. Will be giving a talk about @proteomeXchange and @pride_ebi in a couple of hours!

[Yasset Perez-Riverol @ypriverol]

We are currently working with multiple databases that systematically reanalyze data from PRIDE to link their peptide evidence to PRIDE Spectrum Viewer.

[Yasset Perez-Riverol @ypriverol]

Release day at @pride_ebi. We released the possibility to visualize & retrieve spectra using USIs for private submissions. https://t.co/12KNeFoX6n. You can now put in the supplementary information USIs to your novel claims: peptides, PTMs, SAAVs & the reviewer can check them.