LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana

Nucleic Acids Res. 2011 Jan;39(Database issue):D230-4. doi: 10.1093/nar/gkq927. Epub 2010 Nov 11.

Abstract

LocDB is a manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Currently, it contains entries for 19,604 UniProt proteins (HS: 13,342; AT: 6262). Each database entry contains the experimentally derived localization in Gene Ontology (GO) terminology, the experimental annotation of localization, localization predictions by state-of-the-art methods and, where available, the type of experimental information. LocDB is searchable by keyword, protein name and subcellular compartment, as well as by identifiers from UniProt, Ensembl and TAIR resources. In comparison to other public databases, LocDB as a resource adds about 10,000 experimental localization annotations for HS proteins and ∼900 for AS proteins. Over 40% of the proteins in LocDB have multiple localization annotations providing a better platform for development of new multiple localization prediction methods with higher coverage and accuracy. Links to all referenced databases are provided. LocDB will be updated regularly by our group (available at: http://www.rostlab.org/services/locDB).

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Arabidopsis Proteins / analysis*
  • Data Mining
  • Databases, Protein*
  • Humans
  • Intracellular Space / chemistry
  • Proteins / analysis*

Substances

  • Arabidopsis Proteins
  • Proteins