The Mouse Genome Informatics (MGI, www.informatics.jax.org) group implements the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice and maintains the international authoritative resource for the identity and names of mouse genes, genetic markers, alleles, chromosome aberrations, genomic features, and mouse strains. Nomenclature follows the established guidelines, but there is input from others to develop accurate and informative names and symbols that will be useful to and used by the scientific community.
Each gene and genome feature is given a genome feature type using the Sequence Ontology (SO, http://www.sequenceontology.org/browser/obob.cgi). Feature types provide information that cannot always be included in nomenclature. Example SO feature terms include protein-coding, miRNA, long noncoding RNA, and pseudogene. MGI petitions the SO to create additional feature types when new ones are necessary. Every mouse strain, allele, gene and genome feature receives a unique MGI_ID. Some, depending on the object, receive a list of synonyms including common ‘lab’ names, published alternate names, and previous official names. These aid researchers in identifying an object of interest in as many ways as possible. Designations have evolved for spontaneous, induced, targeted, endonuclease-mediated, and gene-trapped alleles of endogenous genes. Transgenic alleles have their own symbols distinct from the others. The different nomenclature rules for allele symbols help investigators distinguish among these types.
The representation of Quantitative Trait Loci or QTL is an area of focus undergoing refinement and expansion. QTL identified from literature need official nomenclature and mapping coordinates.
Robust homology information is crucial for translational researchers. MGI collaborates with human and rat nomenclature committees and subject matter experts to unify the nomenclature of homologs. MGI participates in the Consensus CDS (CCDS) project, a collaborative effort to identify a core set of human and mouse protein-coding regions that are consistently annotated and of high quality, hosted at NCBI https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi. The Consensus CDS (CCDS) project is working toward convergence on a standard set of gene annotations. Updated nomenclature makes homology relationships clear.
This work is supported by NIH grant HG000330.