These are chat archives for elsiklab/bovinemine

6th
Nov 2015
Aditi
@tayala
Nov 06 2015 21:41
hey guys …just checking in
Deepak
@deepakunni3
Nov 06 2015 21:41
hello
Aditi
@tayala
Nov 06 2015 21:42
hows it going
Deepak
@deepakunni3
Nov 06 2015 21:42
its going ok. I am working on a DBSNP parser to consume the DBSNP ASN flat file
for BovineMine
Aditi
@tayala
Nov 06 2015 21:43
oh great… yeyyy
Deepak
@deepakunni3
Nov 06 2015 21:43
so that we don’t have to compute SNP effects ourselves
it all comes from DBSNP
what about you?
Aditi
@tayala
Nov 06 2015 21:43
i finished the orthodb stuff. The parser was not the problem
the file was a problem
it all had protein information for all the genes
Deepak
@deepakunni3
Nov 06 2015 21:44
wait..which orthodb?
Aditi
@tayala
Nov 06 2015 21:44
orthodb 8
Deepak
@deepakunni3
Nov 06 2015 21:44
oh
orthoDB 8 has 2 files
Aditi
@tayala
Nov 06 2015 21:44
yes
Deepak
@deepakunni3
Nov 06 2015 21:44
one is annotations and other is genes
Aditi
@tayala
Nov 06 2015 21:44
yes
Deepak
@deepakunni3
Nov 06 2015 21:45
the only thing missing from ODB8 is protein domain information for each gene
it was provided in ODB7
so you got to parse it?
Aditi
@tayala
Nov 06 2015 21:45
the genes were actually protein ids
not gene ids
Deepak
@deepakunni3
Nov 06 2015 21:45
oh, right! Ensembl proteins
Aditi
@tayala
Nov 06 2015 21:46
yes … i am still have to go thru the parser and see if the parser loads the domain information
and so then i will have to merge the files
Deepak
@deepakunni3
Nov 06 2015 21:47
right
cool, thats great.
Aditi
@tayala
Nov 06 2015 21:48
there are still a few ids in orthodb 8 that have gene ids but are “retired”
so i left them as protein ids
Deepak
@deepakunni3
Nov 06 2015 21:48
oh
Aditi
@tayala
Nov 06 2015 21:48
mostly rat
and homo sapiens
Deepak
@deepakunni3
Nov 06 2015 21:48
nah. You’ll have to eliminate them. else we wil have protein IDs in the Gene table
Aditi
@tayala
Nov 06 2015 21:49
ok kool.
Aditi
@tayala
Nov 06 2015 21:59
yes doing this for bovinemine was ok
i am dreadding hymenopteramine
Deepak
@deepakunni3
Nov 06 2015 22:00
Yeah. We’ll worry about that when we get there :no_mouth:
heres to hoping OrthoDB 9 is released by then
Aditi
@tayala
Nov 06 2015 22:00
with geneids
Deepak
@deepakunni3
Nov 06 2015 22:01
nevermind. I was being too optimistic.