The recent leading article1 and subsequent correspondence2,4 on nomenclature illustrate problems that the scientific community is largely failing to address. A general reluctance to adopt any form of nomenclature regulation will ensure a continuing increase in idiosyncratic names being associated with genes. To try to overcome this problem, the International Society for Plant Molecular Biology, through its Commission of Plant Gene Nomenclature (CPGN), has undertaken to unify gene nomenclature within ‘plants’5.
To achieve this goal, all plant nuclear-encoded sequences in the SwissProt and SPTREMBL databases have been grouped by cluster analysis and gene family analysis. This analysis is soon to be expanded to incorporate all eukaryotic organelle sequences. Each gene family has been assigned a unique alphanumeric identifier, whether or not it has an acceptable name. Assigning to each gene family a name that will reflect the function of the proteins within the family is a big task, and to attempt this retrospectively for the many gene families that do not have names will be time-consuming.
The assignment of unique ‘gene family numbers’ has many immediate advantages: it unifies families between species but could also be used in a wider context to unify nomenclature within the eukarya. Gene family numbers can be linked to expressed sequence tags (ESTs) and used to identify the location of the EST on chromosomal maps in place of the myriad of meaningless EST accession numbers. Gene family names would eventually replace the gene family numbers, making maps intelligible.
The CPGN's database Mendel (http://jiio6.jic.bbsrc.ac.uk) holds some 3,500 sequence records relating to approximately 300 gene families. The current analysis, when complete, will expand the number of gene families to nearer 2,000, adding a further 12,500 records. This information will be released during 1998 and will be reciprocally cross-linked to European Molecular Biology Laboratory sequence records.
In my experience, most people in the scientific community do not know of attempts to standardize nomenclature. Here surely is a role for the journals, which could not only promote the existence of nomenclature databases but could also insist on authors submitting the recognized ‘name’ or, in its absence, the gene family number besides the sequence accession number. This would inevitably force the pace of change in unifying nomenclature.
The CPGN would be pleased to collaborate with other nomenclature projects to help promote unification of nomenclature within the eukarya.
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Trends in Genetics (1998)