This HOWTO describes a method for loading sequence annotation data in GFF3 format into a Chado database.
An easy way to load data into the database is to use a
GFF3 file and the script
load/bin/gmod_bulk_load_gff3.pl. A good set of sample data is the GFF3
file prepared by the nice folks at the Saccharomyces Genome
Database:
http://downloads.yeastgenome.org/curation/chromosomal_feature/saccharomyces_cerevisiae.gff
This file contains
Gene Ontology (GO) annotations, so if you didn’t load
GO when you executed make ontologies you will get many warning
messages about being unable to find entries in the
dbxref table. If you want
to load GO you should be able to execute make ontologies and select
Gene Ontology for installation.
You will need to have an entry for your species in the Chado organism
table. To add a new
organism, run the tool that came with Chado, gmod_add_organism.pl
This script will ask you what information about your organism:
Both genus and species are required; please provide them below
Organism's genus?
Organism's species?
Organism's abbreviation? []
Comment (can be empty)?
Unless your GFF3 is sorted by location with grouped gene models (gene, mRNA, CDS/exon/UTR), you must first do this. Use this gmod_gff3_preprocessor.pl.
> gmod_gff3_preprocessor.pl --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
Then execute gmod_bulk_load_gff3.pl:
>gmod_bulk_load_gff3.pl --organism yeast --gfffile saccharomyces_cerevisiae.sorted.gff
This loads the GFF3 file. The loading script requires
GFF3 as it has tighter control of the syntax and requires
the use of a controlled vocabulary (from
Sequence Ontology Feature Annotation (SOFA)),
allowing mapping to the relational schema. In addition to supplying the
location of the file with the --gfffile flag, the --organism tag
uses the common name (common_name field) from the Chado organism
table. Do
perldoc gmod_bulk_load_gff.pl for more information on adding other
organisms and databases, as well as other available command line flags.
Note that gmod_load_gff3.pl is also available, but is limited in how
much it has been supported and in how flexible it currently is. It is a
good example of how to write code using
Class::DBI classes that are
created at the time of install. For more information on using these
classes, see Modware for a
Class::DBI-based
middleware/API.
A recent update (April 2007) to bp_genbank2gff3.pl extends it to
handle Swiss and EMBL format input, along with GenBank. You can now
create GFF3 entries of UniProt sequences suited to
loading into
Chado, including
most of the protein description, Dbxref, and related fields useful in
annotating genome matches. Use the --format Uniprot flag to specify
this input format (--format EMBL can also be useful).
>bp_genbank2gff3.pl --noCDS --in uniprot-subset.dat --format Uniprot
>gmod_bulk_load_gff3.pl --database mygenome --gff uniprot-subset.dat.gff --organism fromdata
Use the --organism fromdata flag to load UniProt with many organisms.
See the related HOWTO Load RefSeq Into Chado.
Please send questions to the GMOD developers list:
gmod-devel@lists.sourceforge.net
Or contact the GMOD Help Desk