Dear Lenin,
I've recently generated the item xml from Ensembl 66 human core
database and I don't have any problem loading it in. I just checked
the xml file, but there is no NCBI gene id bit in it. What version
of InterMine are you with? Can you paste a bit of your xml with the
ncbi number field?
Thanks
Fengyuan
On 10/04/12 12:57,
[hidden email] wrote:
Hi all,
We had successfully integrated data from ensembl for Mus
musculus by
downloading the mus_musculus core and creating the XML file
according to
instructions in the intermine wiki. But when we followed the
same procedure
for Homo sapiens, we get the following error.
Problem while loading item identifier 3_39 because
Duplicate objects from the same data source; o1 =
"Gene:657514719" (in database), o2 = "Gene:657515089" (in
database), source1 = "<Source: name="ensembl-human",
type="null", skeleton=false>", source2 = "<Source:
name="ensembl-human", type="null", skeleton=false>"
It looks like the database created using human ensembl data
has two
entries with the same ncbi gene number (4831), but different
Ensembl ids
(ENSG00000011052, ENSG00000243678)
While loading mouse data, the ncbi-gene number field was not
populated,
but while loading human data, it is getting populated, with
the resultant
errors while merging other sources based on ncbiGenenumber.
Any ideas on why the human and mouse XML files generated from
ensembl are
different and how to solve this problem?
Thanks and Regards,
Lenin
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