[InterMine Dev] CrossReferences

Dr. Intikhab Alam intikhab.alam at kaust.edu.sa
Wed Feb 22 14:20:34 GMT 2012


Dear at dev.intermine,


How can one properly cross refence Interpro, GO or uniprot accessions from
intermine-items-large-xml-file type source?


I am building a mine using sources like intermine-items-large-xml-file on
top of interpro, go-annotation etc. First I could not properly link
seqfeatures to the chromosome to properly do post-process like
transfer-sequences. Now I have learned that unless I define the relevent
chromosome, link it to the datasource in the xml and reference Location
with feature attribute and furthermore use 'exons', 'cds', 'gene' in the
Transcript, I can not see Gene Models and sequences for the Gene,
Transcript, Exon or CDS.

How can I properly crossreference Interpro and GO Ids, If I am loading
'Gene', 'Transcript', 'Exon' ,'CDS' and 'Protein' using
intermine-items-large-xml-file type source with Ids for Interpro and
GO-Annotation AND interpro, GO-Annotation and loaded in the database using
their standard sources? When Interpro and GO-Annotation are loaded using
their standard source loaders in intermine, is there a way to define the
datasource for Interpro and GO-Annotation in my
intermine-items-large-xml-file type source, that is required for
crossrefernce I guess? If not what is the best way to do this?

Regards,

Intikhab





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