Hi Björn I have just added some documentation that describes loading in two examples one of these is the one you have used (NC_008783): http://www.sanger.ac.uk/Software/Artemis/v11/chado/dbloading.shtml
I did not experience the problem you seem to have with feature types. However I had to manually add 'processed_transcript' to the SO CvTerm. I am not sure what feature types = 1 is in you case but Artemis currently only looks at these types to build the database manager for features that contain residues that can be launched: %chromosome% %sequence% supercontig ultra_scaffold golden_path_region contig It may be better to try to fix the feature types problem you had and then reloading. Regards Tim On 2/24/09 5:41 PM, "Björn Nystedt" <bjorn.nyst...@ebc.uu.se> wrote: > Hi, > I am trying to set up a GMOD chado database to read/write using Artemis. I > admit not being a very experienced database user, so maybe I am missing > something obvious. Anyway. > > I start Artemis using > art -Dchado="localhost:5432/annotation?bjorns" > -Djdbc.drivers=org.postgresqlver -Dibatis > and feeds my database password. > This appear to work ok in the sense that there are no error messages. However, > in the database list at the top left, there is only an unnamed folder, and > clicking this folder nothing happens except an error appears in the terminal > 'Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException > ...' > > > *GMOD > The database I am using is a postgresql (v8.1.16, as I understand there was a > problem with gmod and v8.3?), setup with the GMOD schema (gmod-1.0, from > http://www.postgresql.org/download/): > perl Makefile.PL > make > sudo make install > make load_schema > make prepdb > make ontologies > This appear to work as far as I can decide. > > * TEST DATASET > A test dataset was loaded into the database by first manually setting the > organism: > INSERT INTO organism (abbreviation, genus, species, common_name, > organism_id) VALUES ('B.bacilliformis', 'Bartonella', 'bacilliformis', 'BB', > 8783); > then converting a genbank file to gff and load the gff data into the database > perl bp_genbank2gff3.pl NC_008783.gbk --noCDS -o . > gmod_bulk_load_gff3.pl --organism 'BB' --noexon --gfffile > NC_008783.gbk.gff --recreate_cache > > After the upload the database does contain data that makes sense as far as I > can tell, and it is possible to backup the database. (There is for some reason > a problem with feature types in gmod_bulk_load_gff3.pl: for now I made an ugly > hardcoding to set all feature types = 1. line755) > > > Any idea on how to get Artemis to find the data in the database is > appreciated! > > > Best > Björn Nystedt > > _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
