7. UniProt

We want to pay tribute to the UniProt team for their amazing resource their provide to the scientific community. pyuniprot only provides methods to download and locally query open accessible UniProt data.

7.1. About

Citation from UniProt website (about) [08/11/2017]:

“The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).

UniProt is a collaboration between the European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR). Across the three institutes more than 100 people are involved through different tasks such as database curation, software development and support.

EMBL-EBI and SIB together used to produce Swiss-Prot and TrEMBL, while PIR produced the Protein Sequence Database (PIR-PSD). These two data sets coexisted with different protein sequence coverage and annotation priorities. TrEMBL (Translated EMBL Nucleotide Sequence Data Library) was originally created because sequence data was being generated at a pace that exceeded Swiss-Prot’s ability to keep up. Meanwhile, PIR maintained the PIR-PSD and related databases, including iProClass, a database of protein sequences and curated families. In 2002 the three institutes decided to pool their resources and expertise and formed the UniProt consortium.

The UniProt consortium is headed by Alex Bateman (PI), Cathy Wu, and Ioannis Xenarios, supported by key staff, and receives valuable input from an independent Scientific Advisory Board.”

Note

Please note that PyUniProt not covers all parts of UniProtKB. UniRef and UniParc are in the moment not acessible via the library. Only Swiss-Prot is included, TrEMBL will follow in the next version of PyUniProt.

7.2. Citation

Latest UniProt publication:

The UniProt Consortium UniProt: the universal protein knowledgebase Nucleic Acids Res. 45: D158-D169 (2017) (PDF)