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Related glossaries include Model & other organisms.

Carbohydrate nomenclature
IUPAC-IUBMB Joint Commission on Biochemical Nomenclature, Nomenclature of Carbohydrates, Recommendations,  1996    http://www.chem.qmw.ac.uk/iupac/2carb/

IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), Nomenclature of glycoproteins, glycopeptides and peptidoglycans, Recommendations 1985. http://www.chem.qmw.ac.uk/iupac/misc/glycp.html

Enzyme Nomenclature
A classification according to the Enzyme Commission (EC) of the IUBMB (International Union of Biochemistry and Molecular Biology). Enzymes are allocated four numbers, the first of which defines the type of reaction catalyzed, the next two define the substrates, and the fourth is a catalogue numbers. Categories of enzymes are EC 1, Oxidoreductases; EC 2 Transferases; EC 3 Hyedrolases; EC 4 Lyases, EC 56 Isomerases; EC 6 Ligases (Synthetases). [IUPAC Bioinorganic]

Enzyme Nomenclature, Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, July 2000] http://www.chem.qmw.ac.uk/iubmb/enzyme/
Links to individual enzyme documents, includes citations for published versions.

Gene nomenclature - integrating
While the Gene Ontology^TM Consortium http://www.geneontology.org/   Functional genomics glossary is not dealing specifically with gene nomenclature their efforts at integrating terminology are an important step being able to compare genes in any number of organisms (plants, model organisms, and animals including humans).  

Human gene nomenclature
There is "currently no official nomenclature for human genes, however, the Human Gene Nomenclature Committee (part of HUGO) is currently trying to establish a nomenclature standard and does have a recommended format. The Human Gene Nomenclature Committee is the accepted authority for establishing these standards.  For new genes lacking official nomenclature the research community is encouraged to use the Nomenclature Committee web form to submit a proposed gene symbol and name, thus creating a community provided name.  In general, the research community does try to conform to using pre- existing names but these names might not be the current official nomenclature name so situations do arise where a single gene is being called by multiple names.  There is no enforcement of this suggested nomenclature method and investigators are free to name a gene as they wish.   [dbSNP FAQ, NCBI, US]  http://www.ncbi.nlm.nih.gov/SNP/get_html.gene nocgi?whichHtml=faq

Guidelines for Human Genome Nomenclature, HUGO 1997   http://www.gene.ucl.ac.uk/nomenclature/guidelines.html#2.2

HGNC Gene Family Nomenclature Guidelines, HUGO Gene Nomenclature Committee http://ash.gene.ucl.ac.uk/nomenclature/genefamily.shtml

Human Gene Nomenclature Database Search, HUGO http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl   Can be restricted to approved symbols.

Standardized Human Gene Nomenclature, NCBI News, Fall/Winter 2000 http://www.ncbi.nlm.nih.gov/Web/Newsltr/FallWinter2000/nomenclature.html

Human gene mutation nomenclature
Mutations "Recommendations for a nomenclature system for human gene mutations, Nomenclature Working Group Human Mutation 11(1):1-3 1998 http://www.interscience.wiley.com/jpages/1059-7794/nomenclature.html

See also the further note on Human Gene Nomenclature at the end of this section.

Plant and animal gene nomenclature
Other Nomenclature Guidelines (for non-human species), HUGO  http://www.gene.ucl.ac.uk/nomenclature/moreguides.html   Includes plants (Arabadopsis, rice) model organisms, cows and chickens,

Model organisms The Gene Ontology^TM project is a collaboration between the Arabadopsis, C. elegans, Drosophila, mouse and Saccharomyces people. http://www.geneontology.org  Gene definitions See also Model organisms glossary.

C. elegans Nomenclature: http://www.cbs.umn.edu/CGC/Nomenclature/nomenguid.htm

Drosophila Nomenclature: http://fly.ebi.ac.uk:7081/docs/nomenclature/lk/nomenclature.html

Mouse Genome Nomenclature, Jackson Lab, US  http://www.informatics.jax.org/mgihome/nomen/

Rat Genetic Nomenclature, Rat Genome Database, Goteborg University, Sweden  http://ratmap.gen.gu.se/ratmap/WWWNomen/Nomen.htmlRatsites

Saccharomyces cerevisae Nomenclature: SGD Gene Naming Guidelines, Stanford University, US http://genome-www.stanford.edu/Saccharomyces/gene_guidelines.html

Zebrafish nomenclature Guidelines  http://zfin.org/zf_info/nomen.html

Protein nomenclature
SWISS- PROT Protein Sequence Data Bank, List of nomenclature related references for proteins, Amos Bairoch.  http://www.expasy.ch/cgi-bin/lists?nomlist.txt

Nomenclature of glycoproteins, glycopeptides and peptidoglycans, Recommendations, IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), 1985. http://www.chem.qmw.ac.uk/iupac/misc/glycp.html

Nomenclature Rules for Recombinant Proteins, IUPAC http://www.itb.uni-stuttgart.de:8080/IUPAC/nomenclature/nomen.html   IUBMB and IUPAC are setting up a task force to address protein isoforms, protein glycoforms, genome-derived proteins, artificial proteins derived from gene shuffling.

Nomenclature and Symbols for Amino Acids and Peptides, Recommendations, IUPAC and IUBMB and IUPAC-IUB Joint Commission on Chemical Nomenclature 1983 http://www.chem.qmw.ac.uk/iupac/AminoAcid/

See also Enzyme Nomenclature.

Species nomenclature: Taxonomy, NCBI, US  http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/

Taxonomic databases are rather controversial since the soundness of the taxonomic classifications done by one taxonomist will be directly questioned by next taxonomist!  Various efforts are going on to create a taxonomy resource (e.g. "The Tree of Life" project  (http://phylogeny.arizona.edu/tree/life.html), "Species 2000" (http://www.sp2000.org/), International Organization for Plant Information (http://iopi.csu.edu.au/iopi/), Integrated Taxonomic Information System (http://www.itis.usda.gov/itis/), etc.). The most generally useful taxonomic database is that maintained by the NCBI [see above] http://www.ncbi.nlm.nih.gov/Taxonomy/   This hierarchical taxonomy is used by the Nucleotide Sequence Databases, SWISS-PROT and TrEMBL, and is curated by an informal group of experts. [Introduction to Molecular Biology Databases, R. Apweiler, R. Lopez, B. Marx, 1999] http://www.ebi.ac.uk/swissprot/Publications/mbd1.html

Bibliography

Alpha glossary index

HGNC Nomenclature: Genes, weights and measures, animals, elements, and planets.  H. Wain, E. Bruford, A. Duncanson, R. Lovering, S. Povey   July 2000
The authority charged with approving and implementing human gene names and symbols is the Human Gene Nomenclature Committee (HGNC)  which is a sub- committee of HUGO (The Human Genome Organisation). This was formed in the 1970’s (first reported by Shows et al., 19791) when it was realised that a consistent, standardised gene nomenclature would be vital to the collaborative effort of maintaining databases of genes. Nomenclature committees were soon established for both the human and mouse genes and guidelines (White et al., 19972 and Maltais LJ et al., 19973)   published in conjunction with the reports from the HGM (Human Genome Mapping) meetings. In a further development, databases, initially the Genome Database (GDB)  and the Mouse Genome Database (MGD), also implemented "approved" gene nomenclature as part of their curation system.

Since the inception of the HGNC, the numbers of databases have continued to expand with many more now available online. This means that standardised gene symbols are even more important as they ensure correct labelling of any individual gene across the breadth of databases available. All the major databases containing information on human genes now use the HGNC standard for approved symbols. Thus, when searching with the symbol ABCC1 information about only that gene will be retrieved from LocusLink, GDB, OMIM, GeneCards, GenBank and GENATLAS. This standardisation will become more crucial once the whole of the human genome is sequenced; there are now over 10,400 approved gene symbols in the HGNC online database ... However, it is not just human gene databases which are making use of the information and invaluable curation skills of the HGNC, but also many other organism gene databases. Where possible, these try to use the same gene symbols for confirmed orthologous genes in order to maintain consistency and searchability. ... 

There are a number of journals which now insist on the use of approved gene symbols. These include: Genomics, Nature Genetics, The Annals of Human Genetics, Mammalian Genome, Cytogenetics and Cell Genetics  and of course, Radiation Research.  There are also a number of other journals which mention nomenclature in their instructions to authors. Thus the penultimate barrier to accurate information retrieval is being overcome, as approved symbols can now be found in the literature databases such as PubMed contained in the titles and abstracts. Some journals have tried to include all known aliases of a particular gene in a publication to ensure understanding by all parties. This is unnecessary and confusing, so our recommendation is to use the approved symbol alongside the alias favoured by the author in the title and/ or abstract and to use the favourite symbol (preferably the approved one) in the rest of the paper.   http://www.gene.ucl.ac.uk/users/hester/Radresedit.html