CaMKiNet

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CaMKiNet

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/CamKinet/

What is the URL of the data resource/software?

http://camkinet.embl.de/v2/home/

Who is the owner of the data resource/software?

Toby J. Gibson and Manjeet Kumar

What are the annotations provided?

The resource provides Calcium/Calmodulin-dependent protein kinases (CaMKs) and their substrate relationships. High quality manually annotated information (for instance, curator assessment, reliability and conservation etc.) is catalogued for each relationship.

How regularly are these annotations updated?

Annually

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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?

We do not provide any raw score as the data is manually annotated.

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

Confidence assessment is provided at three levels while curating: True Positive (TP), False Positive (FP), and Unknown (U) category. The TPs are the sites which have the highest confidence. Phosphosites in Unknown category should be evaluated carefully by keeping reliability, conservation and disorder score into consideration.

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

The reliability assessment could be considered as confidence level. They are provided for each annotated phosphosite in the resource. The levels are decided based on the quality of available evidence as well by the curator while doing manual annotation. It is divided in three levels - Certain, Likely and Unlikely where Certain is the highest and unlikely is the lowest.

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

CaMKinet is a manually annotated resource and data could be used for the benchmarking purposes.

How are these annotations collected/generated?

Annotators read the literature, extract evidences, assay details and methods used for the experimental characterization of a given phosphosite and the relevant kinase. Protein sequence regions having phosphosites are analyzed for the conservation and disorder to assign quality. The annotation procedure is similar to what ELM uses and the details are present in this reference [Methods Mol. Biol. 2141:73-102].