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Tips & FAQs for the Biopharmaceutical glossaries
Evolving terminology for emerging technologies
Suggestions? Comments? Questions? Mary Chitty 781 972 5416 mchitty@healthtech.com
Last revised March 23, 2012

 



1. What can you do with the search engine?
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. What can you do with the search engine?  It does support truncation (use an asterisk *).  It is sensitive to punctuation. In particular, try words and phrases with and without hyphens if you don't retrieve any results.

You can't search with numbers.  You won't find 2D gel electrophoresis (although it is there).  I've tried to put in cross references to two-D however.

It isn't case- sensitive. It doesn't seem to support searching by phrases. Two words come up with fewer results than either one of the words alone. This implies a Boolean AND function, but I'm not convinced of this.  I don't think there are Boolean OR or NOT functions.  

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. 

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 

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 

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
Of course computational chemistry about 670,000 is also a useful term. 

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.
Nov 19, 2009  cancer genomics about 77,500  oncogenomics about 515,000  

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.  And the please fill out this form seems to interfere with links.  

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   Bibliography

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