On Sep 1, 2005, at 10:47 AM, KEVIN ZEMBOWER wrote:
Further research on the PubMed site now leads me to believe that
Endnote must have written a client that allows it to search PubMed
on port 80 and get answers in XML format. I'm going to ask this
question of the PubMed support list, but can anyone on this list
tell me off the top of their head if this is correct or not?
You might be interested in checking out the National Library of
Medicine's Entrez API [1]. It basically provides a RESTful interface
for the many databases, including pubmed.
If this is correct, I'm faced with a problem. About a quarter of
the entries in POPLINE are monographs and the rest are articles
appearing in periodicals. Should I try to force this into a MARC
format and use a Z39.50 server to allow access? Or, should I write
an HTTP API and allow searches on port 80 and return information in
XML? I'd like to be as similar to any standard or de facto
standard, such as PubMed, as possible, to aid in adoption and ease
of use. Is there a well-accepted standard for articles in journals
similar to MARC if MARC shouldn't be used? Should I, or even can I,
write a Z39.50 server that returns a result in MARC if it was a
monograph, or in XML if it was an article?
If you are trying to make it easy for folks to interactively search
your set of records with EndNote I would find out exactly what
mechanism(s) EndNote supports. I think you're right, that Z39.50 is
supported for searching library catalogs.
From my admittedly limited exposure to EndNote I think that
researchers are accustomed to searching an external database for
articles, saving citations off, and then importing into EndNote. For
example in Pubmed, after searching, you can select Medline display,
and save the results off to a file, and then import with EndLink.
You're right the metadata isn't MARC, it looks like:
PMID- 16138271
OWN - NLM
STAT- In-Data-Review
DA - 20050902
PUBM- Print
IS - 0948-2393
VI - 209
IP - 4
DP - 2005 Aug
TI - [Morbidity and mortality of extremely low gestational age
infants in
schleswig-holstein.]
PG - 135-43
AB - BACKGROUND: Regional, population-based outcome studies of
extremely
preterm infants may help to assess the quality of neonatal
care across
centres and explain variation. PATIENTS AND METHODS: We
included all
extremely low gestational age infants (< 27 + 0 gestational
age = ELGA) of
six paediatric hospitals in Schleswig-Holstein born during
1997 to 1999.
The surviving children were evaluated at the corrected age of
three to six
years with the developmental test ET 6 - 6. The end point
major disability
was determined as subnormal scores in the developmental test
ET 6 - 6 (< 2
SD), or any of the following diagnoses: cerebral palsy,
blindness,
deafness, epilepsy and/or hydrocephalus requiring a shunt
system. RESULTS:
130 infants with gestational age (GA) < 27 + 0 weeks were
identified. 85
survived until discharge and 82 survived until follow-up. 63
children (77
% of all possible cases) participated in the developmental
test. Neonatal
survival increased with gestational age: 0/1 GA = 22 weeks,
3/10 GA = 23
weeks, 12/25 GA 24 = weeks, 28/43 GA = 25 weeks, 42/51 GA = 26
weeks. At
follow-up 24 children had a major disability, among those were
14 children
with multiple major disabilities. There was no significant
correlation
between major disability and gestational age. CONCLUSIONS: In
a regional
neonatal care system only infants of 25 to 26 weeks gestation
but not
those of lower GA show good survival rates. Major disability
of extremely
preterm infants seems to be independent of gestational age.
AD - Klinik fur Kinder- und Jugendmedizin, Universitatsklinikum
Schleswig-Holstein, Campus Lubeck.
FAU - Rapp, M
AU - Rapp M
FAU - Thyen, U
AU - Thyen U
FAU - Muller-Steinhardt, K
AU - Muller-Steinhardt K
FAU - Kohl, M
AU - Kohl M
LA - ger
PT - Journal Article
TT - Morbiditat und Mortalitat extrem fruhgeborener Kinder in
Schleswig-Holstein - Nachuntersuchung von extrem fruhgeborenen
Kindern
unter 27 + 0 Schwangerschaftswochen im korrigierten Alter von
drei bis
sechs Jahren in Schleswig-Holstein -
PL - Germany
TA - Z Geburtshilfe Neonatol
JID - 9508901
SB - IM
EDAT- 2005/09/03 09:00
MHDA- 2005/09/03 09:00
AID - 10.1055/s-2005-871306 [doi]
PST - ppublish
SO - Z Geburtshilfe Neonatol 2005 Aug;209(4):135-43.
If you've got a web front end on your DB perhaps you could offer the
same functionality: provide a mechanism for saving off citations in a
format that EndNote can import. As Ashely suggests it may be
possible for you to bundle this type of metadata in a Z39.50
response, but I have no idea if EndNote supports extracting that sort
of metadata from a Z39.50 response.
Search & Retrieve by URL (SRU) [2] is a relatively simple RESTful
protocol for doing search over the web. It was developed by the
Library of Congress (and others) to provide a modern alternative to
Z39.50. Although it is simpler, and easier to integrate with it still
has it's complexities, and it doesn't appear to be widely deployed yet.
You might also want to take a look at OpenSearch [3] which is a very
simple protocol developed by Amazon and others for enabling search
over the web. It's nice because they leverage the already widely
deployed RSS for bundling results. So if you decided to try it you'd
automatically be enabling rss readers everywhere to target your
database as a current awareness service.
Finally, I know this list is specifically about the use of perl in
libraries, and I'm taking quite a liberty asking these questions
here. Is there another, more broadly focused list that I should be
asking questions like this on?
Since part of your question is about xml the xml4lib list might be a
good venue as well [4]. Thanks for writing, I'd be interested to hear
what you end up doing.
//Ed
[1] http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
[2] http://www.loc.gov/z3950/agency/zing/srw/sru.html
[3] http://opensearch.a9.com/
[4] http://lists.webjunction.org/xml4lib/
