UniProt

The UniProt Knowledgebase (UniProtKB) has been created from Swiss-Prot, TrEMBL and PIR-PSD. It consists of two parts, one containing fully manually annotated records and another one with computationally analysed records awaiting full manual annotation. The two sections will be referred to as the Swiss-Prot section of the UniProt Knowledgebase (UniProtKB/Swiss-Prot) and TrEMBL section of the UniProt Knowledgebase (UniProtKB/TrEMBL), respectively. PIR-PSD release 80.0 of 31-Dec-2004 has been fully integrated into these sections. This was the last release of PIR-PSD.

This directory contains the following subdirectories:

1. Directory /knowledgebase

subdirectory /complete: This directory contains the eight-weekly updates of the UniProt Knowledgebase, consisting of UniProtKB/Swiss-Prot (fully annotated curated entries) and UniProtKB/TrEMBL (computer-generated entries enriched with automated classification and annotation). Both, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL, are available separately in flat file, XML and FASTA format.

subdirectory /complete/docs: This directory contains various UniProt documents.

subdirectory /embeddings: This directory contains raw embeddings for UniProtKB/Swiss-Prot and some reference proteomes of model organisms.

subdirectory /genome_annotation_tracks: This directory contains the genome annotation tracks files which are updated in conjunction with UniProtKB.

subdirectory /idmapping: This directory contains the idmapping data files which are updated in conjunction with UniProtKB.

subdirectory /pan_proteomes: This directory contains the pan proteomes data files which are updated in conjunction with UniProtKB.

subdirectory /proteomics_mapping: This directory contains the proteomics mapping files which are updated in conjunction with UniProtKB.

subdirectory /reference_proteomes: This directory contains the reference proteomes data files which are updated in conjunction with UniProtKB.

subdirectory /taxonomic_divisions: This directory contains the same data as provided in the /complete subdirectory, split into taxonomic divisions.

subdirectory /variants: This directory contains the variants data files which are updated in conjunction with UniProtKB.

2. Directory /uniparc

This directory contains the eight-weekly update of UniParc, the UniProt Archive of sequences from UniProtKB and many other databases.

3. Directory /uniref

This directory contains the eight-weekly updates of the UniProt Reference Clusters (UniRef). There is a subdirectory for each of the three UniRef databases (which are based on different sequence identity cut-offs): uniref100 (100%), uniref90 (90%) and uniref50 (50%).