Hi, With apologies for the cross-post, but I'll take an answer from either camp if it solves my problem.
I'm using Artemis v11, and Chado/scripts from GMOD-1.0, with PostgreSQL 8.3 My problem at the moment is this: I have a genome annotation with gene models that look like they satisfy the Sequence Ontology parent-child relationships, and are correct. The upload script for Chado modifies these gene models in a way that I'm not entirely happy with; I would prefer to keep the original gene model information. When viewing the information from Chado in Artemis, Artemis appears to make invalid assumptions about the gene model in Chado; it does not do this when reading the annotation from a local .gff3 file. My example case: I have a GFF3 format file with entries like this: supercont1.1 . gene 6164086 6165743 . + . ID=7000001843685266;Name=conserved%20hypothetical%20protein;Alias=PITG_01056 ; supercont1.1 . mRNA 6164086 6165743 . + . ID=7000001843685267;Parent=7000001843685266;Alias=PITT_01056; supercont1.1 . five_prime_UTR 6164086 6164127 . + . ID=7000001843685267.UTR5p1;Parent=7000001843685267 supercont1.1 . exon 6164086 6164456 . + . ID=7000001843685267.exon1;Parent=7000001843685267 supercont1.1 . CDS 6164128 6164456 . + . ID=7000001843685267.cds1;Parent=7000001843685267 supercont1.1 . exon 6164548 6165169 . + . ID=7000001843685267.exon2;Parent=7000001843685267 supercont1.1 . CDS 6164548 6165169 . + . ID=7000001843685267.cds2;Parent=7000001843685267 supercont1.1 . exon 6165239 6165415 . + . ID=7000001843685267.exon3;Parent=7000001843685267 supercont1.1 . CDS 6165239 6165415 . + . ID=7000001843685267.cds3;Parent=7000001843685267 supercont1.1 . exon 6165477 6165743 . + . ID=7000001843685267.exon4;Parent=7000001843685267 supercont1.1 . CDS 6165477 6165743 . + . ID=7000001843685267.cds4;Parent=7000001843685267 This defines a gene, transcript mRNA, and exons that comprise a 5`UTR with CDS. This all seems to me to be correct and in line with Sequence Ontology definitions. The recommended upload script, both at the GMOD site (http://gmod.org/wiki/Load_GFF_Into_Chado), and at the Artemis site (http://www.sanger.ac.uk/Software/Artemis/v11/chado/dbloading.shtml), is gmod_bulk_load_gff3.pl. When I use this script, as is documented in the perldoc, CDS features are converted to polypeptide features, and CDS and UTR features are combined into exon features (unless I use the --noexon flag when calling the script). In general terms I would prefer this not to happen, and to keep separate UTR and CDS features within the database, but there doesn't appear to be an option to upload the gene models without this conversion. As no information is lost, I can live with this, so long as the downstream interpretation makes the correct inferences regarding UTR and CDS. Unfortunately, this does not seem to be the case with Artemis. As noted at http://www.sanger.ac.uk/Software/Artemis/v11/chado/overview.shtml#GENE the gene model that Artemis assumes defines exons differently to Chado's upload script (and, incidentally, differently to the Sequence Ontology itself: http://www.sequenceontology.org/miso/current_cvs/term/SO:0000147), considering them to be equivalent to CDS features. This, as you might imagine, causes some issues for us. Artemis manages to open up the GFF3 file directly without any issues, but as we'd quite like to have multiple users modify the same annotation, this isn't an option for us. I would be happy with any of the following kinds of solution: * pointers to what I'm doing wrong (other than not using Apollo ;) ) * a script that uploads our GFF3 data into Chado in a form that preserves our current gene models for viewing in Artemis (I guess you use one of these at the Sanger - would you be able to make one of these publicly-available, or point me to one?) * a modification to Artemis that infers CDS and UTRs correctly from the exon/polypeptide data in Chado, as uploaded by the recommended upload script. * anything else that make this work. Thanks for your attention, L. -- Dr Leighton Pritchard MRSC D131, Plant Pathology Programme, SCRI Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA e:lpr...@scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard gpg/pgp: 0xFEFC205C tel:+44(0)1382 562731 x2405 ______________________________________________________ SCRI, Invergowrie, Dundee, DD2 5DA. 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