The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data at EMBL-EBI @emblebi
Hinxton, Cambridge
Joined April 2010
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@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. ebi.ac.uk/pride/ws/archive/v…
PRIDE at EBI retweeted
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.
PRIDE at EBI retweeted
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. github.com/PRIDE-Archive/pri…
PRIDE at EBI retweeted
#HUPO2024 is here. This week, we are releasing the v3 of @pride_ebi API ebi.ac.uk/pride/ws/archive/v… . Apart from major upgrades of the existing endpoints, the killing feature is streaming. #reactiveprogramming #proteomics #opendata 🧵
PRIDE at EBI retweeted
You can read about the project here: github.com/PRIDE-Archive/pri… 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.
PRIDE at EBI retweeted
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. github.com/bigbio/proteomics…
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!
PRIDE at EBI retweeted
During January, we worked on a new submission mechanism for @pride_ebi using the @globus protocol (ebi.ac.uk/pride/markdownpage…). In summary:
PRIDE at EBI retweeted
@DeeptiJaiswal, the lead curator of @pride_ebi, has created a short video tutorial on how to transfer data to PRIDE using Globus. youtube.com/watch?v=VRNumsnY…
This is a great job opportunity to join our team!
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
embl.org/jobs/position/EBI02…
PRIDE at EBI retweeted
Just had a great time presenting at #HUPO2023 about #lesSDRF! If you want to use it, add to it or have some feedback ➡️ lessdrf.streamlit.app
@compomics @hupo_org @pride_ebi
Many congratulations Henning!
#HUPO2023 Many congratulations to Henning Hermjakob (@HenningHermjak1) for the Distinguished Service Award @emblebi. I have really learnt a lot from him over the years!
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
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.
PRIDE at EBI retweeted
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.
PRIDE at EBI retweeted
Paper out: Tissue-based absolute quantification using large-scale TMT and LFQ experiments analyticalsciencejournals.on…. Thanks, @OpenMS and #quantms teams.
PRIDE at EBI retweeted
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!
PRIDE at EBI retweeted
We are currently working with multiple databases that systematically reanalyze data from PRIDE to link their peptide evidence to PRIDE Spectrum Viewer.
PRIDE at EBI retweeted
Release day at @pride_ebi. We released the possibility to visualize & retrieve spectra using USIs for private submissions. ebi.ac.uk/pride/archive/usi. You can now put in the supplementary information USIs to your novel claims: peptides, PTMs, SAAVs & the reviewer can check them.
PRIDE at EBI retweeted
For those that need statistics about public proteomics data, here are some cool endpoints in PRIDE:
- Data Volume: ebi.ac.uk/pride/ws/archive/v…
- Monthly submissions: ebi.ac.uk/pride/ws/archive/v…
- Submissions per Country: ebi.ac.uk/pride/ws/archive/v…