Scop3P

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Scop3P

This page provides a description of the annotations provided by this PDBe-KB Consortium Member. These annotations are available via public FTP, from the PDBe graph database, the PDBe graph API, and on the PDBe-KB aggregated views of proteins.

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Basic Information

What is the FTP URL of the provided annotations (JSON format)?

ftp://ftp.ebi.ac.uk/pub/databases/pdbe-kb/annotations/Scop3P/

What is the URL of the data resource/software?

https://iomics.ugent.be/scop3p/index

Who is the owner of the data resource/software?

Lennart Martens, Wim Vranken

What are the annotations provided?

Human phosphorylation sites identified by re-processing large scale public proteomics datasets

How regularly are these annotations updated?

Twice a year

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Description of the data

Is there a "raw_score" provided? How to interpret it? Does it have a value range? Does it have a unit?

None

Is there a "confidence_score" provided? How to interpret it? Does it have a value range?

Phosphosites are labelled with the respective source information (""UP"", ""PRIDE"" ,""UP, PRIDE"") under ""annotation_source"" UP: evidence of phosphorylation at UniProt level PRIDE: evidence of phosphorylation from re-processed proteomics experiments UP, PRIDE: phosphosite evidence in both UniProt and re-processed projects

Is there a "confidence_level" provided? How is it decided?

"Phosphosites are annotated with three different confidence classification (high, medium and curated) high: if the site has annotation from both UniProt (UP) and re-processed proteomics projects (PRIDE) medium: if the site is identified only from re-processed proteomics projects (PRIDE) curated: if the site has only UniProt level evidence "

Are there benchmarking datasets? Are they available publicly? If yes, what is the URL?

Phosphosite information can be accessed from the following REST-API: https://iomics.ugent.be/scop3p/swagger-ui/#/api-controller/getModificationsUsingGET

How are these annotations collected/generated?

Proteomics projects were obtained from PRIDE database. The MGF files containing spectral information were searched using "ionbot" (a data-driven search engine developed at CompOmics group, Ghent, Belgium). Identified phosphosites were filtered at 1% FDR (false discovery rate) with high localization probability. Phosphosite obtained from UniProt/Swiss-Prot annotations were then combined to find the resource-specific and overlapping sites.