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Genomics, Proteomics and Informatics Information Sources
and Pharmaceutical Industry Definitions
486 Pharmaceuticals Companies involved in drug research, development, exploitation and distribution other than those classified elsewhere (e.g. Biotechnology)
Non- Cyclical Consumer Goods 48 Pharmaceuticals & Biotechnology, FTSE Global Classification System, 2002 http://www.ftse.com/indices_marketdata/english-global-classification-system2002.pdf
Biotechnology definition of Biotechnology company
Venture capital definition
NAICS North American Industry
Classification 2002 definition
The NASDAQ Biotechnology Index contains companies that are classified according to the FTSE™ Global Classification System as either biotechnology or pharmaceutical which also meet other eligibility criteria. The NASDAQ Biotechnology Index is calculated under a modified capitalization- weighted methodology. http://www.answers.com/topic/nasdaq
Overviews Biotechnology, genomics
BIO Biotechnology Industry Organization, Introductory Guide to Biotechnology http://www.bio.org/aboutbio/guidetoc.html needs updating
Genomics, Bioinformatics, and Proteomics, PhRMA http://science.bio.org/genomics.news.html
The Geee! in Genome, Canada http://nature.ca/genome/
Life Science Databases
Medline/PubMed, NLM http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
EMBASE: http://www.embase.com/ Excerpta Medica Pharmacological and biomedical literature
Nature, Nature Publishing,1859- http://www.nature.com/nature/
PNAS Proceedings of the National Academy of Sciences, 1915- http://www.pnas.org/
BMC Biology, BioMedCentral, 2003- http://www.biomedcentral.com/bmcbiol/ Original research articles and methodology articles in any area of biology but with a focus on the biomedical sciences.
Briefings in Functional Genomics and Proteomics, Henry Stewart http://www.henrystewart.com/journals/fgp/ Reviews the techniques, protocols and approaches in genome and proteome research. The journal aims to provide a centralised resource for researchers in the fields of genomics and proteomics as well as give guidance to scientists new to these areas. Papers range in scope and depth from the introductory level to specific details of protocols and analyses encompassing bacterial, plant, animal and human data. Detailed subject areas covered by the journal include: microarray technology, gene and protein expression profiling, differential display, electrophoresis, genotyping, transgenic systems, mutation screens, protein spectrometry, comparative genomics, phage display and combinatorial libraries.
Current Genomics, Bentham, 2000- http://www.bentham.org/cg/ Human and functional genomics.
Genetics, Genetics Society of America, 1916- http://www.genetics.org/current.shtml
Journal of Structural and Functional Genomics, Springer, 2000- http://www.springerlink.com/link.asp?id=106605 Kihara Memorial Yokohama Foundation for the Advancement of Life Sciences, Japan was original sponsor.
Mutation Research, Elsevier 1964- http://www.sciencedirect.com/science?_ob=JournalURL&_cdi=4918&_auth=y&_acct=C00...
Omics, Mary Ann Liebert, 1996- http://www.liebertpub.com/OMI/default1.asp Covers genomics (the quantitative study of genes, regulatory and noncoding sequences), transcriptomics (RNA and gene expression), proteomics (protein expression), and metabolomics (metabolites and metabolic networks). The Journal explores advances in the era of post-genomic biology and medicine, including pharmacogenomics (the quantitative study on how genetics affects hosts' responses to drugs), and physiomics (physiological dynamics and functions of whole organisms). Integrative, quantitative, experimental, and computational approaches bring new knowledge, novel methods, and innovative technologies to engender a better understanding of complex biological systems and processes. Was Microbial and comparative genomics
Trends in Genetics, Elsevier, 1985- http://www.trends.com/tig/default.htm Aspects of current research in genetics, developmental biology and genomics. Reviews that synthesise for a non- specialist readership current topics in these fields. Perspective articles, in which novel hypotheses are discussed, and comment pieces, which feature key recent developments in genetics. Genome Analysis section, a forum for original observations concerning the function, organisation and evolution of genomes.
Need for full text for text mining, bibliomics, copyright and other economic issues.
Scientific meetings are
an important source of current information
and proteomics organizations
Office of Biotechnology, NIH http://www4.od.nih.gov/oba/
National Institute of Biomedical Imaging and Bioengineering http://www.nibib.nih.gov/index.htm
American Institute for Medical and Biological Engineering http://www.aimbe.org/
International Union of Crystallography http://www.iucr.org/
International Council of the Electrophoresis Societies http://www.aesociety.org/ICES.html
European Society for
Magnetic Resonance in Biology and Medicine http://www.esmrmb.org/
and medicinal chemistry journals
Analytical Biochemistry, Elsevier, 1960- http://www.elsevier.com/locate/issn/0003-2697 Methods in the biological and biochemical sciences. Methods in: Analytical techniques, Membranes and membrane proteins, Molecular genetics: cloning, sequencing, and mutagenesis, Novel methods of protein purification, Immunological techniques applicable to biochemistry, Immunoassays that introduce a unique approach, Cell biology, General cell and organ culture, Pharmacological and toxicological research techniques, Analytical Biochemistry. Also review articles and Notes and Tips: including helpful "kitchen tricks.
Annual reports in Medicinal Chemistry, Elsevier, 1965- http://www.harcourt-international.com/serials/medicinalchemistry/
Biological chemistry, Walter de Gruyter, 1996- http://www.degruyter.de/rs/272_3059_ENU_h.htm General biochemistry, pathobiochemistry, evolutionary biotechnology, structural biology, molecular and cellular biology, molecular medicine, cancer research, virology, immunology, plant molecular biology and biochemistry, and experimental methodologies. Was Biological Chemistry Hoppe Seyler
Bioorganic and Medicinal Chemistry, Tetrahedron, Elsevier, 1993- http://www.sciencedirect.com/science?_ob=JournalURL&_cdi=52206 Molecular interactions in key biological targets such as receptors, channels, enzymes, nucleotides, lipids and saccharides. The aim of the journal is to promote a better understanding at the molecular level of life processes, and living organisms, as well as the interaction of these with chemical agents
Bioorganic and Medicinal Chemistry Letters Tetrahedron, Elsevier, 1991- http://www.sciencedirect.com/science/journal/0960894X Preliminary experimental or theoretical research results of outstanding significance and timeliness on all aspects of science at the interface of chemistry and biology and on major advances in drug design and development
* Chemical and Engineering News, American Chemical Society http://pubs.acs.org/cen/
Current Medicinal Chemistry, Bentham Science, 1994- http://www.bentham.org/cmc/cmcconts.html Medicinal chemistry and rational drug design.
Current Medicinal Chemistry Anti-Cancer Agents, Bentham Science, 2001- http://www.bentham.org/cmcaca/index2.htm Medicinal chemistry and rational drug design for the discovery of new anti-cancer agents.
Current Topics in Medicinal Chemistry, Bentham Science, 2001- http://www.bentham.org/ctmc/index2.htm Review of areas of keen and topical interest to medicinal chemists and others in allied disciplines. Each issue is solely devoted to a specific topic, containing six to nine reviews, which provide the reader a comprehensive survey of that area.
European Journal of Medicinal Chemistry, Elsevier, 1974- http://www.sciencedirect.com/science/journal/02235234
Journal of Enzyme Inhibition and Medicinal Chemistry, Taylor and Francis, 2002- http://www.tandf.co.uk/journals/titles/14756366.html
* Journal of Medicinal Chemistry, American Chemical Society, 1963- http://pubs.acs.org/journals/jmcmar/
Mini-Reviews in Medicinal Chemistry, Bentham, 2001- http://www.bentham.org/mrmc/index2.htm
Trends in Biochemical Sciences, Elsevier, 1976- http://www.elsevier.com/locate/issn/09680004 Review articles, Recent developments in the fields of biophysics, microbiology, plant sciences and medical science. Protein Sequence Motif section is for short original reports of novel motifs shared between sets of proteins.
IUPAC International Union of Pure and Applied Chemistry http://www.iupac.org/dhtml_home.html
Royal Society of
Chemistry, UK http://www.rsc.org/
Synthetic Organic Chemical Manufacturers Association http://www.socma.com/
IEEE Transactions on Nanobioscience http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?puNumber=7728
International Journal of Mass Spectrometry, Elsevier http://www.elsevier.com/locate/ijmsip/
Journal of Mass Spectrometry, Wiley http://www3.interscience.wiley.com/cgi-bin/jhome/6043
Journal of the American Society of Mass Spectrometry, JASMS, Elsevier http://www1.elsevier.com/homepage/saa/webjam/
Mass Spectrometry Reviews, Wiley http://www3.interscience.wiley.com/cgi-bin/jhome/49879
Pharmaceutical Science and Technology Today, Elsevier http://www.trends.com/pstt/default.htm
Rapid Communications in Mass Spectrometry, Wiley http://www3.interscience.wiley.com/cgi-bin/jhome/4849
Trends in Biotechnology, Elsevier, 1983- http://www.elsevier.com/locate/issn/01677799Audience: All biotechnologists who take an integrated, multidisciplinary approach to the applied biosciences. Of particular interest to industrial or academic scientists active in R&D in molecular biotechnology, gene transfer and expression, applied microbiology, environmental biotechnology, fermentation and bioprocessing, rDNA therapeutics and vaccines, plant biotechnology, patenting and regulatory issues.
and development databases
IDRAC Intelligent Regulatory Database http://www.liquent.com/regintelligence_overview.asp
Drug metabolism and disposition, ASPET American Society of Pharmacology and Experimental Therapeutics, 1973- http://dmd.aspetjournals.org/
Drug Metabolism Reviews, Informa, 1972 http://www.informaworld.com/smpp/title~content=t713597246
Drug News & Perspectives http://www.prous.com/journals/advpubdnp.html
European Biopharmaceutical Review, Samedan Ltd. http://www.samedanltd.com/homepage/ebr.htm quarterly
International Immunopharmacology, Elsevier http://www.elsevier.com/inca/publications/store/6/2/1/3/3/0/index. Merger of International Journal of Immunopharmacology and Immunopharmacology
Journal of pharmacology and experimental therapeutics, ASPET, 1909 http://jpet.aspetjournals.org/
Pharmaceutical Statistics, Wiley http://www3.interscience.wiley.com/cgi-bin/jhome/93012805
Pharmacological Reviews, ASPET, 1949- http://pharmrev.aspetjournals.org/
Prous Daily Drug News.com http://www.prous.com/home_daily/
Research Collaboratory for Structural Bioinformatics, http://www.rcsb.org/databases.html Protein and nucleic acids databases
SNP Consortium http://snp.cshl.org/ Public private cooperative effort. Expect to see more of these.
Genomics jumpstation http://highveld.com/f/fgenomics.html
WWW Resources for Model Organisms, Pam M. Gannon HMS Beagle July 24, 1998 http://news.bmn.com/hmsbeagle/35/webres/insitu.htm Reviews of websites for E. coli, yeast, C. elegans, Drosophila, and mouse
Chemical research in Toxicology, American Chemical Society, 1988- http://pubs.acs.org/journals/crtoec/ All aspects of the chemical basis of toxicological responses. It publishes papers devoted to identification of novel toxic agents and reactive intermediates, development of specific and sensitive new methods for detection of modification of biological macromolecules by toxic agents, characterization of the alteration of macromolecular structure and function by interaction with chemical agents, experimental and theoretical studies of chemical factors that control reactivity with specific macromolecules, and metabolism of toxic agents as it contributes to their biological effects.
Drug safety: Expert evaluations in pharmacovigilance, pharmacoepidemiology, benefit-risk and risk management, Adis, 1990- http://www.ingentaconnect.com/content/adis/dsf Reviews on the epidemiology, clinical features, prevention and management of adverse effects of individual drugs or drug classes. Benefit- risk assessments provide you with an in-depth review of adverse effect and efficacy data for a drug in a specific disease. Drug Safety also features reviews covering drug use in particular 'at- risk' patient groups, and concept reviews of current thinking in pharmacovigilance, risk management and medication error prevention. Articles focus on the practical aspects of ensuring the safest possible use of drugs, including analysis and interpretation of adverse effects, post- marketing surveillance and pharmacoepidemiology.
Human and experimental toxicology, Arnold Publishers, 1990- http://www.arnoldpublishers.com/journals/pages/exp_tox/09603271.htm All aspects of experimental and clinical studies of functional, biochemical and structural disorder. Official journal of the British Toxicological Society.
International Journal of Toxicology, Taylor & Francis, 1997- http://www.tandf.co.uk/journals/titles/10915818.html Assessments of the toxicity hazards of industrial chemicals, pharmaceutical agents, environmental contaminants and other entities, and explores their mechanisms of action and relevance to human health. Includes mechanisms of toxicity, risk assessment and safety evaluation, carcinogenicity, reproductive and genetic toxicity, epidemiology and clinical toxicity, new approaches to toxicological testing, alternatives to animal testing, regulatory toxicology
Toxicology and applied pharmacology, Elsevier, 1959- http://www.elsevier.com/locate/issn/0041-008X Research pertaining to action on tissue structure or function resulting from administration of chemicals, drugs, or natural products to animals or humans. Articles address mechanistic approaches to physiological, biochemical, cellular, or molecular understanding of toxicologic/pathologic lesions and to methods used to describe these responses. Papers concerned with alternatives to the use of experimental animals are encouraged.
Clinical trials Clinical trials informatics
trials journals and news
Clinical Trials: Journal of the Society for Clinical Trials, Arnold Journals, 2004- http://www.sctjournal.com/ Design, conduct, analysis, synthesis, history, ethics, regulation and clinical or policy impact of all types of clinical trials and related medical research methodologies
Clinical trials tracker, MarketLetter Publications Ltd. http://www.marketletter.com/index.htm?patent_bulletin.htm Current news on compounds in clinical development, what’s going on in clinical regulatory matters around the world, clinical trials initiation, status, regulatory approvals and disapprovals.
CW Weekly, CenterWatch http://www.centerwatch.com/bookstore/pubs_profs_cwweekly.html Business headlines, financial information, market intelligence, drug pipeline and clinical trials
Controlled Clinical Trials, Elsevier, 1980- http://www.elsevier.com/locate/conclintrial Design, methods and operational aspects of clinical trials, No longer the official journal of the Society for Clinical Trials
HIV Clinical Trials, Thomas Land, 2000- http://www.thomasland.com/app/home/main.asp?wasp=2dyrtjvwmp2yd226ua5y HIV/AIDS therapeutics and clinical research.
Drug discovery journals
Discovery and Development Organizations
EMEA European Agency for the Evaluation of Medicinal Products, Biotechnology Working Party http://www.emea.eu.int/pdfs/human/bwp/662802en.pdf
FDA CBER http://www.fda.gov/cber/
Statisticians in the Pharmaceutical Industry http://www.psiweb.org/public/public...p
ABPI Association of British Pharmaceutical Industry, UK members http://www.abpi.org.uk/links/
IFPMA International Federation of Pharmaceutical Manufacturing Associations http://www.ifpma.org/
PhRMA members http://www.phrma.org/whoweare/members/
BioTEC Canada http://www.biotech.ca/EN/intcdngov.html
Business Information sources Pharmaceuticals
Biotechnology Investment Today http://www.investinbiotech.com/
EDGAR Online Inc http://www.edgar-online.com/start.asp Business, financial and competitive information derived from U.S. Securities and Exchange Commission data
Health News Daily, FDC Reports, Elsevier http://www.healthnewsdaily.com/FDC/Daily/hnd/TOC.htm Articles from the Pink Sheet [Prescription Pharmaceuticals and Biotechnology], Gray Sheet [Medical Devices, Diagnostics and Instrumentation] and Tan Sheet [Non Prescription Pharmaceuticals and Nutritionals].
International Journal of Biotechnology, InderScience Publishers http://www.environmental-expert.com/magazine/inderscience/ijbt/ The objectives of the journal are to develop, promote and coordinate the science and practice of biotechnology. It also aims to help professionals working in the field, engineering and business educators and policy- makers to contribute, to disseminate information and to learn from each other's work. The international dimension is emphasized in order to overcome cultural and national barriers and to meet the needs of accelerating technological change and changes in the global economy.
Journal of Biolaw and Business. NY: Aspen Law & Business. Monthly http://www.biolawbusiness.com/ Biotechnology and life science law, business, regulation and policy.
Journal of Commercial Biotechnology, Henry Stewart, 1994- http://www.henrystewart.com/journals/jcb/ Biopharmaceutical, agrochemical and environmental industries -- financing, bioethics, public relations, innovation, partnering, technology transfer, market analysis, cost containment, corporate strategy, mergers & acquisitions, intellectual property, product development, venture capital, regulation, human resources and licensing. Was Journal of Biotechnology in Healthcare
MedAdNews Engel Publishing, http://www.medadnews.com/index_f.asp September issue is annual Top 50 Pharmaceuticals directory. Top 100 Biotech companies July Business and marketing activities of the pharmaceutical industry.
Pharmaceutical Executive, Advanstar http://www.pharmexec.com/pharmexec/static/staticHtml.jsp?id=28166 Purpose is to provide innovative, practical information and analysis about business and marketing ideas, strategies, and tactics for pharmaceutical industry leaders. Articles should keep readers in the vanguard of product development and management; global marketing and advertising; regulatory affairs; sales management; customer communication tools; business, legal, and financial issues; trends, and the healthcare delivery system.
Pharmaceutical law and industry report, BNA http://www.bna.com/products/health/plir.htm Regulatory and litigation developments affecting the pharmaceutical and biotech industries.
Biotech Rumor Mill http://www.biofind.com/rumor/
InPharm News, Wiley http://www.inpharm.com/External/InpH
Pharmacy Choice http://www.pharmacychoice.com/ web portal
EDGAR, SEC US public companies http://www.sec.gov/edgar.shtml
EDGAR Online Inc http://www.edgar-online.com/investor/ Business, financial and competitive information derived from U.S. Securities and Exchange Commission data
PhRMA Industry profile http://www.phrma.org/publications/publications/profile02/
Non-Federal statistical websites http://www.fedstats.gov/other.html
Univ. of Michigan Statistical Resources on the Web http://www.lib.umich.edu/govdocs/stats.html
As the term has traditionally been used, has referred to studies that uncover the genetically controlled pathways influenced by a single specific compound. Also used to describe a method pioneered by Stuart Schreiber (Harvard Medical School, Howard Hughes Medical Institute involving a phenotypic screen employing a vast library of small molecules that have been introduced into a cellular assay. ... The coverage of such studies can be genomic, but the detailed activity information they provide is at the genetic level (one gene within a particular pathway) http://www-schreiber.chem.harvard.edu [CHI Structural Proteomics report]
chemical genetics: "Chemical genetics approach" first coined [by Rebecca Ward, at Harvard University] on the inaugural cover of Chemistry and Biology nine years ago. Her term reminds us that to understand a life process you should perturb it and determine the consequence and that such an approach should strive to have the broad power and generality of genetics. Stuart L. Schreiber, The Small Molecule Approach to Biology, Chemical & Engineering News, March 3, 2003 http://pubs.acs.org/cen/coverstory/8109/8109genomics.html
Chemical genetics, Stuart Schreiber, Tetrahedron Prize Lecture, 1998 http://www-schreiber.chem.harvard.edu/home/tetrahedron/tetrahedron.html
Describes the use of small synthetic molecules, that elicit a phenotypic change by direct protein interaction, to identify key genes involved in a specific biological pathway of interest. In many cases existing drugs are used as the chemical probes whose overall effect is well established but whose mode of action is not well understood. Chemical genetic experiments therefore, present an opportunity to clarify the specific mode of action of well- known therapeutics.
Emerging medical genomics
Driven by pathogen variability, immune genes have become the most polymorphic loci known, with some genes having over 500 alleles. The main function of these genes is to provide protection against pathogens and they achieve this through complex pathways for antigen processing and presentation. However, even subtle changes in these pathways can lead to genetic miscommunication and result in disease, particularly autoimmune disease. This genetic balancing act also presents a major challenge to transplant medicine where the aim is to minimise the rejection of transplants while not having to compromise the patient's immune system. Stephan Beck, Team 50 Immunogenomics Lab, Wellcome Trust Sanger Institute, UK http://www.sanger.ac.uk/Teams/Team50/
Rocha, Luis M. ."Integrative Technology for Bioinformatics". Los Alamos National Laboratory Internal Report LAUR 01-6859, http://www.c3.lanl.gov/~rocha/bioinformatics/intbio.html
Opportunities in Molecular Biomedicine in the Era of Teraflop Computing, March 3 & 4, 1999, Rockville, MD, NIH Resource for Macromolecular Modeling and Bioinformatics; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana- Champaign http://www.ks.uiuc.edu/Publications/Reports/teraflop/teraHTML.html
We have coined the term Bioinformatics for the study of informatic processes in biotic systems. Our Bioinformatic approach typically involves spatial, multi- leveled models with many interacting entities whose behavior is determined by local information. [Theoretical Biology Group, Univ. of Utrecht, Netherlands, Paulien Hogeweg Director http://www-binf.bio.uu.nl/
Original definition was "the study of informatic processes in biotic systems" Paulien Hogeweg MIRROR beyond MIRROR, puddles of LIFE, in Artificial Life, ed. C.G. Langton, Addison Wesley, 297-316, 1988 [Nick Saville's homepage, Theoretical Biology and Bioinformatics, Utrecht Univ., Netherlands, 1997
OED online definition cites Hogeweg 1978
More Cheminformatics definitions
Chemoinformatics is an integral part of the discipline of knowledge management. [Nicholas J. Hrib, Norton P. Peet "Chemoinformatics: are we exploiting these new science?" Drug Discovery Today 5 (11): 483- 485, Nov. 2000]
Going by the numbers in Google.com cheminformatics seems to be the currently most used form of this word, overtaking chemoinformatics. See the Glossary FAQ question #3 for details and methodology. update numbers
A general term meant to include all forms of molecular transactions and processes that are part of biochemical systems. Some of these pathways may involve linear processing, but many involve complex branches, convergences, and even cycles. .... There are several different classes of biochemical pathways: metabolic pathways, signal transduction cascades, genetic networks, and drug metabolism pathways. In addition, protein interaction data links protein data objects, and can therefore also be conceptualized as graphs. Although the relationship of protein- interaction maps with biochemical pathways is undeniable, it is not obvious. ... the design of adequate models for bio- process representation, manipulation and simulation is still a very open field of research. In conclusion, we will need to examine and discuss the relationships between all pathway information, protein interaction data, and biological process information in order to successfully produce informatics specifications for any of these kinds of data. Biopathways Consortium "Definition" http://www.biopathways.org/
Life sciences informatics
Life science companies are dealing with very large computational data sets. Some are now approaching half terabyte sizes and upward Life science companies also immensely concern themselves with security, because their data represent their crown jewels. Other major concerns expressed by this industry include the stability, scalability, and security of an operating environment. Life science companies and regulatory bodies such as the FDA are more concerned than ever with operating environments that decay with use: When under computational stress, these fragile operating systems have a habit of crashing, and when these systems crash, they tend to corrupt data. ...
Post-genomic, proteomic, chemical information, and other data sets have created a major appetite for solutions to deal with this tremendous amount of data. Scientists are now asking their IT professionals for the ability to better conceptualize and interpret the meaning of this vast information. To do this, scientists need tools for 3D visualization with a tremendous degree of high definition and accuracy. The next step is to take disparate data sets, render them into 3D values, see the DNA and RNA interface, watch protein folds, and then put a therapeutic small molecule in there and see how it relates within a virus that environmentally influences a different process. Scientists Are Demanding Solutions for Dealing with the Post-Genomic, Proteomic, and Chemical Data Deluge: An Interview with Howard Asher, Director, Global Life Sciences Group, Sun Microsystems, CHI GenomeLink 30 http://www.healthtech.com/newsarticles/issue30_1.asp
Wiley Bioinformatics http://www.wileyeurope.com/WileyCDA/Section/id-4548.html
Wiley Genomics http://www.wiley.co.uk/genomics/
Wiley Proteomics http://www.wiley.co.uk/genomics/proteomics.html
Information Science Technologies, CORDIS, European Union http://www.cordis.lu/ist/
W3C World Wide Web Consortium: http://www.w3.org/ Develops interoperable technologies (specifications, guidelines, software, and tools) to lead the Web to its full potential. W3C is a forum for information, commerce, communication, and collective understanding.
Web Services Activity, W3C http://www.w3.org/2002/ws/
CORBA Common Object Request Broker Architecture, OMG http://www.omg.org/gettingstarted/corbafaq.htm
FDA, Electronic standards for the transfer of regulatory information, Glossary of Abbreviations and Terms http://www.fda.gov/cder/m2/pdf/glossary.pdf
Finishing Standards for the Human Genome Project,
Genome Sequencing Center, School of Medicine, Washington Univ. St. Louis,
Version September 7, 2001
ICH International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use ICH: A decade long effort ... This harmonization of many aspects of an application forms the basis for a satisfying and successful relationship among the United States, Canada, the European community and Japan. Our countries share the goal of harmonizing our standards and simplifying the regulatory process that impacts a global marketplace. Jane E. Henney, FDA, Life After PDUFA, FDAMA and ICH, Millennial World Congress, San Francisco CA, Apr. 16, 2000 http://www.fda.gov/oc/speeches/2000/pharmsciences41600.html
MIAME Minimum Information About a Microarray Experiment: MIAME aims to outline the minimum information required to unambiguously interpret microarray data and to subsequently allow independent verification of this data at a later stage if required. MIAME is not a dogma for microarray experiments to follow, but just a set of guidelines. This set of guidelines will then assist with the development of microarray repositories and data analysis tools. [MIAME homepage 2003] http://www.mged.org/Workgroups/MIAME/miame.html
NISO Z39.19 Standard for Structure and Organization of Information Retrieval Thesauri http://www.niso.org/standards/resources/Z39-19.html
OASIS Organization for the Advancement of Structured Information Systems: A not- for- profit, global consortium that drives the development, convergence and adoption of e-business standards. http://www.oasis-open.org/who/
Open source http://www.opensource.org/advocacy/faq.php
RefSeq Reference sequence standards for the naturally occurring molecules of the central dogma, from chromosomes to mRNAs to proteins. Toward this goal, intermediate larger genomic regions, contigs, are also produced. RefSeq standards provide a foundation for the functional annotation of the human genome. They provide a stable reference point for mutation analysis, gene expression studies, and polymorphism discovery. RefSeq, LocusLink, NCBI, US http://www.ncbi.nlm.nih.gov/RefSeq/
Standards and ontologies for functional genomics, http://www.sofg.org/
Chris Stoeckert, Microarray Databases: Standards and Ontologies, Chipping Forecast II, Nature Genetics 32: supplement, 469 – 473, Dec. 2002 [requires free registration] http://www.nature.com/ng/journal/v32/n4s/pdf/ng1028.pdf
BSML Bioinformatic Sequence Markup Language http://www.bsml.org/
CML Chemical Markup Language Wikipedia http://en.wikipedia.org/wiki/Chemical_Markup_Language http://www.bisti.nih.gov/bistic2.cfm
DAML DARPA Agent Markup Language http://www.daml.org/
DAML + OIL http://www.w3.org/TR/daml+oil-walkthru/
MAGE-ML MicroArray and Gene Expression Markup Language http://www.w3.org/Math/whatIsMathML.html
MatML Materials Markup Language http://www.ceramics.nist.gov/matml/matml.htm
Tissue Engineered Medical Products Standards TEMPS: The standards process for tissue engineered medical products is underway within the American Society for Testing and Materials (ASTM) Committee F-04, Division IV Tissue Engineered Medical Products (http://www.astm.org/) or Committee F04 on Medical and Surgical Materials and Devices. The Executive Roster was established. Information describing the process and progress will be presented at this FDA site. Up dated information and current draft documents can be viewed at http://lindacuster.com/temps Additional information may be obtained at the Pittsburgh Tissue Engineering Initiative site (www.ptei.org FDA, Center for Devices & Radiologic Health, US, Tissue Engineered Medical Products Standards TEMPS, 2002 http://www.fda.gov/CDRH/Tisseng/temps.html
VRML Virtual Reality Modeling Language http://www.w3.org/MarkUp/VRML/
XACML Extensible Access Control Markup Language
XML eXtensible Markup Language http://www.w3.org/XML/
XML in 10 points http://www.w3.org/XML/1999/XML-in-10-points
Robin Cover, Core Standards for Markup Languages, 2002 http://xml.coverpages.org/coreStandards.html
Taxonomies and ontologies
Directories such as Yahoo or the Open Directory Project can be called taxonomies – they are examples of navigational taxonomies. Ontologies is a term originally from philosophy, but used by the Artificial Intelligence AI community for some decades now. As used by the W3C community implies machine processable and understandable as well as machine readable.
Data Mine http://www.the-data-mine.com/
SIGKDD, Special Interest Group Knowledge Discovery in Data and Data Mining, Association for Computing Machinery http://www.acm.org/sigkdd/
Molecular Biology Toolkit, SDSC San Diego Supercomputer Center http://mbt.sdsc.edu/
Micropatent, Information Holdings, Inc. http://www.micropat.com/
on Molecular Medicine
BMC Medical Informatics and Decision Making, BioMedCentral, 2001- http://www.biomedcentral.com/bmcmedinformdecismak/ Original research articles in information management, systems and technology in healthcare and the study of medical decision making
BMC Medical Research Methodology, BioMedCentral, 2001- http://www.biomedcentral.com/bmcmedinformdecismak/ Original research articles in information management, systems and technology in healthcare and the study of medical decision making
BMC Medicine, BioMedCentral, 2003- http://www.biomedcentral.com/bmcmed/ Original research articles, technical advances and study protocols in any area of medical science or clinical practice.
Nature Reviews Cancer, Nature Publishing, 2001- http://www.nature.com/nrc/ Impact factor 13.6
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