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 9
http://servlet.sanger.ac.uk:8080/das/ensembl830/sequence?segment=1:1000,1200
change to
http://www.ensembl.org/das/Homo_sapiens.NCBI36.reference/sequence?segment=1:1000,1200

pg 12 table 1.1
AGAVE http://www.agavexml.org/
BioML http://www.proteometrics.com/BIOML/ (looks abandoned)
BSML http://recentris.com/downloads.html
MAGE-ML http://www.mged.org/Workgroups/MAGE/mage-ml.html
PEML ?
PSI-MI http://www.psidev.info/
SBML http://sbml.org/
XFF ?

pg 46
XEBML(now EMBL XML) http://www.ebi.ac.uk/embl/xml/

http://www.ebi.ac.uk/cgi-bin/xembl/XEBML.pl?id=AY064249&format=Bsml
change to
http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/embl/AY064249/EMBLXML
it is not clear that EBI still produces BSML output, more info at http://www.ebi.ac.uk/cgi-bin/dbfetch

pg 142
TIGR DAS Viewer Sounds a lot like gbrowse
BioJava DAS Client http://www.spice-3d.org/dasobert/


pg 153
http://genome.cse.ucsc.edu/cgi-bin/das/hg12/dna?segment=13:30875977,30876100
you need to use hg16 or newer

pg 162
looks like wombase is using biomart queries instead of das
http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-das-client/trunk/examples
thanks to Michael Han, Wormbase Group, Sanger Institute

pg 249
http://cabio.nci.nih.gov/servlet/GetXML?query=Gene&crit_name=BRCA2
change to
http://cabioapi.nci.nih.gov/cabio41/GetXML?query=Gene&Gene[@symbol=BRCA2]

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