Nomenclature
Chemical and Biochemical Nomenclature
The recognized authority for the names of chemical compounds is Chemical Abstracts (CAS) and its indexes. The Merck Index Online (https://www.rsc.org/merck-index) is also an excellent source. For guidelines on the use of biochemical terminology, consult Biochemical Nomenclature and Related Documents (Portland Press, London, United Kingdom, 1992) and the Instructions to Authors of the Journal of Biological Chemistry and the Archives of Biochemistry and Biophysics (first issues of each year).
For enzymes, use the recommended (trivial) name assigned by the Nomenclature Committee of the International Union of Biochemistry (IUB) as described in Enzyme Nomenclature (Academic Press, Inc., New York, NY, 1992) and its supplements and at http://www.sbcs.qmul.ac.uk/iubmb/enzyme/. If a nonrecommended name is used, place the proper (trivial) name in parentheses at first use in the abstract and text. Use the EC number when one has been assigned. Authors of papers describing enzymological studies should review the standards of the STRENDA Commission for information required for adequate description of experimental conditions and for reporting enzyme activity data.
For nomenclature of restriction enzymes, DNA methyltransferases, homing endonucleases, and their genes, refer to the article by Roberts et al.
Drug Nomenclature
Chemical or generic names of drugs should be used; the use of code numbers or trade names is generally not permitted. When code names or corporate proprietary numbers are to be used, either the chemical structure of the compound or a published literature reference illustrating the chemical structure, if known, must be provided at the first occurrence of the code name or number. For compounds not identified by generic nomenclature, all previous or concurrent identification numbers or appellations should be listed in the manuscript.
Nomenclature of Organisms
Mice. For mouse strain and genetic nomenclature, ASM encourages authors to refer to the guidelines set forth by the International Committee on Standardized Genetic Nomenclature for Mice, available on the Mouse Genome Informatics home page and in Genetic Variants and Strains of the Laboratory Mouse, 3rd ed. (M. F. Lyon et al., ed., Oxford University Press, Oxford, England, 1996).
Viruses. Names used for viruses should be those approved by the International Committee on Taxonomy of Viruses (ICTV) and reported on the ICTV website. In addition, the recommendations of the ICTV regarding the use of species names should generally be followed: when the entire species is discussed as a taxonomic entity, the species name, as with other taxa, is italic and has the first letter and any proper nouns capitalized (e.g., Tobacco mosaic virus, Murray Valley encephalitis virus). When the behavior or manipulation of individual viruses is discussed, the vernacular (e.g., tobacco mosaic virus, Murray Valley encephalitis virus) should be used. If desired, synonyms may be added parenthetically when the name is first mentioned. Approved generic (or group) and family names may also be used.
Bacteria. Binary names, consisting of a generic name and a specific epithet (e.g., Escherichia coli), should be used for all bacteria. Names of categories at or above the genus level may be used alone, but specific and subspecific epithets may not. A specific epithet must be preceded by a generic name, written out in full the first time it is used in a paper. Thereafter, the generic name should be abbreviated to the initial capital letter (e.g., E. coli), provided there can be no confusion with other genera used in the paper. Names of all taxa (kingdoms, phyla, classes, orders, families, genera, species, and subspecies) are printed in italics; strain designations and numbers are not. Two sites on the World Wide Web list current approved bacterial names: Prokaryotic Nomenclature Up-to-Date and List of Prokaryotic Names with Standing in Nomenclature. For guidelines regarding new names and descriptions of new genera and species, see the articles by Tindall and Stackebrandt et al. If there is reason to use a name that does not have standing in nomenclature, the name should be enclosed in quotation marks in the title and at its first use in the abstract and the text and an appropriate statement concerning the nomenclatural status of the name should be made in the text. “Candidatus” species should always be set in quotation marks.
Fungi and parasites. Authors should use nomenclature consistent with community databases, including SGD, CGD, AspGD, PomBase, the Broad Institute genomic databases, and the EuPathDB family of databases. “Classification and Nomenclature of Human Parasites” offers useful information on current parasite nomenclature.
Genetic Nomenclature
To facilitate accurate communication, it is important that standard genetic nomenclature be used whenever possible and that deviations or proposals for new naming systems be endorsed by an appropriate authoritative body. Review and/or publication of submitted manuscripts that contain new or nonstandard nomenclature may be delayed by the editor or the Journals Department so that they may be reviewed.