i am using fmp 13 to access the pubmed database as well and was happy to see that there are others doing it. i am replying to this thread because my problem is kind of similar.
The thing is, a year ago my setup was working fine: i would generate an url with a formula request xml from pubmed (via the eutils esearch feature) and the resulting xml would be parsed by a custom xslt and the values then would be imported without any problem.
the url would look like this:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&retmax=10000&usehistory=y&term=Aortic stenosis [tiab] AND 2016 [dp]
Going back to this database today my scripts all gave me the error that a whitespace was expected in line 1 column 50.
i tried opening the pubmed URL in a browser. copied the resulting content to the text editor and saved it as a utf-8 xml file. when i select this xml file as the source (instead of the URL) everything is working fine.
i have no idea why this all worked about 12 month ago and doesn't work anymore. furthermore i would really like to get this working again...
have you had the same problems? any ideas?
i guess maybe pubmed changed something in the encoding, or the upgrade to macOS sierra.