MicroRNA Gene Ontology annotations

You might have noticed some additional information on the mature miRNA pages in the last few weeks. See for example:

http://mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000123
http://mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000069

The new section “QuickGO function” contains a set of high quality manual annotations of Gene Ontology terms for mature miRNAs, the vast majority of which come from the work of Rachael Huntley et al. at the UCL Functional Gene Annotation group. The annotation has been an Herculean biocuration task — more than 4000 GO terms assigned to nearly 400 miRNAs, all from expert reading of primary literature. Human miR-21 is the star — 244 GO terms:

http://mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0000076

We’re pulling these data from the EBI’s QuickGO database. Their webservices make this straightforward (thanks Tony!). It’s also worth noting that the GO terms are actually assigned to RNAcentral IDs. RNAcentral maintains mappings of IDs between RNA sequence databases, including miRBase. Again, this legwork makes the task of providing these annotations much easier than it would otherwise be.

Functional information has been generally lacking in miRBase. These GO data have already made a significant difference to this, and we’re planning more. Look out for functional statements from text mining of the primary literature, coming to a web browser near you soon.

Rachael et al.’s latest paper on GO annotation of miRNAs is in the preprint section at RNA:

Expanding the horizons of microRNA bioinformatics.
Rachael P Huntley, Barbara Kramarz, Tony Sawford, Zara Umrao, Anastasia Z Kalea, Vanessa Acquaah, Maria-Jesus Martin, Manuel Mayr and Ruth C Lovering.
RNA 2018

See also:

Guidelines for the functional annotation of microRNAs using the Gene Ontology.
Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D’Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC.
RNA 2016 22:667-676.

The GOA database: Gene Ontology annotation updates for 2015.
Huntley RP, Sawford T, Mutowo-Muellenet P, Shypitsyna A, Bonilla C, Martin MJ, O’Donovan C.
Nucleic Acids Research 2014 43:D1057-D1063.

QuickGO: a web-based tool for Gene Ontology searching.
Binns D, Dimmer E, Huntley R, Barrell D, O’Donovan C, Apweiler R.
Bioinformatics 2009 25:3045-3046.