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The triggers contained in the apollo-triggers.plpgsql file assign names according
to the following rules:
1. If the feature has 'prefix:temp' in the uniquename, it gets renamed using a
db sequence for generating uniquenames. Note that 'prefix' is a MOD
specific string set at the time the chado database is created.
a. If the feature is a gene and the name has 'prefix:temp' in it, it
is set equal to the uniquename, otherwise it is left as is.
b. Otherwise if the feature is not a gene and the feature name has
'prefix:temp' in it, it is set to null so that it can be renamed later.
2. When features are given parents via a part_of or producedby relationship
(via an insert into feature_relationship), the child feature's name
is created based on the gene's uniquename. The rules are these:
a. If it is a transcript type (ie, mRNA, tRNA, miRNA) or a polypeptide,
the name is of the form "gene_uniquename-type_nameNN" where NN
is the next available number for that feature type associated
with that gene (see the examples below).
b. If the feature is an exon, it is given a name based on the gene's
uniquename and fmin and fmax for the exon.
EXAMPLE CASE
feature tmp name tmp uname final name final uname
gene null RICE:temp3 RICE0001 RICE0001
gene RICE:temp4 RICE:temp4 RICE0002 RICE0002
gene Adh RICE:temp5 Adh RICE0003
mRNA null RICE:temp1 RICE0003-mRNA1 RICE0004
mRNA Adh cononical RICE:temp33 Adh cononical RICE0005
mRNA RICE:temp2 RICE:temp2 RICE0003-mRNA2 RICE0006
exon null RICE:temp38 RICE0003:33-76 RICE0007
exon RICE:temp1 RICE:temp1 RICE0003:2-25 RICE0008
protein null RICE:temp34 RICE0003-protein1 RICE0009
protein cftr-delF508 RICE:temp44 cftr-delF508 RICE0010
miRNA null RICE:temp22 RICE0001-miRNA1 RICE0011
mRNA Adh-mRNA1 RICE:temp9 Adh-mRNA1 RICE0012
protein Adh-protein1 RICE:temp8 Adh-protein1 RICE0013
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