Friday, November 14, 2008
Errata to XML for Bioinformatics by Ethan Cerami
This book is a great introduction to parsing XML and XML-based webservices for bioinformatics. Unfortunately a lot of the URLs in book have changed and some of the services listed in it have already died. I will try to provide the updated examples below as I continue through the book.
If anyone has the source code to this book please send it to me!
pg 12 table 1.1
BioML http://www.proteometrics.com/BIOML/ (looks abandoned)
XEBML(now EMBL XML) http://www.ebi.ac.uk/embl/xml/
it is not clear that EBI still produces BSML output, more info at http://www.ebi.ac.uk/cgi-bin/dbfetch
TIGR DAS Viewer Sounds a lot like gbrowse
BioJava DAS Client http://www.spice-3d.org/dasobert/
you need to use hg16 or newer
looks like wombase is using biomart queries instead of das
thanks to pg 249