QUESTIONS ABOUT THE PPS GLOSSARY
prepared by Lesley West, PPS glossary team
Questions are summarised here. See answers to questions after this summary.
1. How do I check if a term is in the glossary?
2. How do I add a term to the PPS glossary?
3. How do I autoindex my documents?
4. Whom do I talk to about glossary terms?
5. What index terms are needed?
6. What about case sensitive index terms?
7. What about older terms like gyrase?
8. What does approved by curator mean?
9. Can I unmark a document after autoindexing?
10. What about related terms?
11. What happens to hyphenated glossary terms?
12. What is the glossary URL for?
13. What is under development?
1. How do check if a term is in the glossary?
Glossary terms have a unique mnemonic id. Thus, Il-1-beta is identified as
il1beta in the PPS glossary. Search for the single term of interest (i.e.
il1beta) or similar terms in the URL:
http://www.cryst.bbk.ac.uk/PPS/glossary/search.html.
To see the index for protein structure, check the alphabetical list in the
URL:
http://www.cryst.bbk.ac.uk/PPS/glossary/porteinstruct/_index.html.
2. How do I add a term to the PPS glossary?
Every term in the vsns PPS course material is in the glossary but mainly
undefined at present. Please add your definition or a placeholder
definition. Adding a new term is easy. If everyone adds a term, we will soon
have a valuable glossary, provided you follow the simple guidance given in
this FAQ. First do check the term is not already present in another form. If
your term is absent, then enter the details using:
http://www.cryst.bbk.ac.uk/PPS/glossary/additem.html.
Alternatively, you may simply need to edit an existing term. In this latter
case, email the vsns-pps-glossary list server (see point 4) or the curators
at pps-gloss@crystal.desy.de.
3. How do I autoindex my documents?
You must have forms browser working under a GUI, e.g. Netscape etc.
Automatic indexing is easy. Follow the instructions in the URL:
http://www.cryst.bbk.ac.uk/PPS/glossary/markup.html.
4. Who do I talk to about glossary terms?
Join the list server vsns-pps-glossary. Email general queries and request
once you are a member:
vsns-pps-glossary@www.cryst.bbk.ac.uk.
If you need to contact the curators, email them at
pps-gloss@crystal.desy.de. We are currently producing a list of people
responsible for particular areas. We will include the list here as soon as
possible.
5. What index terms are needed?
Index terms reflect those occurring in PPS documents. Don't worry about case
in indexing terms (e.g. tertiary and Tertiary). At present indexing is case
insensitive. Thus, only enter lower case index terms (e.g. tertiary). Where
the indexing term consists of more than one word, add index terms with care.
For example, nuclear magnetic resonance is an indexing term but NOT magnetic
or resonance. Indexing terms should contain whitespace if appropriate. Thus
greekkey (the glossary term) should have indexing term 'greek key', *not*
greekkey.
6. What about case sensitive index terms?
NO ambiguity is possible. Thus at present case sensitive terms are excluded
from the glossary. PMR is building tools to allow case sensitive index terms
e.g. pH and PH (pleckstrin homology).
7. What about older terms like gyrase?
Where there is an older term (e.g. gyrase) don't create a separate entry,
but do add the term to the newer synonym, e.g.
topoisomerase
synonyms Gyrase (Superseded)
indexing terms gyrase dna gyrase.
8. What does approved by curator mean?
Currently there is no approval of glossary terms by curators. However, PMR
is adding a flag. Unapproved terms simply need further information or
possible quality checks. Thus at present all terms are unapproved. You may
find this flag useful when adding a term you want defined in the glossary.
For example, you want the term torsion but you are unsure of its
definition. Just add the term (provided it is not already present) then
ensure the approval flag is set to No (?Not sure exactly how this will
work yet - may automatically set all terms to No).
9. Can I unmark a document after autoindexing?
Not at present. However, PMR is developing a tool to unmark documents
10. What about related terms?
At present related terms are not linked. PMR is including a separate section
into the glossary. There must be a glossary entry for each related term. For
example, assuming alphahelix and 310helix.html exist, link both terms by
adding the see also sections:
alphahelix
synonym 5/18 helix
see also 3/10 helix.
11. What happens to hyphenated glossary terms?
Hyphenated terms will split at present into two words, e.g. C3'-endo will
split into C3 and endo.
In one dictionary for autoencoding, we ended up taking the hyphen (-) out of
the stop list. However, this brings other problems. We are looking into this
further. Note that hyphenated terms are included as index terms.
12. What is the glossary URL for?
If you know another dictionary or glossary defines the same term, then enter
the URL for that term in the glossary URL box. We are hoping to work
co-operatively with other glossaries to ensure maximum use of resources.
Some terms *may* come from other glossaries in the future.
13. What is under development?
PMR is currently developing the following tools:
rename term
change name
delete synonym
delete paragraph in description
alter order of paragraphs in description
delete URL
delete GIF
delete indexing term
approve term