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Research glossary & taxonomy
Evolving terminology for emerging technologies
Suggestions? Comments? Questions? Mary Chitty MSLS
mchitty@healthtech.com
Last revised
January 10, 2020
Informatics
term index:
Related glossaries include Business Biopharmaceutical
Alliances Business of biopharmaceuticals
Biopharmaceutical Finance Clinical Molecular
Diagnostics Molecular Medicine Biologics Drug discovery &
development
Informatics Algorithms Bioinformatics
Cheminformatics Drug
discovery informatics Clinical &
medical informatics
Technologies Technologies
overview Advances in technologies often accompany research breakthroughs.
Complex
biological problems often require integrative and multidisciplinary approaches
for their solution. However, individual laboratories may lack the necessary
breadth of expertise and resources to achieve this goal. The collaboration of
investigators with different intellectual and technical approaches may promote
the novel insights required to achieve significant research advances. NIGMS
Support for Collaborative Science 2009 http://grants1.nih.gov/grants/guide/notice-files/NOT-GM-08-130.html
applied research:
Applied research means the effort that (a) normally follows basic research, but
may not be severable from the related basic research; (b) attempts to determine
and exploit the potential of scientific discoveries or improvements in
technology, materials, processes, methods, devices, or techniques; and (c)
attempts to advance the state of the art. When being used by contractors in cost
principle applications, this term does not include efforts whose principal aim
is the design, development, or testing of specific items or services to be
considered for sale; these efforts are within the definition of "development,"
given below.
https://wayback.archive-it.org/5902/20160210164701/http://www.nsf.gov/statistics/randdef/fedgov.cfm
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, Definitions
of Research & Development
https://wayback.archive-it.org/5902/20160210164701/http://www.nsf.gov/statistics/randdef/fedgov.cfm
biomedical
research:
(In this document, the term “biomedical” will be used in the broadest sense
to include biological, biomedical, behavioral, social, environmental, and
clinical studies that relate to understanding health and disease.)
Centers
of Excellence for Big Data Computing in the Biomedical Sciences (U54), July 2013
http://grants.nih.gov/grants/guide/rfa-files/RFA-HG-13-009.html
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 [no longer on web]
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 nanofabrication- bottom- up
contract research organization (CRO):
a company that provides support to the pharmaceutical, biotechnology,
and medical
device industries in the form of
research services outsourced on
a contract basis. A CRO may provide such services as biopharmaceutical
development, biologic
assay development, commercialization, preclinical
research, clinical
research, clinical
trials management, and pharmacovigilance.
CROs are designed to reduce costs for companies developing new medicines
and drugs in niche
markets. They aim to simplify entry
into drug markets, and simplify development, as the need for large
pharmaceutical companies to do everything ‘in house’ is now redundant.[citation
needed] CROs also support
foundations, research institutions, and universities, in addition to
governmental organizations (such as the NIH, EMA,
etc.).[1]
Many CROs specifically provide clinical-study and clinical-trial support
for drugs and/or medical devices.[2][3]
… The International
Council on Harmonisation of Technical Requirements for Registration of
Pharmaceuticals for Human Use, a 2015
Swiss NGO of pharmaceutical companies and others, defined a contract
research organization (CRO), specifically pertaining to clinical
trials services as:[6]:10 "A
person or an organization (commercial, academic, or other) contracted by
the sponsor to perform one or more of a sponsor's trial-related duties and
functions." Wikipedia 2018 Nov 10
https://en.wikipedia.org/wiki/Contract_research_organization
See also drug discovery &
development, Contrast Clinical Trials
Clinical Research Organization CRO
cutting- edge: See under bleeding edge
data
sharing: NIH Data Sharing
Policy, 2007 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
development:
Development, as used in this part, means the systematic use of scientific and
technical knowledge in the design, development, testing, or evaluation of a
potential new product or service (or of an improvement in an existing product or
service) to meet specific performance requirements or objectives. It includes
the functions of design engineering, prototyping, and engineering testing; it
excludes subcontracted technical effort that is for the sole purpose of
developing an additional source for an existing product.
https://wayback.archive-it.org/5902/20160210164701/http://www.nsf.gov/statistics/randdef/fedgov.cfm
Related terms: applied research, basic research
Early Stage Investigator Policies: This policy represents a change in NIH
New Investigator policies designed to encourage early transition to
independence. Under this policy, New Investigators within ten years of
completing their terminal research degree or within ten years of completing
their medical residency will be designated Early Stage Investigators
(ESIs). Traditional NIH research grant (R01s) applications from ESIs will
be identified and the career stage of the applicant will be considered at the
time of review and award.
Definition
of Early Stage Investigator: A Program Director/Principal Investigator who
qualifies as a New Investigator is considered an Early Stage Investigator (ESI)
if he/she is within 10 years of completing his/her terminal research
degree or is within 10 years of completing medical residency (or the
equivalent). http://grants.nih.gov/grants/new_investigators/index.htm#earlystage
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
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
risk high reward research NIH:
Four unique NIH Director's awards are available for exceptionally
creative scientists who
propose highly
innovative approaches with high-impact potential to
major challenges in biomedical research:
https://commonfund.nih.gov/highrisk
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. Oxford English Dictionary
Related term: top- down.
Horizon 2020: the financial instrument implementing the Innovation
Union,
a Europe
2020 flagship
initiative aimed at securing Europe's global competitiveness.
http://ec.europa.eu/programmes/horizon2020/en/what-horizon-2020
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
forward genetics
information
silos:
The cultural aspects impeding communication
between different groups can be immense, are often not recognized or
articulated, and greatly impede interdisciplinary
research. Wikipedia http://en.wikipedia.org/wiki/Information_silo
Institutional Review Board:
Regulatory
interdisciplinary
research: Health research traditionally has been
organized much like a series of cottage industries, lumping researchers into
specialty areas, where their efforts remain disconnected from the greater whole
by artificial barriers constructed by technical and language differences between
different disciplines and departmentally-based specialties. But, as science has
advanced over the past decade, two fundamental themes are apparent: the study of
human biology and behavior is a wonderfully dynamic process, and the traditional
divisions within health research may in some instances impede the pace of
scientific discovery. The broad goal for the IR program therefore, is to
change academic research culture, both in the extramural research community and
in the extramural program at the NIH, such that interdisciplinary approaches are
facilitated. Interdisciplinary Research NIH Common Fund http://commonfund.nih.gov/interdisciplinary/overview.aspx
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
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 https://www.nist.gov/publications/redefinition-kilogram-decision-whose-time-has-come-0
longitudinal research:
Studies done over time, with data
collected from the same population.
meta-analysis
Clinical informatics
Next generation researchers initiative
On August 31, 2017,
NIH announced policy details in the NIH Guide Notice: “Policy
Supporting the Next Generation Researchers Initiative (NOT-OD-17-101)”. The
policy amends the definitions of, and policies supporting, early stage
investigators (ESIs). In addition, it creates a new policy for early
established investigators (EEIs), previously referred to as mid-career
investigators, and describes how NIH will monitor the implementation of
the policy to determine the impact on ESI and EEI diversity in the NIH
portfolio
https://grants.nih.gov/ngri.htm
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
Increase has certainly continued
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:
The nominal
group technique (NGT)
is a group process involving problem identification, solution generation, and
decision making.[1] It
can be used in groups of many sizes, who want to make their decision quickly, as
by a vote, but want everyone's opinions taken into account (as opposed to
traditional voting, where only the largest group is considered).[2] The
method of tallying is the difference. Wikipedia accessed 2018 Feb 6
https://en.wikipedia.org/wiki/Nominal_group_technique
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
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
problem driven research: Applied research, contrast with
basic
research and discovery- driven, hypothesis- driven. Are
there other nuances?
R&D research & development:
Narrower terms: applied research,
basic research, development; Alliances
pre- competitive R&D
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" Oxford English Dictionary
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
Broader term: Alliances joint venture
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
nanofabrication- top- down
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
Bibliography
FDA Critical path
https://www.fda.gov/ScienceResearch/SpecialTopics/CriticalPathInitiative/default.htm
NIH Acronym list, 2013 http://grants.nih.gov/grants/acronym_list.htm NIH Definitions related to
technology transfer and research tools,
https://www.mmrrc.org/about/NIH_research_tools_policy/appendb.htm
NIH Glossary Grants and Funding Glossary
http://grants.nih.gov/grants/glossary.htm
NIST
Glossary of DOE Design of Experiments https://www.itl.nist.gov/div898/handbook/pri/section7/pri7.htm
Office of Extramural Research, NIH Glossary Grants and Funding Glossary http://grants.nih.gov/grants/glossary.htm
RePORT
Expenditures and Results (RePORTER)
includes NIH SBIR awards
Twelve tips for engaging with biologists, as told by a physicist,
Sarah Bohndiek, Nature Jan 2020
https://www.nature.com/articles/d41586-019-03961-y
Learn the language Just as with a foreign language, the fastest way to
become fluent in the language of a new scientific discipline is to embed
yourself inside it and practise regularly. For me, learning the language
was the most important reason why I moved from physics to biochemistry for
my first postdoc. … Get comfortable
being uncomfortable… Ask questions … Embrace uncertainty … Learn
statistics …. Avoid equations during presentations
Thirteen tips for engaging with physicists, as told by a biologist, Ken Kosik, Nature Jan 2020
https://www.nature.com/articles/d41586-019-03960-z
When physicists say they do not understand
something that you have said about biology, it’s possible that you do not
understand that topic either.
‘Understanding’ operates at different
planes in different disciplines, and when a physicist seeks understanding,
what they hope to grasp might differ from the knowledge that a biologist
seeks.
… Seek common ground… Scale matters …
Avoid jargon … Skip some details. …
Manage expectations …
Physicists
laugh a lot
Not only is the humour of physicists
arcane, but almost anything unexpected can provide a jocular moment.
Theirs are the ultimate inside jokes, which are often not obviously funny.
But laugh along anyway — even if you don’t find the humour, they won’t
know the difference.
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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