The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program

Schneider, Michel; Lane, Lydie; Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Bougueleret, Lydie; Bairoch, Amos Marc

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Title		The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program
Authors		Schneider, Michel Lane, Lydie Boutet, Emmanuel Lieberherr, Damien Tognolli, Michael Bougueleret, Lydie Bairoch, Amos Marc
Published in		Journal of Proteomics. 2009, vol. 72, no. 3, p. 567-573
Abstract		The UniProt knowledgebase, UniProtKB, is the main product of the UniProt consortium. It consists of two sections, UniProtKB/Swiss-Prot, the manually curated section, and UniProtKB/TrEMBL, the computer translation of the EMBL/GenBank/DDBJ nucleotide sequence database. Taken together, these two sections cover all the proteins characterized or inferred from all publicly available nucleotide sequences. The Plant Proteome Annotation Program (PPAP) of UniProtKB/Swiss-Prot focuses on the manual annotation of plant-specific proteins and protein families. Our major effort is currently directed towards the two model plants Arabidopsis thaliana and Oryza sativa. In UniProtKB/Swiss-Prot, redundancy is minimized by merging all data from different sources in a single entry. The proposed protein sequence is frequently modified after comparison with ESTs, full length transcripts or homologous proteins from other species. The information present in manually curated entries allows the reconstruction of all described isoforms. The annotation also includes proteomics data such as PTM and protein identification MS experimental results. UniProtKB and the other products of the UniProt consortium are accessible online at www.uniprot.org.
Keywords		Abstracting and Indexing as Topic — Arabidopsis/chemistry — Databases, Protein — Internet — Knowledge Bases — Mass Spectrometry — Oryza sativa/chemistry — Plant Proteins/analysis/chemistry/classification — Proteome/analysis/chemistry/*classification
Identifiers		DOI: 10.1016/j.jprot.2008.11.010 PMID: 19084081
Full text		Article - Limited access to UNIGE Other version: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689360/pdf/nihms112545.pdf
Structures		Faculté de médecine / Section de médecine fondamentale / Département de biologie structurale et bioinformatique
Research group		Calipho (80)
Citation (ISO format)		SCHNEIDER, Michel et al. The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. In: Journal of Proteomics, 2009, vol. 72, n° 3, p. 567-573. https://archive-ouverte.unige.ch/unige:20086