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More genomics overviews
More databases   Bibliographic   Drug discovery & development    pipeline
More journals   Key top journals chemical journals  genomics   medicinal chemistry   technologies     drug discovery and development   pharmacology & metabolism   toxicogenomics
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More Organizations    Analytical & medicinal chemistry   drug discovery & development   biotechnology  bioinformatics
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Biotechnology and Pharmaceutical Industry Definitions
FTSE [London Stock Exchange] definition Biotechnology company
482 Biotechnology Companies, the majority of whose research involves the use of living material as its means of drug discovery and diagnostics development. The majority of its revenue is derived from either the sale or of these drugs and/or diagnostics tools. 

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 

Nature Biotechnology definition of Biotechnology company
Nature Biotechnology's definition of a biotechnology company is broad. We focus on companies whose future business would rely heavily on R&D in the life science areas, and that spend at least 10% of their revenue on R&D. Pharmaceutical companies are excluded, although we appreciate that this is unfairly discriminatory because they also invest large sums in R&D and are intimately involved in the biotechnology sector. Other companies classified as biotechnology companies include those providing support services, such as database providers (Incyte Pharmaceuticals, Palo Alto, CA), manufacturers of microarrays and other high-tech equipment (Affymetrix, Santa Clara, CA); Aclara, Mountain View, CA) and clinical research service organizations (Parexel, Waltham, MA; Quintiles Transanational S. San Francisco, CA.)  Nature Biotechnology Nature Biotechnology  21, 607 - 612, 2003 doi:10.1038/nbt0603-607 2003 

Biotechnology: Venture capital definition
Developers of technology promoting drug development, disease treatment, and a deeper understanding of living organisms. Includes human, animal, and industrial biotechnology products and services. Also included are biosensors, biotechnology equipment, and pharmaceuticals. Industry Definitions, PriceWaterhouseCoopers/ Thomson Venture Economics/ National Venture Capital Association, MoneyTreeTM Survey, 2003

NAICS North American Industry Classification 2002 definition
541710 Research and Development in the Physical, Engineering, and Life Sciences
This industry comprises establishments primarily engaged in conducting research and experimental development in the physical, engineering, and life sciences, such as agriculture, electronics, environmental, biology, botany, biotechnology, computers, chemistry, food, fisheries, forests, geology, health, mathematics, medicine, oceanography, pharmacy, physics, veterinary, and other allied subjects.

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. 

More Overviews Biotechnology, genomics
About Biotech About Biotech/Biomedical,

BIO Biotechnology Industry Organization, Introductory Guide to Biotechnology needs updating

Genomics, Bioinformatics, and Proteomics, PhRMA

The Geee! in Genome, Canada

Life Science Databases
Bibliographic databases
Entrez, NLM portal
Text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others (27 databases as of Sept. 30, 2003)

Medline/PubMed, NLM


EMBASE:   Excerpta Medica Pharmacological and biomedical literature

Key top journals
Cell, Cell Press, 1974- 

Nature, Nature Publishing,1859-

PNAS Proceedings of the National Academy of Sciences, 1915-

Science, AAAS, 1883-
Science Online

More genomics journals
Annual Review of Genomics and Human Genetics, Annual Reviews 2000-

BMC Biology, BioMedCentral, 2003- 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  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- Human and functional genomics.

Genetics, Genetics Society of America, 1916- 

Journal of Structural and Functional Genomics, Springer, 2000-  Kihara Memorial Yokohama Foundation for the Advancement of Life Sciences, Japan was original sponsor.

Mutation Research, Elsevier 1964-

Omics, Mary Ann Liebert, 1996- 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- 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.

Life Science Publishing
There are enormous ongoing changes in publishing. 

HighWire Press Useful semi-automated taxonomy indexes  indexes 300+ HighWire journals, PubMed, National Library of Medicine, NIH   
Public Library of Science PLOS
PubMed Central

Need for full text for text mining, bibliomics, copyright and other economic issues.

Scientific meetings are an important source of current information
BioMedNet conference reporter
Nature Science Update/conferences
Science Meetings

Genomics and proteomics organizations
European Union
CORDIS Community Research and Development Information Service European Union’s Sixth Framework Program FP6 Life Sciences, genomics and biotechnology for health
Life Science, Genomics and Biotechnology for Health, CORDIS, 6th Framework [2002-2006] European Union , EMBO  a next generation scientific information platform that will interlink genomic and other factual data with the life sciences research literature
Biotechnology Ireland, Bioresearch Ireland Kingdom
BBSRC Biotechnology and Biological Sciences Research Council, UK 
MRC Medical Research Council, UK

US government
DOE, Department of Energy, Genome Programs
Involvement dates from post WWII work with radiation and gene mutations, predates NIH involvement. NIH National Institutes of Health
NHGRI National Human Genome Research Institute
NIGMS National Institute of General Medical Sciences, NIH
NCRR National Center for Research Resources, NIH

International organizations
HUGO Human Genome Organization 
HUPO Human Proteome Organization
Proteome Society
ASBMB American Society of Biochemistry and Molecular Biology
Protein Society 
RNA Society

Technologies organizations
IBio, UK,  Biotechnology portal
Biotechnology Regulatory Atlas Guides SMEs [small and medium- sized enterprises] and start-up companies to effective compliance strategies, equipping them to minimise the risks and costs arising from knowledge gaps.

BECON Bioengineering Consortium: The focus of bioengineering activities at the NIH. The Consortium consists of senior- level representatives from all of the NIH institutes, centers, and divisions plus representatives of other Federal agencies concerned with biomedical research and development. BECON is administered by the National Institute of Biomedical Imaging and Bioengineering (NIBIB).

Office of Biotechnology, NIH
Guidelines for Research Involving Recombinant DNA Molecules

National Institute of Biomedical Imaging and Bioengineering

ABRF Association of Biomolecular Resource Facilities

American Institute for Medical and Biological Engineering

International Union of Crystallography

International Council of the Electrophoresis Societies

American Society of Mass Spectrometry
International Mass Spectrometry Society

European Society for Magnetic Resonance in Biology and Medicine
International Society for Magnetic Resonance in Medicine
Japanese Society for Magnetic Resonance in Medicine

Analytical and medicinal chemistry journals
Analytical Chemistry,
American Chemical Society, 1947- Analytical measurements and the best new ways to increase accuracy, selectivity, sensitivity, and reproducibility. Coverage includes the latest peer- reviewed research and significant applications in bioanalysis, electrochemistry, mass spectrometry, microscale systems, environmental analysis, separations, and spectroscopy. Features and news articles about new analytical concepts, novel apparatus, research published in other international journals, developments in computers and on the Web, and evolving approaches to analytical chemistry education.

Analytical Biochemistry, Elsevier, 1960-  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-

Biological chemistry, Walter de Gruyter, 1996-  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- 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-   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

Current Medicinal Chemistry, Bentham Science, 1994-  Medicinal chemistry and rational drug design. 

Current Medicinal Chemistry Anti-Cancer Agents, Bentham Science, 2001-  Medicinal chemistry and rational drug design for the discovery of new anti-cancer agents.  

Current Topics in Medicinal Chemistry, Bentham Science, 2001-  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- 

Journal of Enzyme Inhibition and Medicinal Chemistry, Taylor and Francis, 2002-  

* Journal of Medicinal Chemistry, American Chemical Society, 1963-  

Mini-Reviews in Medicinal Chemistry, Bentham, 2001-  

Trends in Biochemical Sciences, Elsevier, 1976- 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.

Chemistry Organizations
American Chemical Society portal

IUPAC International Union of Pure and Applied Chemistry

Royal Society of Chemistry, UK
Biomedical and environmental

Synthetic Organic Chemical Manufacturers Association

More Technologies journals
Assay and drug development technologies, Mary Ann Liebert

IEEE Transactions on Nanobioscience

International Journal of Mass Spectrometry, Elsevier

Journal of Mass Spectrometry, Wiley

Journal of the American Society of Mass Spectrometry, JASMS, Elsevier

Mass Spectrometry Reviews, Wiley

Pharmaceutical Science and Technology Today,  Elsevier

Rapid Communications in Mass Spectrometry, Wiley

Trends in Biotechnology, Elsevier, 1983- 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. 

Technologies websites
U.S. Congress, Office of Technology Assessment, The OTA Legacy: 1972-1995 (Washington, DC: April 1996) <URL:> New technologies can be useful, but knowing the lessons of the older technologies is helpful as well.

Drug discovery and development databases
ADIS R&D Insight
IMS R&D Focus, IMS
NDA Pipeline, FDC Reports
PharmaProjects, PJB, UK
Prous Drug Data Report
Prous Drugs of the Future

IDRAC Intelligent Regulatory Database

Drug metabolism and pharmacology and other journals
Current Drug Metabolism, Bentham, 2000

Drug metabolism and disposition, ASPET American Society of Pharmacology and Experimental Therapeutics, 1973-

Drug Metabolism Reviews, Informa, 1972  

Drug News & Perspectives

European Biopharmaceutical Review, Samedan Ltd. quarterly

International Immunopharmacology, Elsevier Merger of International Journal of Immunopharmacology and Immunopharmacology

Journal of pharmacology and experimental therapeutics, ASPET, 1909

Pharmaceutical Statistics, Wiley

Pharmacological Reviews, ASPET, 1949-

Prous Daily Drug

Nature, Encyclopedia of Life Sciences

Research Collaboratory for Structural Bioinformatics, Protein and nucleic acids databases

SNP Consortium Public private cooperative effort.  Expect to see more of these.

Genomics jumpstation

WWW Resources for Model Organisms, Pam M. Gannon HMS Beagle July 24, 1998  Reviews of websites for E. coli, yeast, C. elegans, Drosophila, and mouse

Toxicology journals
Cell biology and toxicology, Kluwer, 1984-  Cell biology, genetic, molecular and cellular toxicology.  The scope of publication includes scientific reports dealing with the basic biology and with the physiological, pharmacological, and toxic response of cellular systems. Studies of subcellular and cellular systems derived from both prokaryotic and eukaryotic cell types are appropriate. Studies of toxic effects may include, but are not limited to, cytotoxicity, mutagenicity, carcinogenicity, and teratogenicity. Moreover, investigations on the development of cell systems for these purposes are relevant. In particular, the journal welcomes approaches to cellular studies or molecular structure activity correlations that provide sound scientific information leading to the reduced use of experimental animals.

Chemical research in Toxicology, American Chemical Society, 1988- 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-  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-  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- 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-  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

Clinical trials journals and news
Applied Clinical trials, Advanstar

Clinical Trials: Journal of the Society for Clinical Trials, Arnold Journals, 2004- 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. 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  Business headlines, financial information, market intelligence, drug pipeline and clinical trials

Controlled Clinical Trials, Elsevier, 1980-  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- HIV/AIDS therapeutics and clinical research.

Drug discovery journals
Journal of Biopharmaceutical Statistics, Marcel Dekker, 1991-  Quality applications of statistics in biopharmaceutical research and development and statistical methodology. Covers drug, device, and biological research and development, drug screening and drug design, assessment of pharmacological activity, pharmaceutical formulation and scale- up, preclinical safety assessment, bioavailability, bioequivalence, and pharmacokinetics, phase I, II, and III clinical development, premarket approval assessment of clinical safety, postmarketing surveillance, manufacturing and quality control, technical operations, regulatory issues 

Drug Discovery and Development Organizations
American Society of Pharmacology and Experimental Therapeutics ASPET

EMEA European Agency for the Evaluation of Medicinal Products, Biotechnology Working Party

FDA CDER Many biologics products were transferred from CBER to CDER as of July 2003 

Statisticians in the Pharmaceutical Industry

ABPI Association of British Pharmaceutical Industry, UK members

IFPMA International Federation of Pharmaceutical Manufacturing Associations

PhRMA members

BioTEC Canada 
Canada's Research Based Pharmaceutical Companies  50+ companies

More Business Information sources Pharmaceuticals
, PJB  Management trends, business strategies, financial challenges, scientific breakthroughs, and other industry- specific issues. still published?

Biotechnology Investment Today

EDGAR Online Inc  Business, financial and competitive information derived from U.S. Securities and Exchange Commission data

Health News Daily, FDC Reports, Elsevier 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   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  Biotechnology and life science law, business, regulation and policy. 

Journal of Commercial Biotechnology, Henry Stewart, 1994- 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, September issue is annual Top 50 Pharmaceuticals directory. Top 100 Biotech companies July  Business and marketing activities of the pharmaceutical industry.

Pharmaceutical Executive, Advanstar 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  Regulatory and litigation developments affecting the pharmaceutical and biotech industries.

Biotech Rumor Mill 

InPharm News, Wiley


Pharmacy Choice web portal 

EDGAR, SEC US public companies

EDGAR Online Inc Business, financial and competitive information derived from U.S. Securities and Exchange Commission data

PhRMA Industry profile

Non-Federal statistical websites

Univ. of Michigan Statistical Resources on the Web

Special topics  Data mining   Markup Languages   Ontologies and taxonomies  semantics and syntax – integrating data   Standards   Visualization 

More on chemical genomics
(Sometimes referred to as chemical genomics) was most likely first used by Vertex Pharmaceuticals to describe its parallel drug design approach, which involves using structures of proteins in a given family to design drugs for the family as a whole. The Vertex approach is truly parallel (i.e., involving multiple targets at once) and combines structural biology, biased library design and screening, and structure- based drug design. At its limit, chemogenomics represents the discovery and description of all possible compounds that can interact with any protein encoded by the human genome. The term chemogenomics is slowly (and somewhat grudgingly) catching on. Broadly, it now appears to mean "taking a combinatorial approach to screening protein targets by family/ class." Detailed protein structure information is used to design libraries that are "biased" to contain compounds that are more likely to interact with a particular protein family (hence, it is a "genomic" approach). This screening methodology helps researchers identify the best small molecule compound to bind to a target (hence it is a "chemical" approach). [CHI Structural Proteomics report]

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) [CHI Structural Proteomics report]

Chemical genomics
Some groups (e.g., NeoGenesis) have used this term to describe the broader meaning of chemogenomics (i.e., target- oriented libraries screened against small molecules). Other experts believe this term is a better name for what Stuart Schreiber refers to as chemical genetics. [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  

Chemical genetics, Stuart Schreiber, Tetrahedron Prize Lecture, 1998

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 specialties
The goal of this PGA [Program for Genomic Applications] is to begin linking genes to function, dysfunction and structural abnormalities of the cardiovascular system caused by clinically relevant, genetic and environmental stimuli. The principal biological theme to be pursued is how the transcriptional network of the cardiovascular system responds to genetic and environmental stresses to maintain normal function and structure, and how this network is altered in disease [to] generate a high quality, comprehensive data set for the functional genomics of structural and functional adaptation of the cardiovascular system by integrating expression data from animal models and human tissue samples, mutation screening of candidate genes in patients, and DNA polymorphisms in a well characterized general population Such a data set will serve as a benchmark for future basic, clinical and pharmacogenomic studies. National Heart, Lung & Blood Institute, NIH, US "Genomics of Cardiovascular Development, Adaptation, and Remodeling (CardioGenomics)" 2001

Proteins differentially  expressed in normal and failing human hearts. Cardiogenomics, Myogen, US  

Technology allows the monitoring of ever denser and longer serial biological and physical environmental data. This in turn allows the recognition of time structures, chronomes, including, with an ever broader spectrum of rhythms, also deterministic and other chaos and trends. Chronomics thus resolves the otherwise impenetrable "normal range" of physiological variation and leads to new, dynamic maps of normalcy and health in all fields of human endeavor, including, with health care, physics, chemistry, biology, and even sociology and economics. F. Halberg et. al. "Essays on chronomics spawned by transdisciplinary chronobiology. Witness in time: Earl Elmer Bakken" Neuroendocrinology Letters 22 (5): 359- 384 Oct. 2001

Pharmacokinetic parameters are generally assumed to be invariate with the time of day, although circadian variation of drug metabolism and drug response is known. As proposed, chronopharmacokinetics considers the implications of the chronovariability of pharmacokinetic parameters. In order to investigate chronovariation in the rate of disappearance of a substance from the approximate a linear course until very low blood levels are attained. ... It is concluded that: 1) rhythmicity within elimination curves can only be determined by repetition of the experiment at different times of the diel period; 2)the expectation that a rate-constant estimated at one time of the day may be valid for another part of the day carries with it an unknown risk. No pharmacokinetic analysis can be considered definitive unless chronopharmacokinetic variation of parameters is considered. FM Sturtevant, Chronopharmacokinetics of ethanol. I. Review of the literature and theoretical considerations, Chronobiologia 3(3): 237- 262, Jul-Sept 1976

Gene Therapy
The term 'gene therapy' encompasses at least four types of application of genetic engineering for the insertion of genes into humans. The scientific requirements and the ethical issues associated with each type are discussed. Somatic cell gene therapy is technically the simplest and ethically the least controversial. The first clinical trials will probably be undertaken within the next year [1986]. Germ line gene therapy will require major advances in our present knowledge and it raises ethical issues that are now being debated. In order to provide guidelines for determining when germ line gene therapy would be ethical, the author presents three criteria which should be satisfied prior to the time that a clinical protocol is attempted in humans. Enhancement genetic engineering presents significant, and troubling, ethical concerns. Except where this type of therapy can be justified on the grounds of preventive medicine, enhancement engineering should not be performed. The fourth type, eugenic genetic engineering, is impossible at present and will probably remain so for the foreseeable future, despite the widespread media attention it has received. W. French Anderson "Human gene therapy: scientific and ethical considerations" J Med Philosophy 10 (3): 275- 291, Aug. 1985

Research in the Immunogenomics Laboratory is focused around the study of the organisation, function and evolution of vertebrate defense genes, particularly those encoded by the Major Histocompatibility Complex (MHC) and the Leukocyte Receptor Complex (LRC). Both complexes form integral parts of the immune system. The MHC is the most important genetic region in relation to infection and common disease such as autoimmunity.

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

Technology based on applications of cells and molecules of the immune system. A major research interest is the application of human recombinant antibodies and antibody fragments in medical and industrial applications, as well as studies of mechanisms underlying somatic mutations in B cells and IgE switch in allergy. The use of synthetic antibodies in proteome analysis, including protein array technology is also pursued as well as gene array analysis of the transcriptome. B cell malignancies is one focus in antibody and gene therapy projects as well as viral infection in molecular breeding projects. [Dept. of Immunotechnology, Lund Univ., Sweden, 2002

The concept of using the immune system to treat disease, for example, developing a vaccine against cancer. Immunotherapy may also refer to the therapy of diseases caused by the immune system, allergies for example. [NHGRI]

CNS disorders affect a vast patient population and represent a huge area of unmet therapeutic need. In the United States alone, Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS) afflict more than 6.5 million people. Drug discovery efforts for the most prevalent CNS diseases have met with varying success; it is estimated that billions of dollars are spent every year on prescription drug sales, however, many current therapies merely treat the symptoms but do not provide cures. CHA Cambridge Healthtech Advisors,  Neurogenomics and Neurotherapeutic Strategies: New Directions in Platforms, Targets, and Therapeutic Approaches report, 2005 

Protein profiling related to CNS cells, tissues and neurodegenerative and neuropsychiatric conditions.

More Informatics definitions

Selected Bioinformatics reports
EU US Large Scientific Databases  Annapolis MD Sept. 8-10, 1999

Rocha, Luis M. [2001]."Integrative Technology for Bioinformatics". Los Alamos National Laboratory Internal Report LAUR 01-6859,

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

More bioinformatics definitions
The earliest Medline reference I've found to bioinformatics is William Bain's "Bioinformatics in Europe - the federation strikes back" in Trends in Biotechnology 11(6): 217- 218 June 1993.

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

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

Molecular informatics
The effective use of information derived from genomics and proteomics is of central importance and the ability to identify the most important data, to assess its accuracy and to be aware of any assumptions and limitations of hypotheses and predictive models is absolutely essential. Whereas the development of predictive models based on analogy has been very successful in chemistry and cheminformatics, the complex nature of biomolecular systems limits similar transference within bioinformatics. Without a critical analysis, in- silico discovery will be unable to be effectively integrated in the field of molecular informatics. The following themes will be covered: knowledge discovery and data mining, rational drug design, prediction of small molecule bioavailability (ADME Tox) properties, protein structure and function determination, new methods of drug- target modeling, cellular metabolism, and the use of high- throughput methods (biochips) for acquiring gene expression and protein binding information. Beilstein- Institut, Molecular Informatics: Confronting Complexity International Workshop May 13- 16 2002

More Cheminformatics definitions
An emerging area, which annotates small molecules and also libraries with structure – function, synthesis, and all other relevant data used to design and develop better drugs. ["Combinatorial Chemistry" Nature Biotechnology 18:  Supplement Oct. 2000, from Nature Biotechnology 16, 691– 693, 1998]

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 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

Although there is no consensus definition of "program" or "networks", these terms are most often encountered and understood in the context of the regulatory interactions that link groups of genes and gene products in developmental processes.  Many of these linkages have recently been elucidated in considerable detail for key events in a variety of species. Sean Carroll "Communications breakdown?" (book review) Science 291: 1264-1265, Feb. 16, 2001

The term biochemical pathways has principally referred to metabolic pathways, which are the pathways by which a cell converts compounds that enter it into cellular components (e.g., small molecules and macromolecules including proteins, nucleic acids, storage carbohydrates, and fatty acids) and by which the cell derives energy. Signaling pathways are biochemical pathways that regulate cellular characteristics and processes such as physiology, proliferation, changes in shape and motility, differentiation, adhesion, and intercellular interactions. High- content screening approaches can be used to help elucidate pathways. CHI High- Content Screening report, 2002 

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"

Life sciences informatics
Informatics are essential at every step of genomics-based drug discovery and development. The commercial landscape of life sciences information technology has changed dramatically in the last few years. Bioinformatics, in particular, has gone through a dramatic boom/bust. While IT companies are looking to the drug discovery and development arena as a new market opportunity, pharmaceutical companies  are faced with rising pressure to reduce (or at least control) costs, and have a growing need for new informatics tools to help manage the influx of data from genomics, and turn that data into tomorrow's drugs. Key IT tools, such as high- performance computing, Web services, and grids, are being used to improve the speed and efficiency of drug discovery and development. True breakthroughs are still lacking, particularly in key areas such as gene prediction, data mining, protein structure modeling and prediction, and modeling of complex biological systems. However, most experts agree that IT and bioinformatics are essential to reaching the improved productivity the pharmaceutical industry craves.  CHI Life Sciences Informatics: From Data to Drugs report, 2003

Biopharmaceutical informatics
Drug companies go through a very arduous and regulated discovery, applied research, and development process-typically spanning five years of laboratory research and ten years of clinical studies .. multinational clinical studies, which need to be done with tremendous precision over a very long period of time. The study parameters must be identical for every patient (many times numbering 10,000 patients, followed for five or more years), and all the participating hospitals essentially have to behave in exactly the same way for the trial to be valid. ..  The life science industry is conservative by nature, and therefore it is a late- adopting industry. It is very sensitive to standards because of the legacy according to which these companies have to maintain data and information. Major pharmaceutical companies typically adopt a 100-year minimum document retention policy, ...each of the industry's four industrial sectors - the pharmaceutical, the biotech, the medical device, and the diagnostics sector - has a different set of needs and desires, as well as its own requirements for unique IT solutions.  ... 

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

More Informatics websites
Government Computer News Searchable

Wiley Bioinformatics

Wiley Genomics

Wiley Proteomics

More bioinformatics organizations
BISTI Consortium: Established in May 2000 to serve as the focus of biomedical computing issues at the NIH ...  composed of senior-level representatives from the NIH centers and institutes and representatives of other Federal agencies concerned with bioinformatics and computational applications.  The mission of the BISTI Consortium is to make optimal use of computer science and technology to address problems in biology and medicine by fostering new basic understandings, collaborations, and transdisciplinary initiatives between the computational and biomedical sciences.

Information Science Technologies, CORDIS, European Union

W3C World Wide Web Consortium:  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.

Semantic web/web services terminology
Semantic Web, W3C
Semantic Web Community Portal

Web Services Activity, W3C

RDF Resource Description Framework
SOAP Simple Object Access Protocol

CDISC Clinical Data Interchange Standards Consortium: An open, multidisciplinary, non- profit organization committed to the development of industry standards to support the electronic acquisition, exchange, submission and archiving of clinical trials data and metadata for medical and biopharmaceutical product development.

CORBA Common Object Request Broker Architecture, OMG

FDA, Electronic standards for the transfer of regulatory information, Glossary of Abbreviations and Terms

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

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]

NISO Z39.19 Standard for Structure and Organization of Information Retrieval Thesauri

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.

Open source

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  

Standards and ontologies for functional genomics,

Chris Stoeckert, Microarray Databases: Standards and Ontologies, Chipping Forecast II, Nature Genetics 32: supplement, 469 – 473, Dec. 2002 [requires free registration]  

Markup languages
BIOML Biopolymer Markup Language

BSML Bioinformatic Sequence Markup Language

CML Chemical Markup Language Wikipedia

DAML DARPA Agent Markup Language 


MAGE-ML MicroArray and Gene Expression Markup Language

MatML Materials Markup Language

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 ( 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 Additional information may be obtained at the Pittsburgh Tissue Engineering Initiative site ( FDA, Center for Devices & Radiologic Health, US, Tissue Engineered Medical Products Standards TEMPS, 2002

VRML Virtual Reality Modeling Language

XACML Extensible Access Control Markup Language

XML  eXtensible Markup Language

XML in 10 points
XML for molecular biology, Paul Gordon, 

Robin Cover, Core Standards for Markup Languages, 2002 

Taxonomies and ontologies
Frustrations with search engines and information retrieval (and information overload) have led to increased interest in specialized taxonomies. A form of controlled vocabulary, with hierarchical relationships (broader terms, narrower terms) which provide additional suggestions for browsing, as do lateral relationships (related terms) and preferred terms. While there is theoretical interest in natural language processing, a very small percentage of web search engine queries actually use natural language processing successfully.

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.

Reusable ontologies
A key enabler for electronic Commerce, Richard Fikes, Knowledge Systems Lab, Stanford Univ.

Shared ontologies
3.1 Shared ontologies, W3C, Requirements for a web ontology language, work in progress

Shared taxonomies 
Clearly reusable and/or shared ontologies and taxonomies are still at a fairly nascent stage of development.

Semantics and syntax – integrating data

Special topics
Data and databases

Information capture, management and interpretation

Data mining
BioMedCentral for data mining

Data Mine


SIGKDD, Special Interest Group Knowledge Discovery in Data and Data Mining, Association for Computing Machinery

Information visualization resources on the web, 2002

Molecular Biology Toolkit, SDSC San Diego Supercomputer Center

Intellectual Property 

Micropatent, Information Holdings, Inc.

Intellectual Property Organizations
European Patent Office
IPO Intellectual Property Owners Association 
Licensing & Executives Society
US Patent and Trademark Office
WIPO World International Patent Organization

more on Molecular Medicine
BMC Cancer, BioMedCentral, 2001-  All aspects of research relating to cancer, including molecular biology, genetics, pathophysiology, epidemiology, clinical reports, and controlled trials.

BMC Medical Informatics and Decision Making, BioMedCentral, 2001-  Original research articles in information management, systems and technology in healthcare and the study of medical decision making

BMC Medical Research Methodology, BioMedCentral, 2001- Original research articles in information management, systems and technology in healthcare and the study of medical decision making

BMC Medicine, BioMedCentral, 2003-  Original research articles, technical advances and study protocols in any area of medical science or clinical practice. 

Nature Reviews Cancer, Nature Publishing, 2001- Impact factor 13.6

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What are genomics and proteomics? chemical genomics?  pharmacogenomics?   toxicogenomics?  What are bioinformatics? cheminformatics?  informatics?       chisitemap

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