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/

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