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Bioethics, Terminology & nomenclature  -omics & informatics, drug discovery & development & molecular medicine
Mary Chitty mchity@healthtech.com 617-630-1316
no longer being updated

Terminology   Genomics  Proteomics     toxicogenomics   bioinformatics   medicinal & pharmaceutical chemistry   cheminformatics   technologies   molecular medicine    
Nomenclature   human genes   non-human genes   proteins   species 

Bioethics

Bioethics Journals
BMC Medical Ethics, BioMedCentral, 2000-  http://www.biomedcentral.com/bmcmedethics/  Original research articles in the ethics of medical research and practice.

Websites
 Bermuda principles: Agreed upon coordinated rapid release of data into the public domain. Summary of principles agreed at the International Strategy Meeting on Human Genome Sequencing, Bermuda, 25th- 28th February 1996, Sponsored by the Wellcome Trust, HUGO http://www.gene.ucl.ac.uk/hugo/bermuda.htm

Bioethical Issues, BIOME, UK   http://bioresearch.ac.uk/nb/a9ca8522f09837da77d0c1d5b132732b.html

ELSI Resources, CDC Centers for Disease Control and Prevention?, US  http://www.cdc.gov/genetics/links/ethical.htm

Ethical, legal & social issues, DOE Dept. of Energy, Human Genome Project, Oak Ridge National Lab, US  http://www.ornl.gov/hgmis/elsi/elsi...l
Ethical, legal & social issues Research DOE, Human Genome Project, Oak Ridge National Lab, US http://www.ornl.gov/hgmis/research/elsi.html

Genetic privacy: Genetics Privacy and Legislation, HGMIS, DOE, US   http://www.ornl.gov/TechResources/Human_Genome/elsi/legislat.html

Minorities, Race and Genetics: Human Genome Project Information, DOE, US http://www.ornl.gov/TechResources/Human_Genome/elsi/minorities.html

ELSI NHGRI, National Human Genome Research Institute, NIH, US http://www.nhgri.nih.gov/ELSI/

ELSI NIEHS, National Institute of Environmental Health Sciences, NIH, US http://www.niehs.nih.gov/envgenom/elsi.htm

Nature Genome Ethics     

Nuffield Council on Bioethics, Nuffield Trust, Wellcome Foundation, Medical Research Council http://www.nuffieldbioethics.org/home/   Ethical issues arising from developments in medicine and biology, including genetic screening, stem cell research, xenotransplantation, GMOs, genetics and human behaviour, patenting DNA.

Precautionary Principle, AgBioTech InfoNet, 2002 http://www.biotech-info.net/precautionary.html

President's Council on Bioethics, US http://www.bioethics.gov/ Reports and background information on cloning, stem cells, genetic enhancement, patenting human life, biotechnology and public policy, sex selection.

Steven Pinker on why designer babies are unlikely anytime soon.  http://www.bioethics.gov/transcripts/march03/session3.html

Public Agenda: Medical Research http://publicagenda.org/issues/debate.cfm?issue_type=medical_research Discussion guides

Who Owns Life? Center for Bioethics, Univ. of Pennsylvania, US http://www.bioethics.upenn.edu/prog/wol/index.shtml 

Public policy
Genetics and Public Policy Center, http://dnapolicy.org/policy/index.jhtml.html 
Policy and ethics, NHGRI, US  http://www.genome.gov/PolicyEthics/
Nature Policy http://www.nature.com/nsu/categories/technology.html
Science’s Next Wave: Science Policy http://nextwave.sciencemag.org/pol.dtl

Terminology
A note on terminology: Many terms are still evolving and used for a variety of meanings and contexts. Words and phrases in bold are defined in the text. Subtle variations may or may not imply differences in meaning. These topics overlap with other sections of the book and specific resources may fit better elsewhere 

The Bioinformatics section has some discussion of taxonomies and ontologies, and how they offer promise (not yet implemented for the most part) in working towards interoperable data and databases.

Terminology Bibliography
Scientific Resources: Online glossaries, Science Online http://www.sciencemag.org/feature/plus/sfg/education/glossaries.shtml

IUPAC e-news  http://lists.ibiblio.org/mailman/listinfo/iupac-enews Useful for keeping up with new terminology and nomenclature compilations.

Terminology resources:  Biotechnology, Genomics 
Biopharmaceutical glossaries, Mary Chitty, Cambridge Healthtech http://www.genomicglossaries.com/default.asp Pharmaceutical & biotechnology terms & definitions not in most dictionaries, 4,000 terms.

Glossary of Biotechnology for Food and Agriculture, FAO Food and Agricultural Organization, 2002, 3196 terms http://www.fao.org/biotech/index_glossary.asp Not just for food or agriculture

Gene Ontology definitions  Gene Ontology  http://www.geneontology.org/doc/GO.defs

Talking glossary of genetic terms National Human Genome Research Institute, NIH  http://www.genome.gov/glossary.cfm

Genome Glossary, Oak Ridge National Lab, Dept. of Energy http://www.ornl.gov/sci/techresources/Human_Genome/glossary/

Proteomics
SWISS-PROT keywords Swiss Institute of Bioinformatics, Geneva Switzerland and European Bioinformatics Institute, Hinxton, UK, 2001, 800 + definitions.

Print only terminology resources
Bains, William, Biotechnology A-Z, Oxford University Press, 1998. About 400 entries/definitions.  
King’s Dictionary of Genetics, Oxford University Press, 2002, 6th edition
Oxford Dictionary of Molecular Biology and Biochemistry, Oxford University Press, 2000 
Zhang, Yong-he and Meng Zhang, A Dictionary of Gene Technology Terms, Parthenon Publishing, 2001  4500 + definitions.

Toxicogenomics terminology
IUPAC is working on a Glossary for toxicokinetics of chemicals. The terminology will include information on chemical speciation, the chemistry- speciation for toxic substances, analytical methods, analytical equipment, and biological activity of the chemicals. Completion date 2003. http://www.iupac.org/projects/2000/2000-034-2-700.html

International Union of Pure and Applied Chemistry, GLOSSARY FOR CHEMISTS OF TERMS USED IN TOXICOLOGY, Clinical Chemistry Division, Commission on Toxicology, Recommendations. Pure and Appl. Chem., 65 (9):  2003- 2122, 1993. 1200+ definitions.   http://sis.nlm.nih.gov/main.htm  http://www.iupac.org/reports/1993/6509duffus/index.html

Glossary, National Center for Toxicogenomics, NIEHS, US http://www.niehs.nih.gov/dert/trc/glossary.htm   30+ definitions

Glossary of IRIS [Integrated Risk Information System] Terms, Environmental Protection Agency, 2003, 130+ terms http://www.epa.gov/IRIS/help_gloss.htm

Biotechnology Intellectual property Terminology

Technologies terminology
Microarrays and protein chips glossary  http://www.genomicglossaries.com/content/microarrays.asp

Bioinformatics Terminology 
 Bioinformatics glossary, Mary Chitty http://www.genomicglossaries.com/content/Bioinformatics_gloss.asp

Genome Bioinformatics Terminology, UC Santa Cruz http://bioinfo.hku.hk/ucsc/goldenPath/term.html

Medicinal and Pharmaceutical Chemical Terminology
 IUPAC International Union of Pure & Applied Chemistry, Glossaries and Nomenclature http://www.chem.qmw.ac.uk/iupac/  
IUPAC Combinatorial Chemistry http://www.iupac.org/reports/1999/7112maclean/
IUPAC Computational Drug Design  http://www.iupac.org/reports/1997/6905vandewaterbeemd/
IUPAC Medicinal Chemistry http://www.chem.qmw.ac.uk/iupac/medchem/

Chemical Informatics Terminology
Chitty, Mary, Cheminformatics glossary, Cambridge Healthtech http://www.genomicglossaries.com/content/chemoinformatics_gloss.asp

Goodman, Jonathan, Chemical Informatics Letters Glossary  http://www.ch.cam.ac.uk/MMRG/CIL/gloss.html

Molecular Medicine terminology
Glossary of Clinical Trials Terms, NLM, 2003 http://clinicaltrials.gov/ct/info/glossary 80+ terms  Treatment trials, diagnostic trials, prevention trials, screening trials, quality of life trials

Molecular Diagnostics Terminology
 McNerney, Ruth, Glossary of terms commonly used in molecular diagnostics, Dept. of Infectious and Tropical Diseases, London School of Hygiene & Tropical Diseases, 1999, about 50 terms. http://www.lshtm.ac.uk/pmbu/staff/rmcnerney/homepage/glos.

Nomenclature
The issue here is not only that scientists are truly terrible about sticking to established terminologies. “Scientists would rather share each other's underwear than use each other's nomenclature,” as biochemist Keith Yamamoto is fond of saying. Steven Dickman, Tough Mining: The challenges of searching the scientific literature, PLOS Biology, 1(2) Nov. 2003

Human Gene Nomenclature HUGO Gene Nomenclature Committee http://www.genenames.org/ 
We have approved symbols for nearly one half of the genes in the human genome and, with an estimated 15,000 more genes to name, we still have plenty to do!

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 # 6, NCBI, US http://www.ncbi.nlm.nih.gov/SNP/get_html.cgi?whichHtml=faq#hum%20gen%20nomen

Guidelines for Human Genome Nomenclature, HUGO 2002 http://www.gene.ucl.ac.uk/nomenclature/guidelines.html

HGNC Gene Grouping Family Nomenclature, HUGO http://ash.gene.ucl.ac.uk/nomenclature/genefamily...l

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

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

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

Protein nomenclature and beyond
SWISS- PROT Protein Sequence Data Bank, List of nomenclature related references for proteins, Amos Bairoch.   Definitions

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

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

See also proteomics terminology

Chemical nomenclature
IUPAC Nomenclature: Recommendations on Organic & Biochemical Nomenclature and Symbols http://www.chem.qmul.ac.uk/iupac/
IUPAC Nomenclature of Organic Chemistry, 1979, 1993 recommendations  http://www.acdlabs.com/iupac/nomenclature/  

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