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You are here Biopharmaceutical/ Genomic glossary homepage/Search > FAQs for biopharmaceutical glossaries Tips & FAQs
for the Biopharmaceutical glossaries
1. What can you do with the search engine?
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. The site is supposed to be re-indexed at least once every week. I'm still figuring out just what the search engine is doing, and would welcome your observations. mchitty@healthtech.com Sometimes I use Google, by adding the words healthtech and glossary to whatever I'm looking for instead of the website 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?
3. How do you determine
the relative preferability (or popularity) of variant terms?
May 15, 2002 On Oct. 16, 2001 Searching AltaVista
and Google on July 18, 2000 for variants had these results
By May 23, 2001 the relative predominance had shifted (using Google) to I changed the title of the Cheminformatics/Chemoinformatics Glossary from Chemoinformatics Glossary in Nov. 2001. Computers & computing, Data & information management, Microarray & protein chips categories and -Omes & -omics glossary now have Google word/ phrase counts for most entries. 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. Example AltaVista works (with truncation *) better than Google for biochip* "DNA array*" "gene chip*" microarray* and other variants but Google would usually the first search engine I try for a single word (bioinformatics) or a phrase like "functional genomics". Advanced Search in Google now permits limited Boolean "or" searching, but I haven't used this feature much yet. As far as I can tell Google still does not permit truncation.) No search engine covers the entire web (or even a majority of it) and several weeks to months are needed before some sites are indexed (particularly noticeable with very recent events. 4. Why did you change the name to glossaries and taxonomies? What is a
taxonomy anyway? 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? 6. Why are you missing some very basic
terms while you include others
which seem even more elementary? 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 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. I kept alphabetical and category indexes manually for about a year, but simply couldn't keep up. Now i really need to switch to a database 8. Why are there terms without any definitions? 9. Why do you quote so much?
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? 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?
12. Why aren't the definitions
shorter? 13. What's your budget for this project? 14. Why are you doing this? 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
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