Tuesday, September 27, 2016

New and improved publications view in UniProtKB!

UniProt Knowledgebase protein entries are a treasure trove of knowledge mined from the most relevant publications. Entries provide not only a quick evidence tag for statements based on publications but also a list of all publications used for curating an entry. In addition to this, entries  used to have a link to computationally mapped publications for an expanded list of publications if you are looking to review as many relevant papers to your protein as possible.

Now presenting a new and improved view of publications! From being a section within the Entry document, publications now have their own tab within the entries (see snapshot above). When you land on a UniProtKB entry, you can see some alternative view options under 'Display' on the left hand side including the 'Publications' view. This expanded space now allows us to provide all relevant publications in one integrated view, the ones used by UniProtKB for curating the entry as well as additional relevant publications that have been computationally mapped.

Filters on the left hand side allow you to quickly narrow down the list to just the UniProtKB reviewed or the computationally mapped ones. You can also filter the publications based on the category of data that they have been cited for/ mapped for. So you can quickly find reviewed and mapped publications for the type of category you're interested in (such as Function, Sequencing, and Structure). Additionally, you can filter to see publications tagged as being from large-scale or small-scale experiments.

You can switch back to the main Entry using the link under the Display section again, or explore the other alternative views of the Feature viewer and the Feature table.

We hope you enjoy this new feature. If you have any questions or feedback for us, write to us on help@uniprot.org.

Tuesday, September 20, 2016

A new Peptide Search tool now in UniProt

Finding matches for a specific peptide sequence is important for protein identification in proteomics studies. It is also important for sequence-based protein retrieval as peptide sequences can often be too short for effective BLAST search. The Protein Information Resource, a UniProt consortium partner, has hosted a Peptide match service for over a decade. This popular tool is now also available directly through the UniProt interface! It can be accessed from the 'Peptide search' link in the UniProt website header.

All you need to provide as input is a peptide sequence at least three amino acids long. Optionally, you can choose to restrict the search to a specific taxonomic group and/or you can specify whether you would like the tool to treat Isoleucine and Leucine as equivalent.

The Peptide search results display proteins that have exact match to the query sequence in a table with filters on the left hand side. The table contains an additional column titled 'Peptide search:...', which shoes the sequence matched and the sequence position where the match begins in the target sequence. Each peptide search job is assigned a unique identifier that can be used to retrieve the results back from UniProt for up to seven days by simple pasting it back into the main search box or by bookmarking the peptide search results URL.

Try out this new tool now and let us know what you think! 

Friday, September 9, 2016

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!