Import problem
Jung
I just installed cpath version 0.6.
The system setup works perfect and loading the provided sample BIOPAX
file(testData/biopax/Apoptosis.owl) works perfect.
As the next step I would like to import the data from KEGG database
With the omo Sapiens.owl I'm getting the error messages shown below.
So any ideas what's going wrong here ?
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I just downloaded from here:
ftp://ftp.genome.jp/pub/db/community/biopax/biopax.tar.gz
and
./admin.pl -d -f ../testData/biopax/KEGG/Homo Sapiens.owl import
The end of
XREF Element references a database which does not exist in cPath:
PubChem Compound. Occurred in: [Element: <bp:DB [Namespace:
http://www.biopax.org/release/biopax-level2.owl#]/>]
XREF Element references a database which does not exist in cPath:
PubChem Compound. Occurred in: [Element: <bp:DB [Namespace:
http://www.biopax.org/release/biopax-level2.owl#]/>]
Gary Bader
cPath checks that external references in BioPAX files are recognized so
that correct hyperlinks can be made to these sources from record web
pages. By default, cPath doesn't know about all databases that are
referenced in all possible BioPAX files, just some commonly used ones.
To skip the validation of external references, use the -x option for the
admin.pl script.
The complete fix is to update the external_db table to add new 'known'
databases and their URL patterns that are used to create links.
Unfortunately, we don't have a nice interface for this functionality
yet, so it has to be done manually e.g. using SQL or software like
phpMyAdmin or Navicat.
If you add any new external databases, send us the updated table and we
can add them to future cPath versions.
Hope that helps,
Gary
--
http://baderlab.org
Terrence Donnelly Centre for Cellular and Biomolecular Research
University of Toronto