Biocuration 2015 Beijing Talk - C-HPP

neXtProt and C-HPP: an update
Lydie Lane, May 21st, 2016
neXtProt and the C_HPP project
• As a reference knowledgebase for C-HPP,
neXtProt:
– integrates the results of HPP experimental studies
(mass spectrometry and antibodies)
– validates protein “existence”
– provides metrics to assess the project progress
– represents the “functional” knowledge on human
proteins as best as possible
neXtProt contents [February 2016]
 20’055 entries representing 41’992 protein sequences (isoforms created by
alternative splicing/initiation)
 All of Swiss-Prot human annotations
PLUS
 Many “terminology” resources: GO, OMIM, NCI Thesaurus, MeSH, etc.
including two that are “home-grown”: CALOHA and the Cellosaurus
 All GOA human protein annotations
 Chromosomal location and exons mapping from Ensembl
 Many additional identifiers (Affymetrix, Antibodypedia, IPI, etc.)
 Variants: about 2.5 million SAPs from COSMIC and dbSNP
 Subcellular localization data from different sources, incl. HPA
 Tissular expression data at mRNA level (microarray/EST) from Bgee (metaanalysis of ArrayExpress/UniGene data)
 Tissular expression data at protein level (IHC) from HPA
 Over 1 million MS/MS peptides from PeptideAtlas (“Human-all” build at 1%
FDR at protein level)
 63 000 phosphorylation sites from PeptideAtlas (“Phosphobuild” at 1% FDR at
protein level)
 30 000 PTM (non phospho) sites from proteomics publications
 All synthetic peptides from SRMAtlas
neXtProt proteomics view
Peptide viewer 1/2
https://search.nextprot.org/entry/NX_ A6NI47 /view/peptides
Peptide viewer 2/2
Unicity checker (beta version)
https://search.nextprot.org/view/gh/MatSchaeff/unicity-checker
Metrics
To comply with HPP Guidelines, our criteria for entry validation
at PE1 based on proteomics data has changed
2 non nested, unique*peptides of 9aa or more are now required !
* without taking SNP into account
A new protein existence viewer
https://search.nextprot.org/view/statistics/protein-existence
search.nextprot.org
• A new search engine with two components:
– A simple “google-like” full text search
– An advanced search capability based on a SPARQL/RDF
technology
• A new API that allows to retrieve precisely any
annotation in neXtProt in XML or JSON and thus also
allows to build applications on top of neXtProt
• A new version of the XML export format (in progress)
Examples of advanced searches
The neXtProt team
Content: Pascale Gaudet, Aurore Britan, Isabelle Cusin, Paula Duek,
Valérie Hinard
Software: Pierre-André Michel, Alain Gateau, Anne Gleizes, Frédéric
Nikitin, Valentine Rech de Laval, Mathieu Schaeffer, Daniel Teixeira
QA: Monique Zahn
Directed by: Amos Bairoch, Lydie Lane