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homepage > About genomic glossaries & taxonomies
Scope How terms were chosen & defined
Origins
About these
biopharmaceutical glossaries & taxonomies These glossaries & taxonomies are a project of Mary Chitty, Library
Director & Taxonomist at Cambridge Healthtech
Institute. We try to follow new and evolving
trends in pharmaceuticals, biotechnology and life sciences, particularly early drug
discovery and development, informatics
including bioinformatics, clinical
trials and Regulatory Affairs and
technologies. Keeping up with new
biopharmaceutical and biomedical technologies and terminology are challenges for everyone these days, including us! When I started this
project in 1999 it seemed as if the web was the only way to keep up with such rapidly
changing concepts. But as they have evolved I have come to
realize that while I keep adding content, what is here doesn't become out of
date nearly as quickly as I expected, and a print version could be very
useful. I'm actively looking for a publisher and offer the Concise
Biopharmaceutical Glossary as a draft manuscript. Scope:
These glossaries are
How terms were chosen and defined
Origins
Technical
Varying purposes demand different degrees of depth
and preparation. By doing your homework, many subjects can become more accessible
than they appear at first glance. Knowing how to ask informed questions
is more important than seeming to know all the answers. Some questions clearly don't have
complete answers yet.
Not comprehensive
Not only for biologists or chemists – and not only for
scientists
The pharmaceutical and biotechnology industries have become much more science
(and information) driven in recent years, but the rate of change (both
technological and cultural) can be pretty slow. Diffusion of Science Driven Drug
Discovery Organizational Change in Pharmaceutical Research, Rebecca
Henderson, Iain Cockburn and Scott Stern
http://www.nber.org/papers/w7359
Cutting edge technology demands considerable investment. Public- private collaborations are increasingly the way the biggest bioscience
projects get done. Progress rarely happens as quickly as people want (or
predict). Advances in molecular biology in the 1970's were responsible
for the growing influence of biotechnology in the 1980's and 1990's -- and while
genomics and proteomics have been more in the lab than in the clinic, hospital
and health professionals' offices, this is very much in the process of changing.
We all need
to know more about how molecular biology will be influencing personal decisions -
and public debate.
Not authoritative or definitive
Descriptive - not prescriptive definitions
Not primarily focused on clinical applications
I urge people using the web for finding information on medical issues to
carefully and critically evaluate where the information is coming from, whether
it is up to date (far too few websites clearly date information) and whether the
provenance of information and suggestions for additional resources are clearly
indicated. For more information on this too seldom discussed topic see
Susan Detwiler's "Charlatans, Leeches, and Old Wives: Medical
Misinformation" Searcher 9(3), Mar. 2001. http://www.infotoday.com/searcher/mar01/detwiler.htm
Go beyond basic research These (relatively) short and selective (30 - 60+ definitions each, or 6 - 8+ printed
pages, if you use the smallest type) glossaries are organized by subject. Some organizations, government
agencies, and cryptic acronyms are included selectively. This website is not so much a dictionary, but a quickly
scannable series of brief guides, arranged to provide suggestions for related and broader and narrower
terms of possible interest. I know this needs to go into a database, and
am working on that (slowly, given my limited budget).
How terms are chosen for inclusion &
defined Neologisms
Hard(er) to find definitions
Categories Subtle nuances Unfamiliar technologies
can be particularly intimidating to the uninitiated. Definitions
of relevant technologies and instrumentation are provided, with various links and
contexts. Some less familiar basic terms (but not particularly new technologies)
may be included selectively.
Old words, new meanings
Other terms have long been used
by biologists, but are now in the process of evolving new meanings
in a genomic context (gene, phenotype, genetic testing). Still others
need a specific genomic context (profiling, scoring, or
threading).
While the central dogma (DNA makes RNA
makes protein(s)) is clearly a continuum, the chasm between people (and
technologies for) working with DNA and proteins is still
vast.
Origins
An early discussion of
which terms to define for a report glossary led a reports editor to suggest that any word in the text not in the standard spell checking
software should be a candidate. This was said (only) half jokingly. As
I began to research terms I was struck by how little overlap there was
in genetic and proteomic terminology, and while the gap is narrowing it is still
an issue.
I had become interested in identifying terminology used by
different specialties with variant meanings when I ran the first Cambridge
Healthtech Bioinformatics
conference in San Francisco in June 1995 (originally started at Florida State University
in 1991). Discussions of communication difficulties between biologists
and computer scientists, and the lack of interoperability between
various databases sounded very familiar to a librarian. These differences
can be particularly elusive, since each group tends to assume the other
is making the same assumptions about nuances and implications, usually
without explicitly verifying those assumptions.
I've taken heart from
Steven Weinberg's Four Golden Lessons, Nature 426: 389, 27 Nov 2003 "How
could I do anything without knowing everything that had already been done? ...
[graduate school] was sink or swim.... I did learn one big thing: that no one
knows everything, and you don't have to. Another lesson to be learned ... is
that while you are swimming and not sinking you should aim for rough
waters. My advice is to go for the messes -- that's where the action
is... My third piece of advice is probably the hardest to take. IT is to forgive
yourself for wasting time... If you want to be creative, then you will have to
get used to spending most of your time not being creative, to being becalmed on
the ocean of scientific knowledge. Finally, learn something about the
history of science, or at a minimum the history of your own branch of science.
The least important reason for this is that the history may actually be of some
use to your ... More importantly, the history of science can make your work seem
more worthwhile to you.
I'm realizing that the
variety of skills and domain expertise needed for breakthroughs in the life
sciences is more than anyone discipline and/'or lifetime(s) can muster.
While new technologies might be helpful, cultural shifts, incentives for
collaborating, and pre-competitive cooperation will also be important.
Incremental changes can be helpful more frequent than true paradigm
shifts. Industrialization, scalability and automating and ramping up processes to move
from the R&D lab into the clinic are under-appreciated challenges, as are
marketing dilemmas that come about with disruptive
technologies.
Style guides
[not necessarily followed] You might consult Wikipedia http://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style
or the CDC Centers for Disease Control Emerging Infectious Diseases Author
Resources
https://wwwnc.cdc.gov/eid/page/author-resource-center
Defining -- and
understanding -- evolving terminology is an iterative process. Definitions
are a work in progress. I look forward to receiving your comments,
suggestions and questions.
Glossaries
& Taxonomies resources
IUPAC Gold Book, Obsolete terms
http://goldbook.iupac.org/lists/list_obsoleted.html
Silo Effect:
The Peril of
Expertise and the Promise of Breaking Down Barriers, Gillian Tett
http://www.simonandschuster.com/books/The-Silo-Effect/Gillian-Tett/9781451644746
Evolving Terminologies for Emerging Technologies
Comments? Questions?
Revisions?
Mary Chitty MSLS
mchitty@healthtech.com
Last revised
October 23, 2018
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Basic Genetics &
genomics has links
to a number of useful websites with excellent introductory material, some specifically
aimed at people without any technical background.
See How
to look for other unfamiliar terms for more extensive sources
and strategies, including a list of useful websites with links, databases
(free and fee- based), recommended search engines and search strategies,
and print books. (The best resources aren't always available on the web.)
The boundaries of this project are semi- permeable and extensible, but not
unlimited.
Biologists and chemists need tools and insights from computer sciences,
engineering, mathematics, physics, and other disciplines. Biology is increasingly
interdisciplinary, but terminological ambiguity and unarticulated assumptions still remain
barriers to clear communication.
Authoritative definitions take years to compile and often seem to languish
in committees. These glossaries are descriptive, not prescriptive.
Words and phrases often come to have a number of different connotations.
I've found it even harder to determine the subtle nuances of seemingly similar
terms. As someone wrote in answer to a question I posed to the Ask A
Linguist service http://linguistlist.org/ask-ling/index.html
"there are no true synonyms" But
I keep running into "information silos" and suspect that there are
numerous synonyms in different disciplines, as well as unacknowledged subtle
(and not so subtle) differences in interpretation. I am always looking for ways
to bridge these information chasms.
"The Oxford English Dictionary
is not an arbiter of proper usage, despite its widespread reputation to the
contrary. The Dictionary is intended to be descriptive, not prescriptive. In
other words, its content should be viewed as an objective reflection of English
language usage, not a subjective collection of usage ‘dos’ and ‘don'ts’.
However, it does include information on which usages are, or have been,
popularly regarded as ‘incorrect’.
These glossaries are deliberately (and I'd argue inevitably) descriptive, not
prescriptive.
Patient resources has some
websites recommended for people looking for information geared
towards patients and medical conditions. Most research covered on this
website has potential for clinical applications, but predicting when, how and
for how many classes of patients research
will move from the lab to the clinic can be a daunting task.
Applied research, drawing upon and going beyond sound basic research is
the focus. Cutting- edge (but not necessarily bleeding edge) research, with
a judicious mix of the visionary and pragmatic, is the aim. Both incremental
changes and what may be true paradigm shifts are included.
When this project started I expected newly coined words to predominate.
In some areas (notably in the Microarrays
glossary and the -Omes
and -omics glossary they do. But as I researched vocabulary
I found that some words had been around longer than I’d expected. Genome
appears in the Oxford English Dictionary (cited 1920). Multiplex
began as a botanical and then a telecommunications term – a 19th century
telegraph word.
A limited number of words and phrases which can be found in specialized
dictionaries of molecular biology, genetics, medicine, cell biology and
engineering are included, particularly if definitions seem problematic
or confusing, or when they are critical to understanding other definitions. I've
also tried to collect any examples I could find of differing meanings used by
specific disciplines, and would welcome any examples you can think of. mchitty@healthtech.com
I'm particularly interested in trying to figure out categories and
classification as our knowledge of biology and physiology extends to previously
inaccessible levels of biochemistry and molecular biology. While medicine
has long been organized by organ or system, and to some extent on the cellular
level, new technologies are revealing relationships among disciplines previously
seen as quite unconnected. See networks and pathways in the Metabolic
engineering glossary as an example, or the way biology is being
reorganized at the biochemical level in the Chemistry glossary
While some terms seem at first glance to be self- evident, closer investigation
revealed specific subtleties. I’m still trying to pin down all the senses
of “characterized”. Robust had always seemed
self- evident
to me from its contexts, but it has a specific statistical meaning.
Some fairly common words or phrases were just hard to locate definitions for (small
molecules, housekeeping proteins.) Some terms come from established technologies only (relatively) recently
relevant to the life sciences (such as mass spectrometry or photonics)
or from somewhat tangential disciplines including computer science,
engineering,
and mathematics.
As big (if not a bigger) challenge as “new” or specialized vocabulary
is the conceptual shift from classical genetics to a more dynamic genomic
“big picture” understanding of genomic applications.
DNA sequences
are essentially linear snapshots. To understand gene function we need to
look at 3D protein structures. To begin to understand physiological
processes we need to examine changes in gene and protein expression
over time (4D) and to know more about genetic variations in
specific populations.
This genomics glossary originated with Cambridge Healthtech’s first Genomic Pathways report. As I read
the first Proteomics report in the summer of 1999 I noticed a number
of terms were defined in the text, and being a librarian, suggested that
a glossary would be a worthwhile addition to future reports (and was invited
to compile one).
Mary Chitty mchitty@healthtech.com
IUPAC,
Guidelines for drafting technical reports and recommendations
https://iupac.org/what-we-do/recommendations/guidelines-for-drafting-reports/
especially the
section on Definitions of terms
http://iupac.org/what-we-do/recommendations/guidelines-for-drafting-reports/#definitions-of-terms
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