Hey Apollo-ers,
We are using Apollo, Chado and XORT to handle the bovine genome
annotation effort, and things are working pretty well.
I am running some tests to make sure everything is working correctly,
and it seems Apollo is not pulling some rank attributes out of Chado
correctly.
When I do a roundtrip test thusly:
1) Annotate gene using Apollo, save as Chado XML
2) Load into Chado using XORT
3) Pull annotation from Chado using Apollo
4) Write to Chado XML ("after" XML file)
and do a diff on the "before" Chado XML (step 1) and "after" Chado
XML
(step 4), the rank attribute of feature_relationship's have changed.
In the "before" Chado XML, the rank attribute of
feature_relationship between
exons and their mRNA in the before Chado XML is always equal to
the order
of the exon: 1st exon has a rank of 1, second exon has a rank of 2
and so on.
In the "after" Chado XML, the rank attribute is always 0.
Example:
Before -
<feature_relationship>
<rank>1</rank>
<subject_id>
<feature>
<is_analysis>0</is_analysis>
<name>Btgn:temp1:Chr6.29:650000-768000:1</name>
After -
<feature_relationship>
<rank>0</rank>
<subject_id>
<feature>
<is_analysis>0</is_analysis>
<name>Btgn:temp1:Chr6.29:650000-768000-RA exon 1</
name>
XORT seems to have correctly loaded the ranks into Chado, so
that's not the
problem:
SELECT feature.name, feature_relationship.rank FROM feature,
feature_relationship WHERE feature.feature_id =
feature_relationship.subject_id AND uniquename LIKE
'Btgn:temp1:Chr6.29:650000-768000%'
name | rank
-------------------------------------+------
Btgn:temp1:Chr6.29:650000-768000-PA | 0
Btgn:temp1:Chr6.29:650000-768000:16 | 16
Btgn:temp1:Chr6.29:650000-768000:15 | 15
Btgn:temp1:Chr6.29:650000-768000:14 | 14
Btgn:temp1:Chr6.29:650000-768000:13 | 13
Btgn:temp1:Chr6.29:650000-768000:12 | 12
Btgn:temp1:Chr6.29:650000-768000:11 | 11
Btgn:temp1:Chr6.29:650000-768000:10 | 10
Btgn:temp1:Chr6.29:650000-768000:9 | 9
Btgn:temp1:Chr6.29:650000-768000:8 | 8
Btgn:temp1:Chr6.29:650000-768000:7 | 7
Btgn:temp1:Chr6.29:650000-768000:6 | 6
Btgn:temp1:Chr6.29:650000-768000:5 | 5
Btgn:temp1:Chr6.29:650000-768000:4 | 4
Btgn:temp1:Chr6.29:650000-768000:3 | 3
Btgn:temp1:Chr6.29:650000-768000:2 | 2
Btgn:temp1:Chr6.29:650000-768000:1 | 1
Btgn:temp1:Chr6.29:650000-768000-RA | 0
I did some Apollo code diving, and found this in
ChadoXmlAdapter.java:
/** Get the rank from a featureprop record.
* <featureprop>
* <rank>0</rank>
* <type_id>
* Returns the rank as a short (default is 0 if it can't be
parsed).
* 12/2005: No longer used (not roundtripping featureprop
ranks). */
Looks like someone else was doing this same roundtrip and decided
that this diff was not a dealbreaker. I found several other places
in the
Apollo code where rank is retrieved from Chado and assigned, but
can't
seem to find the one that is relevant here (i.e. a place where I
can change
the rank manually to something unique like 99999 and have that rank
show up in the "after" XML).
Any advice about why ranks aren't being pulled correctly here,
and, more
importantly, whether this is harmful? Are incorrect
feature_relationship
ranks going to hurt anything? Apollo happily loads these genes with
the wrong ranks, and they display correctly as far as I can tell.
I'd be glad to provide a chado-adapter.xml or connection info if
anyone
wants to connect to our chado and have a look first-hand.
Thanks in advance,
Justin
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