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Biopharmaceutical
Informatics
Map: Finding guide to terms in these glossaries Site
Map There
is room for both big and small science, stated George Kenyon [Univ. of Michigan]
No one group, company or government entity is going to solve these [proteomics]
problems, there is a great need for interdisciplinary collaboration, locally,
nationally and globally. Defining the Mandate of Proteomics in the Post-
Genomics Era, Board on International Scientific Organizations, National Academy
of Sciences, 2002 http://www.nap.edu/books/NI000479/html/R1.html
basic research: The objective of basic research is to gain more comprehensive knowledge or understanding of the subject under study, without specific applications in mind. In industry, basic research is defined as research that advances scientific knowledge but does not have specific immediate commercial objectives, although it may be in fields of present or potential commercial interest. [National Science Foundation, Directorate for Social, Behavioral & Economic Sciences, US definitions for resource surveys 1996] http://www.nsf.gov/sbe/srs/seind96/ch4_defn.htm Bayh- Dole Act: Biopharmaceutical law & intellectual property glossary bleeding edge: (General industry usage) Synonym for "cutting edge," with an added implication of the pioneer's vulnerability. Ex: "We're really on the bleeding edge with this product. Hope it sells through." Being "edgy" is still, however, a desirable Microsoft quality. [Ken Barnes et. al., Microsoft Lexicon, 1995-1998] http://www.cinepad.com/mslex.htm bottom-up: The classical reductionist approach to biology which aims to examine the smallest units to gain insight into the larger ones. Mendelian genetics, which looks at single genes, is a bottom- up approach. Compare top- down. Narrower term: Nanoscience & miniaturization glossary nanofabrication- bottom- up CORDIS Community Research and Development Information Service: Business of biopharmaceuticals glossary CRADA Cooperative Research and Development Act: Biopharmaceutical law & Intellectual property glossary children in research, clinical trials: Drug approvals & clinical trials glossary clinical research: Molecular medicine glossary clinical research informatics: Informatics overview research informatics collaboration, consortium: Biopharmaceutical Alliances glossary conceptual biology: Bioinformatics glossary cutting- edge: See under bleeding edge data sharing: NIH Data Sharing Policy, 2003 http://grants.nih.gov/grants/policy/data_sharing/ Sharing Research Data, National Academies Press, 1985 http://books.nap.edu/catalog/2033.html Delphi technique: A cerebral process -- the Delphi Technique -- to identify and then forecast the outlook for these technologies. The Delphi process, developed shortly after World War II to get a better fix on the future, taps the brainpower of a jury of experts. [Dave Beal, St. Paul Pioneer Press, Scenarios, Minnesota FutureWork] determinism: Molecular Medicine glossary development: The systematic use of the knowledge or understanding gained from research directed toward the production of useful materials, devices, systems, or methods, including the design and development of prototypes and processes. [National Science Foundation, Directorate for Social, Behavioral & Economic Sciences, US definitions for resource surveys 1996.] http://www.nsf.gov/sbe/srs/seind96/ch4_defn.htm Related terms: applied research, basic research discovery driven research: High throughput techniques in DNA sequencing and gene expression have led to a vast increase in quantitative data. This data is extensive and widely available on the internet. By all accounts there is a wealth of information in the data that has not been completely investigated. Traditional biology research is hypothesis driven. However, the best way to exploit the vast databanks is discovery driven. The difference is that for hypothesis driven research you need an encyclopedic knowledge of a very specific area (a particular protein, for example) to be able to suggest and perform unique and interesting experiments. Discovery driven research requires a much broader knowledge, along with the ability to rapidly read the relevant literature and get up to speed on a specific area. [James P. Brody, Assistant Professor, Center for Biomedical Engineering, University of California, Irvine, US] http://brodylab.eng.uci.edu/~jpbrody/comp.html effectiveness research: See under outcomes research electronic notebook: Biopharmaceutical law & Intellectual property glossary experimental design: The use of mathematical and statistical methods to select the minimum number of experiments or compounds for optimal coverage of descriptor or variable space. [IUPAC Computational] false negative, false positive: Microarrays glossary Framework Programme, European Union: Business of biopharmaceuticals glossary funding of genomic research: Biopharmaceutical Finance glossary genomics - research: Genomics glossary glue grants: NIGMS [National Institute of General Medical Sciences, NIH, US] has two initiatives that seek to promote the integrative and collaborative approaches that are increasingly needed to solve complex problems in biomedical science. Because these programs are meant to provide resources to bring people together, they have been nicknamed "glue grants." http://www.nigms.nih.gov/funding/gluegrants.html "gold standard" : Optimal case definition is important in epidemiological research, but can be problematic when no satisfactory gold standard is available. In particular, difficulties arise where the pathology underlying a disorder is unknown or cannot be reliably diagnosed. This problem can be overcome if diagnoses are viewed not necessarily as labels for disease processes, but more generally as a useful method for classifying people for the purpose of preventing or managing illness. With this perspective, the value of a case definition lies in its practical utility in distinguishing groups of people whose illnesses share the same causes or determinants of outcome (including response to treatment). A corollary is that the best-case definition for a disorder may vary according to the purpose for which it is being applied. Assessing case definitions in the absence of a diagnostic gold standard, D Coggon, C Martyn, KT Palmer, B Evanoff, Intl J Epidemiol 34 (4): 949-952 Good Publication Practice: Guidelines for pharmaceutical companies Good Publications Practice Working Group, 2003 http://www.gpp-guidelines.org/ Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule: The first comprehensive Federal protection for the privacy of personal health information. Research organizations and researchers may or may not be covered by the HIPAA Privacy Rule. NIH http://privacyruleandresearch.nih.gov/ See also Molecular medicine clinical research and HIPAA high technology industry: Business of biopharmaceuticals glossary holism: The idea that ``the whole is greater than the sum of the parts.'' Holism is credible on the basis of emergence alone, since reductionism and bottom-up descriptions of nature often fail to predict complex higher- level patterns. [Gary William Flake, Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems, and Adaptation, MIT Press, 1998] http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-intro.html Coined by General J. C. Smuts (1870-1950) to indicate the tendency of nature to produce wholes. First recorded 1926 in Holism & Evolution. [OED] Related term: top- down. hypothesis driven research: The traditional approach of moving from a hypothesis to a specific understanding through research. The era of high- throughput and systematic functional analysis of genes has not rendered hypothesis- or problem driven biological research obsolete or outmoded. Instead, it has created a vast set of new problems to be solved by the traditional biological research approach, centered on human researchers rather than automated systems. However, biologists carrying out hypothesis- or problem driven research often do so utilizing new tools made possible by genomics and other cutting edge systemic technologies (e.g., bioinformatics databases, model organisms for which there are extensive genomics information, and array technology). Related terms: discovery driven research, problem driven research; Functional genomics glossary forward genetics informatics: Biopharmaceutical Information management & interpretation glossary innovation: Task Force on the Future of American Innovation, The Knowledge Economy: Is the United States Losing its Competitive Edge? 2005 http://www.futureofinnovation.org/PDF/Benchmarks.pdf Related term: disruptive technology Institutional Review Board: Clinical trials, drug approvals glossary integration- diagnostics & therapeutics: Business of biopharmaceuticals glossary integration of R&D: R&D is breaking apart across organizations, sites, scientific domains and lab technologies in response to global pressures. Today’s R&D challenge is integration. At this forum, Symyx will present success stories and implementation techniques of how companies are integrating scientific desktops, experimentation systems, and data management across departments, sites and CROs. R&D is breaking apart across organizations, sites, scientific domains and lab technologies in response to global pressures. Today’s R&D challenge is integration. At this forum, Symyx will present success stories and implementation techniques of how companies are integrating scientific desktops, experimentation systems, and data management across departments, sites and CROs. Symyx Software Symposium, April 30- May 2 2008, Boston MA interdisciplinary aspects of research: Terminology and ideas relevant to genomics comes from a wide variety of disciplines: analytical chemistry, biochemistry, bioinformatics, biomechanics, biophysics, biotechnology, cell biology, clinical and research medicine, computer sciences, developmental and structural biology, electrochemistry, electronics, engineering, enzymology, epidemiology, imaging, immunology, mathematics, microbiology, molecular biology, optics, pharmacology, public health, statistics, toxicology, virology and aspects of business, chaos theory, ethics and law are all relevant. Few people (if any) can be truly interdisciplinary and expert in all of these subjects. Universities are struggling with the challenge of (and need to) building bridges between departments. Companies are as well. We all need to learn more to participate in informed public debate. kilogram: Redefinition of the kilogram: An idea whose time has come, Ian Mills et. al, Metrelogia 42: 71-80, 2005 http://www.iop.org/EJ/abstract/0026-1394/42/2/001 knowledge management: Biopharmaceutical Information management & interpretation glossary longitudinal research: Studies done over time, with data collected from the same population. market research: Business of biopharmaceuticals glossary meta-analyses: See meta-analysis. meta-analysis: The use of statistical techniques in a systematic review to integrate the results of included studies. Sometimes misused as a synonym for systematic reviews, where the review includes a meta- analysis. Cochrane Collaboration "Glossary of terms in the Cochrane Collaboration, 2005 http://www.cochrane.org/resources/glossary.htm A quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc., with application chiefly in the areas of research and medicine. MeSH, 1989 meta-regression: Can formally test whether there is evidence of different effects in different subgroups of trials. For example, you can use meta-regression to test whether treatment effects are bigger in low quality studies than in high quality studies. Cochran Collaborative, Diversity and Heterogeneity, 2002 http://www.cochrane-net.org/openlearning/HTML/mod13-5.htm . NCRA, NCRPA: Biopharmaceutical Alliances glossary NIH roadmap: The opportunities for discoveries have never been greater, but the complexity of biology remains a daunting challenge. a framework of the priorities the NIH as a whole must address in order to optimize its entire research portfolio. It lays out a vision for a more efficient and productive system of medical research. It identifies the most compelling opportunities in three main areas: new pathways to discovery, research teams of the future, and re-engineering the clinical research enterprise. Initiatives include building blocks, biological pathways and networks. molecular libraries and imaging, structural biology, bioinformatics and computational biology, nanomedicine. http://nihroadmap.nih.gov/ new paradigms: An investigation by Science revealed that use of the term "new paradigm" in MEDLINE and the ISI database of leading journals increased steadily during the 1990’s, as did its use in NIH and NSF databases of new grants. [J Cohen "The March of Paradigms" Science 283 : 1998-1999 Mar 26, 1999] While many advances are unlikely to be truly new paradigms, a few developments show signs of being more than incremental improvements. Roger Brent compares microarrays to the microscope and telescope because they "enable observation of the previous unobservable" [transcripts expressed under different conditions in cells, tissues, and organisms] [R. Brent, "Functional genomics: learning to think about gene expression data" Current Biology 9: R338-R341, May 1999] This is no overstatement. Related terms: paradigm, paradigm shifts nominal group technique: Research in group dynamics indicates that more ideas are expressed by individuals working alone but in a group environment than by individuals engaged in a formal group discussion. The Nominal Group Technique is a good way of getting many ideas from a group. It has advantages over the usual committee approach to identifying ideas. Group consensus can be reached faster and everyone has equal opportunity to present their ideas. ... The nominal group is a structured group that meets to gather information about a specific concern; that is, to identify problems and priorities. Individuals work alone but in a group setting. [GUIDELINES FOR USING THE NOMINAL GROUP TECHNIQUE, Center for Rural Studies, Univ. of Vermont, 1997] http://crs.uvm.edu/gopher/nerl/group/a/meet/Exercise7/b.html organization of pharmaceutical R&D: Business of biopharmaceuticals glossary outcomes research: The terms "outcomes research" and "effectiveness research" have been used to refer to a wide range of studies, and there is no single definition for either that has gained widespread acceptance. As these fields evolved, it appears that "outcomes research" emerged from a new emphasis on measuring a greater variety of impacts on patients and patient care (function, quality of life, satisfaction, readmissions, costs, etc). The term "effectiveness research" was used to emphasize the contrast with efficacy studies, and highlighted the goal of learning how medical interventions affected real patients in "typical" practice settings (OTA, 1994). Effectiveness studies sought to understand the impact of health care on patients with diverse characteristics, rather than highly homogeneous study populations. While the terms may have different initial roots, there does not appear to be much value in distinguishing these activities, and the field is generally referred to as OER. .. OER evaluates the impact of health care (including discrete interventions such as particular drugs, medical devices, and procedures as well as broader programmatic or system interventions) on the health outcomes of patients and populations. OER may include evaluation of economic impacts linked to health outcomes, such as cost- effectiveness and cost utility. OER emphasizes health problem- (or disease-) oriented evaluations of care delivered in general, real- world settings; multidisciplinary teams; and a wide range of outcomes, including mortality, morbidity, functional status, mental well- being, and other aspects of health-related quality of life. [Outcome of Outcomes Research at AHCPR: Final Report, Agency for Health Care Policy and Research, AHCPR Publication No. 99-R044] http://www.ahrq.gov/clinic/out2res/outcom1.htm outsourcing research & development: Business of biopharmaceuticals glossary paradigm: An archetypal solution to a problem. [News about the passing away of Thomas Kuhn, NY Times obituary, 19 June 1996] http://www.brint.com/kuhnnews.htm Paradigm, Keith Cunningham, 1994. http://capita.wustl.edu/ME567_Informatics/concepts/paradigm.html Narrower terms: new paradigm, paradigm shifts paradigm shifts: The opposite of incremental changes. Related terms: new paradigms, paradigm peer review: The evaluation by experts of the quality and pertinence of research or research proposals of other experts in the same field. Peer review is used by editors in deciding which submissions warrant publication, by granting agencies to determine which proposals should be funded, and by academic institutions in tenure decisions. MeSH, 1994 pharmaceutical industry research: Business of biopharmaceuticals glossary pre-competitive R&D: "Pre- competitive" can hardly be defined in absolute terms. Genetic information that is regarded as pre- competitive by large drug developing companies (like those who participated in the SNP consortium) may be regarded as competitive by e.g. start- up firms who seek to commercialize any new information – provided they can reserve some exclusive right to its use. Thus, it seems that institutional and legal frameworks play a role in defining or constituting certain areas of research as "pre- competitive". Accordingly, the arguments raised in the Working Group infer two types of reasons for considering research as pre- competitive: - Functional prerequisites of successful research that make strategies of private appropriation technically unfeasible - Regulatory conditions that impose normative restrictions on the appropriation of research results ["Arguments, Research Consortia, World Business Council for Sustainable Development (WBCSD) , 2003] http://www.wz-berlin.de/ipr-dialogue/argumentations/hgr/CV_Research_Consortia.htm Precompetitive R&D precludes: (a) exchanging information among competitors relating to costs, sales, profitability, prices, marketing, or distribution of any product, process, or service that is not reasonably required to conduct the research and development that is the purpose of such venture; (b) entering into any agreement or engaging in any other conduct restricting, requiring, or otherwise involving the production or marketing by any person who is a party to such venture of any product, process, or service, other than the production or marketing of proprietary information developed through such venture; and (c) entering into any agreement or engaging in any other conduct that is not reasonably required to prevent misappropriation of proprietary information contributed by any person who is a party to such venture or its results. [David. Hahn, Thomas Sporleder, ADE 601 Glossary Technical Terms for Agribusiness Managers, Ohio State Univ. US*] no longer on the web problem driven research: Applied research, contrast with basic research and discovery- driven, hypothesis- driven. Are there other nuances? proof of concept, proof of principle: Compare definitions in Business of biopharmaceuticals glossary with those below. Example: In 1997, the first high- density single nucleotide polymorphism (SNP) mapping proof- of- principle experiments were performed .. In 2003, the first- generation, whole- genome, high- density SNP maps for pharmacogenetic profiling were generated and tested. The proof of concept study identified individuals with a higher risk of adverse events... [Allen D. Roses, Practice of neurology, Archives of neurology 58 (11): 2025 Nov. 2001 editorial] http://archneur.ama-assn.org/issues/v58n11/ffull/ned10009.html R&D research & development: Narrower terms: applied research, basic research, development; Alliances glossary pre- competitive R&D R&D productivity: Business of biopharmaceuticals glossary reductionism: The development of molecular genetics on the heels of Mendelian genetics has raised the inevitable philosophical question of whether the discovery of DNA represents the ultimate reduction of biological to physicochemical processes. Numerous philosophers of science have approached the issue, especially the basic question of what exactly is meant by "reductionism." A useful exploration of this issue, specifically in relation to genetics, is by Kenneth Schaffner in "Approaches to Reduction," Philosophy of Science, 1967, 34:137-147. In another paper Schaffner argues that molecular biology was not built on a conscious attempt to reduce Mendelian to molecular genetics: ... [Garland E. Alen "Life Sciences in the Twentieth Century" History of Science Society Newsletter, 17 (5) Supplement 1988] http://depts.washington.edu/hssexec/newsletter/1997/allen.html "Often used as a term of abuse for those theories which simplify too much" [OED] research diagnostics: Molecular Medicine glossary research- how to: See Biopharmaceutical Algorithms artificial intelligence How to do research in the MIT AI Lab Practical and useful, not just for artificial intelligence. Other good references? research informatics: The explosion of genomic information, from sequences and gene expression to SNPs and protein structures, is of limited value for pharmaceutical researchers without powerful software capable of interpretation and comparisons. Data mining, multiple location data sharing, and computational enhancements of biological and chemistry projects, as well as integration of these efforts, and legacy information systems, the very different language and perspectives of chemists and biologists, and the organizational issues of compartmentalization remain key topics. Research Joint Venture RJV: Any group of activities, including attempting to make, making, or performing a contract, by two or more persons for the purpose of (a) theoretical analysis, experimentation, or systematic study of phenomena or observable facts, (b) the development or testing of basic engineering techniques, (c) the extension of investigative findings or theory of a scientific or technical nature into practical application for experimental and demonstration purposes … (d) the collection, exchange, and analysis of research information, or (e) any combination of the [above].” RJV members can be from different sectors as well as from different countries. [NCRA quoted in National Science Foundation's Science & Engineering Indicators 1998] http://www.nsf.gov/sbe/srs/seind98/access/c4/c4s3.htm Broader term: Biopharmaceutical Alliances glossary joint venture research tools: We use the term "research tool" in its broadest sense to embrace the full range of resources that scientists use in the laboratory, while recognizing that from other perspectives the same resources may be viewed as "end products." For our purposes, the term may thus include cell lines, monoclonal antibodies, reagents, animal models, growth factors, combinatorial chemistry libraries, drugs and drug targets, clones and cloning tools (such as PCR), methods, laboratory equipment and machines, databases and computer software. .. [NIH Working Group on Research Tools, June 4, 1998] http://www.nih.gov/news/researchtools/ Related term: pre-competitive SBIR Small Business Innovation Research: Biopharmaceutical Alliances glossary social informatics: Biopharmaceutical Information management & interpretation glossary stage gate criteria: Business of biopharmaceuticals TRA Technology Research Associations; technology transfer: Biopharmaceutical Alliances glossary top-down: A systems approach, which looks at the big picture and complexity. Genomics is essentially a top- down approach, the opposite of a bottom- up approach. Our ways of thinking have been so profoundly influenced by bottom- up, reductionist approaches that we are having to learn to think in very different ways to begin to fully exploit genomic data. Narrower term: Nanoscience & miniaturization glossary nanofabrication- top- down translational research: The major concern in the pharmaceutical industry is that the increased investment in discovery R&D, in part driven by the implementation of various “omic” technologies”, has led to the increased number of drug targets and the number of compounds entering development, however has failed to result in an increased number on NCEs. A major contributing factor to this paradigm is the costly late- stage attrition that often results from drug candidates transitioning into clinical trials without sufficient information about safety, efficacy, or pharmacology. Translational Research focuses on implementing bi-directional plans to enable better decision making at the pre- clinical/ clinical interface through more informed lead selection and terminating high- risk projects earlier. NIH's Roadmap specifies at least two kinds of translational research: Translational Research Core Services. This effort will facilitate the translation of basic discoveries to early phase clinical testing. It will provide bench and clinical investigators with cost- effective core services, including the expertise needed to move projects through complex logistical and regulatory barriers, and the technical services to synthesize chemical and biological agents for early phase clinical studies. and Regional Translational Research Centers. These Centers will increase interactions between basic and clinical scientists and accelerate the translational development of new drugs, biomarkers, and treatment strategies from the laboratory bench to clinical testing. New centers will provide essential core infrastructure and support, including specialized cores that provide expertise in biostatistics, clinical pharmacology, pharmacogenetics, and genetics. NIH Roadmap Initiatives http://nihroadmap.nih.gov/initiatives.asp Translational research is one of the most important activities of translational medicine as it supports predictions about probable drug activities across species and is especially important when compounds with unprecedented drug targets are brought to humans for the first time. Translational research has the potential to deliver many practical benefits for patients and justify the extensive investments placed by the private and public sector in biomedical research. Translational research encompasses a complexity of scientific, financial, ethical, regulatory, legislative and practical hurdles that need to be addressed at several levels to make the process efficient. What's next in translational medicine? Littman BH, Di Mario L, Plebani M, Marincola FM. What's next in translational medicine? Clin Sci (London) 112 (4): 217- 227, Feb 2007 Burroughs Wellcome Fund Translational Research http://www.bwfund.org/programs/translational/ Related terms: Molecular Medicine glossary clinical proteomics translational medicine biomarker validation truth: Making new technology work may be easier than using it to discover truth. Roger Brent, "Functional genomics: learning to think about gene expression data" Current Biology 9: R338- R341, 1999 Question from Nature column Lifelines put to Michel Brunet, palaeontologist "What is the one thing about science you wish the public understood better?" Answer "That the 'truth' is always an asymptotic ideal." Dreams of the past, Nature 423 (6939): 121, 8 May 2003 uncertainty: Molecular Medicine glossary women and minorities and research: Inclusion of Women and Minorities As Participants In Research Involving Human Subjects - Policy Implementation Page, NIH, Office of External Research, 2003 http://grants1.nih.gov/grants/funding/women_min/women_min.htm women's health: Molecular Medicine glossary women's health - statistical modeling: Molecular Medicine glossary Bibliography
Alpha biopharmaceutical glossary index How to look for other unfamiliar biopharmaceutical terms IUPAC definitions are reprinted with the permission of the International Union of Pure and Applied Chemistry. |
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