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Tips & FAQs
for the Biopharmaceutical glossaries
1. Why don't you have a search engine?
See
How
to look for other unfamiliar terms if you don't find terms with
these tips. There are always more terms to add, and I'm concentrating on
ones which can't be found in the standard (specialized) print dictionaries cited
in How to look.
2. Do you require a certain number of
times for a term to be found to include it in the glossary? No, but I do like to find terms on the
web or in print to get a sense of the spelling and context. I find Google incredibly useful
for tracking down very recent words. (See the
–Omes
and –Omics glossary) and for any situation where variant
usages (and/or spellings) come into play.
3. How do you determine
the relative preferability (or popularity) of variant terms?
Google
is the best source for this example Feb 22 2011 Google has about 67,900 hits for
druggable Feb 22 2011 and about 20,500 for drugable By May 23, 2001 the relative predominance had shifted (using Google) to cheminformatics about 3000
chemoinformatics about 1270
chemiinformatics about 25.
2009 Nov 19 update
cheminformatics about 269,000
chemoinformatics about 140,000
chemiinformatics about 4,580 I changed the title of the Cheminformatics/Chemoinformatics Glossary from
Chemoinformatics Glossary in Nov. 2001.
Unless indicated otherwise multi- word phrases are
searched in quotation marks, and match the term entry (singular or
plural). Terms with hyphens - for example data mining- gene expression
is searched as "data mining" "gene expression". Example: A Google search on Dec. 15, 2000 showed only about one-third
the number of occurrences of "oncogenomics" as "cancer
genomics",
with no overlap between the two terms. In recent
years the total number of Google hits seems to have decreased for many terms,
and my recording of the numbers is not totally reliable either. I wish I
had a spider to get the numbers for various terms and keep better track.
I'd also like an automated way to help identify terms in life science which are
becoming more prevalent than might be expected. Please let me know if you
could suggest useful software or other means of supplementing my efforts to help
organize this rather chaotic and unstructured [but important and absorbing] body
of knowledge. I've become convinced that no single human lifetime is long
enough to learn everything needed to bring new drugs successfully to [and keep
them there] to market for use in humans. I try to use quotation marks for
multi-word phrases, but don't always succeed - which may account for some of the
apparent discrepancies in numbers.
4. Why did you change the name to glossaries and taxonomies? What is a
taxonomy anyway? You can find various definitions for different kinds of taxonomies in
Ontologies & taxonomies
l. I realized I'd envisioned the
hierarchical nature of the definitions almost from the beginning, and I realized
how helpful additional related terms, narrower terms and broader terms) references
could be. I am still working on
adding to these and would welcome your comments on possible additions (or
modifications, or deletions). I am convinced that there is a fundamental
reorganization of biology going on at both the molecular and biochemical levels,
as we have new technologies, completed genomes and lots of bright and
motivated people working on really difficult problems.
Going to a
meeting (sponsored by the Special Libraries Association, in Northampton MA April
4, 2001) on Taxonomies gave me a lot to think about (and incorporate into this website).
I gave a talk on taxonomies and information overload for the Pharmaceutical division at the
annual Special Libraries Association meeting, June 2002, Los Angeles. Virtual
presentation: Information overload, taxonomies and beyond
http://www.genomicglossaries.com/presentation/SLA_outline.asp
5. How often do you check for dead links?
This is one process that
hasn't scaled for me. I need a more automated solution which checks not
only if the URL has changed, but if the content has. Some sites are only
temporarily unavailable. Other content moves to a different URL. I sometimes leave a
definition in from a no longer working website until I find another (and as good
or better) one. These are the ones with a URL without a live link. Please let me know if you
find any non- working or incorrect links now.
6. Why are you missing some very basic
terms while you include others
which seem even more elementary? My choices are somewhat arbitrary at times.
See Basic genetics
(& genomics) especially the glossary in the Primer
on Molecular Genetics for a good basic glossary and How
to look for other unfamiliar terms for some strategies for finding
terms I don't include (and email
mchitty@healthtech.com to suggest terms you don't find. Often
I just haven't thought about a particular term and would welcome your suggestions.
Some words (like gene or phenotype) are
familiar to almost everyone, but are in the process of being redefined
by genomics. When I realize this I collect a variety of definitions (and
background material) and eventually try to synthesize it and see what I
can make of it. Sometimes I put the research material on the web,
sometimes it is only on my computer and in piles in my office. The
definitions get longer before they get shorter. I don't want to lose
something crucial even if it eventually seems redundant, before I understand
enough to sort out subtleties.
7. Why don't you have an A-Z section of definitions?
I did for some months before the glossaries
were up on the web, but it was unwieldy and labor- intensive.
I was heartened to hear John Simpson, editor of
the Oxford English Dictionary in Boston in the spring of 2000, on
tour talking about the web OED version, and asked him if they were using
a database. (He had talked about the early days of data conversion into
WordPerfect.) He said they couldn't manage without a very sophisticated
one, run by HighWire Press out of Palo
Alto (US), and had profited from consultation
with people at both MIT and Stanford.
8. Why are there terms without any definitions?
These are definitions I'm working on and haven't had time to get in yet. E-mail me if you want a work in
progress definition. I probably have something to send, and would
be interested to know if a term or concept is in demand.
9. Why do you quote so much?
This is essentially a descriptive glossary, not a prescriptive
one. I'm trying to document just how words and phrases are being
used, and to distinguish nuances and differences, particularly if I can
identify the influences of different disciplines.
I also suspect
that there is a fair amount of unrecognized miscommunication as a result
of differing interpretations taken for granted by varying disciplines,
without these being articulated very often.
I'd be interested in
hearing from people who can give me specific examples. The classic
example is bioinformatics, which has biologists and computer scientists
coming at the same data from very different perspectives and assumptions.
10. Aren't some of the terms in rather
odd or idiosyncratic categories? How do you categorize them, and how consistent
are you? Absolutely there are oddities. I move terms around a lot
at times, and have trouble remembering where they are. Even the
broad categories (applications, informatics, technologies and biology
aren't mutually exclusive.
There is a lot of overlap between what
I categorize as applications (genomics, proteomics, etc.) and technologies
(which is both instrumentation and other techniques). Informatics
overlays, and is involved with almost all of the categories. I try
for consistency, but don't claim to be anywhere near it. Please let
me know if you think something is wildly out of place. I do try to
define a term only once (except for those included in the overviews) in
an effort to not have fragmented differing definitions in too many places.
I've tried to make the different sections topical guidebooks
to a field for those less familiar with the general area. - browsable and
scannable (and many sites link to specific sections most relevant to theirs).
I started by circulating paper glossaries before I was ready to put this
up on the web and found that nobody wanted to read 15 pages worth at a
go. It was only when I got the handouts down to one (double- sided)
page that I started to get feedback. As glossaries grow I tend
to split them off, but maintain ample cross- references,.
11. Why don't
the links to specific
definitions in the glossaries always work or even exist?
I've been busy trying to catch up with terms I want to input (a considerable
backlog). I'm writing,
editing, organizing and typing (and
cutting and pasting) as fast as I can. FrontPage bookmarks seem to
disappear at times.
12. Why aren't the definitions
shorter?
I try to keep shortening them, but am also
adding more -- and some of them just haven't had a chance to be edited
down sufficiently. Since I am looking for evolving definitions I
hesitate to discard anything that looks potentially useful. But please
let me know if you can suggest more succinct wording, find redundant sections,
or have any other comments.
13. What's your budget for this project?
Minimal, except for my time, my company contributes the website and software (and supports
some of my time) and a few hundred dollars for print books and subscriptions. (Not everything is
on the web.)
14. Why are you doing this?
I’m having a good time, learning a lot
and putting pieces together in a way I couldn't before. This serves
internal uses - it's (to an extent) the basis for in- house indexing and
information retrieval.
In my job I am always trying to figure out
what are the incremental improvements that make life easier for people
in the labs or clinics, without missing true paradigm shifts (which come
along only occasionally - see new paradigm in the Biotech
& pharmaceutical applications
overview.). As a librarian I’ve spent a lot of time trying
to learning specialized vocabulary in order to be able to ask (reasonably)
intelligent questions.
15.
What happened to the Genomic Glossaries & Taxonomies? This website has
evolved into a Biopharmaceutical Glossary and Taxonomies. Genomics and
proteomics are still part of it.
Mary Chitty mchitty@healthtech.com
Evolving terminology for emerging
technologies
Suggestions? Comments? Questions?
Mary Chitty MSLS 781 972 5416 mchitty@healthtech.com
Last revised
September 18, 2018
<%end if%>
2. Must a term be found a certain number of
times to be included in the glossary?
3. How do you determine the relative prevalence/ popularity of variant terms? Does this change over time?
4. Why is this called Glossaries and taxonomies? What's
a
taxonomy anyway?
5. How often do you check for dead links?
6. Why are you missing some very basic
terms while you include others
which seem even more elementary?
7. Why don't you have an A-Z section of definitions?
8. Why are there terms without any definitions?
9. Why do you quote so much?
10. Aren't some of the terms in rather
odd or idiosyncratic categories? How do you categorize them, and how consistent
are you?
11. Why don't you link to specific
definitions in the glossaries you cross-reference?
12. Why aren't the definitions
shorter?
13. What's your budget for this project?
14. Why are you compiling these glossaries/taxonomies?
15. What happened to the Genomic Glossaries & Taxonomies?
1.
A good
alternative:
Use Google site search
site:www.genomicglossaries.com and whatever you want to look for. Use
parentheses for more precise results and/or try advanced google search. .
There is no space between site: and the URL www. I'm currently revising a
number of glossaries and the term indexes are not always up to date.
Chemoinformatics is another good example. May 15, 2002 cheminformatics 6,340
chemoinformatics 2,200
On Oct. 16, 2001
cheminformatics had about 5,010 (Google) documents,
chemoinformatics about 1,640 (Google) chemiinformatics about 26 (Google)
Google on July 18, 2000 chemoinformatics about 684 cheminformatics
about 39 chemiinformatics about 6
Of course computational
chemistry about 670,000 is also a useful term.
Nov 19, 2009 cancer genomics about 77,500 oncogenomics about
515,000
Bibliography
Back to GenomicGlossaries.com