UniProt COVID-19 portal: Supporting research during the pandemic

 

Responding to the urgency of the pandemic, UniProt created and is continuing to develop a dedicated portal to provide access to the latest pre-release annotations and sequences for proteins related to COVID-19. It is released independently of UniProt’s 8 weekly release schedule. It can be accessed via https://covid-19.uniprot.org/ and all sequences can also be downloaded directly via our FTP site ftp://ftp.uniprot.org/pub/databases/uniprot/pre_release/.

An integrated source of sequence, function and links to specialist resources

 

The portal provides SARS-CoV-2 annotated protein sequences, closest SARS-CoV 2003 sequences and human sequences relevant to the biology of viral infection. The SARS-CoV-2 proteome is annotated based on expert curation of literature and the knowledge extracted from the well-studied SARS-CoV virus. Rule-based automatic annotation also allows us to add information from a broader taxonomic range of viruses. Links to structures, drugs, interactions, molecular pathways as well as many other resources provide integrated information to help understand the biology and investigate routes to treatment.

 

The annotated UniProtKB entries include functional and positional annotations. The microbial infection information and essential positions and structures for the virus infection are also documented in these records. Each protein entry provides annotations such as the catalytic activity and function, Gene Ontology terms, 3D structures, interactions, external links to resources like IntAct, ChEMBL, DrugBank, PDBe-KB, etc, and the ProtVista visualisation of positional annotations on the sequence space. Within entries, the mature products that result from proteolytic cleavage of precursor proteins can be identified with UniProt product identifiers.

Contribute and explore literature about COVID-19

The portal provides access to the latest literature related to the virus and host protein through a link to LitCovid and a link to UniProt’s community literature submissions. Users can also contribute relevant publications through the ‘Add a publication’ link present in each entry.

 

How can you increase the impact of your research papers and contribute to UniProt?

Have you ever wondered how to get your life science data into public resources like UniProt with due credit and citation of your papers? Would you like the broaden the reach and impact of your research papers?  

Biomedical literature is vast, with over one million papers being added to PubMed every year.  Our team of curators triages these and selects relevant papers to create and update our protein entries. This herculean task is sometimes made more difficult when we cannot easily identify exactly which protein(s) a paper is about due to the lack of species, strain and even sequence information! The simple addition of a UniProt accession number in a paper could go a long way to helping both UniProt and other resources to use your work for adding knowledge into our databases and giving you due credit.

If the protein you are writing about is not in UniProt, you can get an accession number for it by submitting it to us through http://www.uniprot.org/help/submissions. Accession numbers are the alphanumeric identifiers that typically look like P12346 or A0A167SS16. Here are a couple of examples of a protein being referenced in this way within the text of a paper:

Remember, accession numbers are different to Entry names and are stable from release to release. Hence, accession numbers are the best identifier for referring to your protein in a manuscript. 

We recommend the format “UniProtKB P12346” to be used in the body of a manuscript, while the UniProtKB accession numbers would also be a suitable column title for a table. We do have procedures in place to identify the accession numbers alone in the text but elucidating that these are from UniProt would help us and readers of your papers to understand and use your work.  

Although we have discussed UniProt accessions here, adding accession numbers for other resources will also help to link up the research literature helping researchers search for and disseminate your work and hence increase its impact further. We are looking forward to working with you to achieve that goal!