Thursday, December 18, 2014

An insight into expert annotation with RS3_HUMAN

UniProt's expert curation consists of manual annotation based on literature and curation tools. You may know that previously unreviewed and automatically generated entries (from TrEMBL) go through expert curation to become reviewed entries in Swiss-Prot. However the curator's role doesn't end at annotating an unreviewed protein entry and making it part of Swiss-Prot. Did you know that reviewed protein entries also undergo revisions by curators? Even well characterised proteins with reviewed Swiss-Prot entries are considered for revision to include information from the latest publications. These revisions can be very valuable as a lot can be learnt from well characterised proteins through important updates such as newly identified enzymatic activities. One such example is the ribosomal S3 protein found in the UniProt entry RS3_HUMAN.

RS3_HUMAN was picked up for revision as it was originally missing a Function annotation. This was the beginning of a comprehensive review during which a UniProt curator read through a number of new publications about this protein. To provide high-quality in-depth experimental annotation, the choice of publications to use is critical. We prioritise publications with (i) a high impact in the scientific community that contain functional data for previously uncharacterized proteins, (ii) new 3D-structural information, (iii) enzymatic reactions that may complete the annotation of known metabolic pathways or networks, (iv) PTMs and their consequences, (v) novel splice variants and (vi) disease-causing variants as well as polymorphisms.

This review resulted in the addition of 26 new publications as sources for the RS3_HUMAN entry. Updates included annotations about function, enzyme activity, interactions, subcellular locations, post translational modifications, etc. You can see the latest function annotation in the entry, now tagged with 16 publications:

To see the full list of updates on any entry, you can use the 'History' button displayed towards the top of the page. In the case of RS3_HUMAN, the History button shows that it was last updated on the 26th of November 2014. To view the exact changes, simply click on the 'Previous versions' link in the dropdown as shown below:

This will bring you the full history page where you can see the version numbers and dates of all changes. To view the exact updates, select the versions that you want to compare. For example, select version 170 with one radio button and version 168 with another and click 'Compare'.

You will then see all the changes, with removed information coloured in red and added information coloured in green. RS3_HUMAN here has a long scrolling page full of green additions, including the Function annotation where it all began!