Hi Justin,
Yes, please provide me with some sample data and access to the database
and I'll explore this issue further.
-Ed
On Tue, 2008-06-10 at 00:20 +0700, Justin Reese wrote:
> 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
> _______________________________________________
> apollo mailing list
> [email protected]
> http://mail.fruitfly.org/mailman/listinfo/apollo
>
_______________________________________________
apollo mailing list
[email protected]
http://mail.fruitfly.org/mailman/listinfo/apollo
