Pubmed XML to Filemaker pro

[oudent]

Hi,

I have NO background whatsoever with XML, but I really want to be able to import data from the online database at pubmed.org to Filemaker pro using XML.

I think I've figured out the command to get filemaker pro 8 to import the record I want from Pubmed, but I guess I need an xslt thing to make it work.

My script command for Importing Records would be:

Import Records [No dialog; http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=9037774&retmode=xml; Add; Windows ANSI]

Does that look right? I'll change it to use a calculation to determine exactly which id # to include.

But then, I get a parsing error:

XML parsing error:

Attibute 'IdType' is not declared for element 'ArticleId'

Line Number: 161

Column Number:31

Which I assume is because I don't have an XSLT style sheet or whatever to convert the data to filemaker's XML grammar.

So, I've looked online for 2 days now, and I just keep finding a bunch of instructions I don't understand, or people suggesting books or courses. I'm a poor graduate student in Microbiology, so there is no way I'm going to be able to pay to get this working, I just want a convenient way to keep track of articles in a certain way that End Note can't do (ie. not crash, and server compatible). Also, I don't have the authorization to install more software on our server so I might as well just use Filemaker Pro 8 as a sudo reference manager that can do a little extra.

Would someone please be able to help?

I should mention that I want this to be Windows and MacOS X compatible, we have a server, so if files need to be linked to I'm sure I can work something out, because I assume and xslt file is usually local and would have to be installed on each computer, or linked to an http address?

If you think you can help, here is all that I want to do...I don't think it is too complicated.

Pubmed, is just a big online database for research article abstracts. Each article has a unique pubmed Id (PMID), which I have a field for in my FM database. I then want to import the pubmed record info into fields like "Article Name" and "Authors", etc in my FM database. Thats it.

How hard can that be?

I have the DTD for pubmed if that helps (I just got it from the address supplied at the top of the XML entry retreived from my Import Records address.

Please, if anyone can help you would make me really happy.

Thanks,

Nick

Edited March 9, 2007 by Guest

[Fenton]

"How hard can it be?" Well, that depends on how much know, and what your definition of hard is. It is not terribly hard, but it is somewhat tedious. There is a lot of information in that xml. The attached xsl will get you started.

pubmed.xsl.zip

[comment]

OFF TOPIC:

That's an interesting method to import the date directly into a date field. The downside is that it relies on the Filemaker file being set to use the m/d/y format.

It would be nice if the DATEFORMAT attribute of the DATABASE element actually meant something to Filemaker - but unfortunately, it is completely ignored.

Incidentally, so is the FOUND attribute of the RESULTSET element. I don't know why you bother to actually count the records. I just put "1" there (it seems it cannot be empty) and the result is the same.