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About these biopharmaceutical glossaries & taxonomies
How terms are chosen for inclusion & defined

Last revised December 23, 2013
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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  But as they have evolved I have come to realize that while I keep adding content, what is here doesn't become out of date nearly as quickly as I expected, and a print version could be very useful.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.  Mary Chitty mchitty@healthtech.com

Scope & Origins: These glossaries are

Technical
Basic Genetics & genomics 
has links to a number of useful websites with excellent introductory material, some specifically aimed at people without any technical background.

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
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.

Not only for biologists or chemists – and not only for scientists
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. 

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
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. 

Descriptive - not prescriptive definitions
"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’." http://dictionary.oed.com/public/help/OED_guide/overview.htm  These glossaries are deliberately (and I'd argue inevitably) descriptive, not prescriptive.

Not primarily focused on clinical applications
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.  

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
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.

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/ non-existent budget).

Neologisms
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.

Hard(er) to find definitions
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

Categories
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 and biology glossary

Subtle nuances
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.  

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
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.

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
This genomics glossary originated with CHI’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).

An early discussion of which terms to define for a report glossary led a CHI 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 try Wikipedia http://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style or the CDC Centers for Disease Control http://www.cdc.gov/ncidod/EID/style_guide_p2_3.htm 

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. 
Mary Chitty  mchitty@healthtech.com  

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