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You are here Biopharmaceutical/ Genomic glossary homepage/Search > Biology > Nomenclature, genes, proteins & species for biopharmaceutical research Nomenclature,
Genes, proteins, species for biopharmaceutical research
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K. Tipton and S Boyce in “History of the enzyme nomenclature system” write that “ambiguities in the words used for common objects or actions have been the basis for many, more- or- less memorable jokes, they can also cause a great deal of confusion … in the sciences ... many groups have stressed the need for standardized, universally accepted systems of nomenclature in chemistry, genetics, enzymology, etc. However, it is the universal acceptance that usually causes the problem. It is rare to find people who will admit that they find nomenclature to be an interesting subject, but many who profess contempt for it will get very excited if it is suggested that their pet nomenclature should be changed in the interest of clarity or uniformity.” Bioinformatics 16(1): 34- 40 Jan 2000 Biology & Chemistry Map: Finding guide to terms in these glossaries Site Map Related glossaries include Functional genomics, Model & other organisms Carbohydrate nomenclature
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 IUPAC Chemical Identifier Project http://www.iupac.org/nomenclature/chem_id_project.html The aim of the Chemical Identifier project is to establish a unique label, the IUPAC Chemical Identifier (IChI), which would be a non- proprietary identifier for chemical substances that could be used in printed and electronic data sources thus enabling easier linking of diverse data and information compilations. Clone nomenclature: Standardized clone names, NCBI http://www.ncbi.nlm.nih.gov/genome/clone/nomen.html drug nomenclature, clinical: RxNorm is a clinical drug nomenclature produced by NLM, in consultation with the Food and Drug Administration (FDA), the Department of Veterans Affairs (VA), and the Health Level 7 (HL7) standards development organization. RxNorm provides standard names for clinical drugs (active ingredient + strength + dose form) and for dose forms as administered. It provides links from clinical drugs to their active ingredients, drug components (active ingredient + strength), and some related brand names. To the extent available from the Food and Drug Administration, NDCs (National Drug Codes) for specific drug products that deliver the clinical drug are stored as attributes of the clinical drug in RxNorm. RxNorm, UMLS, National Library of Medicine, US http://www.nlm.nih.gov/research/umls/rxnorm_main.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/
Gene nomenclature - integrating Genes with multiple aliases seem to be the rule, rather than the exception, whereas genes that have no functional relationship with each other can often bear the same names. As biologists strive to make sense of the growing wealth of genomic information, this messy nomenclature is becoming a bugbear. ... Attempts to impose standard names across the board are meeting stiff resistance, and approaches that would give genes unique ID numbers seem unlikely to take off unless journals enforce the system. But a coalition of leading geneticists may have the answer. The Gene Ontology (GO) Consortium is sidestepping the naming issue by developing 'controlled vocabularies'. These will allow software to scan the genomic databases and link related genes to one another using terms that consistently describe their functions, regardless of what the genes are called. Helen Pearson "Biology's name game" Nature 411: 631-632, 7 June 2001 Human gene nomenclature
HUGO Gene
Nomenclature Committee http://www.genenames.org/ Human gene mutation nomenclature
JT Dunnen, SE Antonarakis SE "Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion" Human Mutation 2000; 15 (1): 7- 12 While a codified mutation nomenclature system for simple DNA lesions has now been adopted broadly by the medical genetics community, it is inherently difficult to represent complex mutations in a unified manner. In this article, suggestions are presented for reporting just such complex mutations. See also the further note on Human Gene Nomenclature at the end of this webpage. Model organisms The Gene OntologyTM 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://wiki.wormbase.org/index.php/UserGuide:Nomenclature post-genomic nomenclature: Ideally, our formalized system of nomenclature is supposed to improve communication among biologists. In reality, it seems to be a major obstacle, especially when misapplied. Although the problem is evident in the literature, it is most severe in the sequence databases, which now serve as the principal source and repository of data used in comparative biology. Moreover, the sequence databases tend to propagate such errors for a variety of reasons. As biological data proliferates and interconnects, it depends increasingly on software infrastructure, and it becomes increasingly obvious that biological names do not meet the requirements of a good identifier, in strict computing terms. A good identifier should be unique and persistent. As an outgrowth of my current DOE funded project, we have been exploring a practical and workable solution that we believe will help solve the problem in a future- roof fashion. Dr. George Garrity – “Carolus Linneaus in the postgenomic era” Contractor Grantee Workshop, DOE Genomes to Life, US, Feb. 9-12, 2003 http://genomicscience.energy.gov/pubs/2003abstracts/comparative.shtml#page=news Protein nomenclature
Species nomenclature: Taxonomy, NCBI, US http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ See also Phylogenomics glossary: species 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/panda/Publications/mbd1.html uBio: An initiative within the science library community to join international efforts to create and utilize a comprehensive and collaborative catalog of names of all living (and once- living) organisms. The Taxonomic Name Server (TNS) catalogs names and classifications to enable tools that can help users find information on living things using any of the names that may be related to an organism. Universal Biological Indexer and Organizer, Marine Biological Laboratory/ Woods Hole Oceanographic Institution Library http://www.ubio.org/index.php HGNC Nomenclature:
Genes, weights and measures, animals, elements, and planets. H. Wain,
E. Bruford, A. Duncanson, R. Lovering, S. Povey July 2000
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. Radiation Research 154, 1-2, 2000 http://www.radres.org/i0033-7587-154-01-0001.pdf 2008 Update http://www.genenames.org/sites/genenames.org/files/documents/PMID17984084.pdf HUGO Gene
Nomenclature Committee http://www.genenames.org/ |
