Hi,
Im new to Biomart and Im having a bit of a problem. I am under the
impression that I do not fully understand how to work with the registry
files.
I have a large query batch that I would like to run using the perl api . but
when connecting through the URL using the following registry
<MartURLLocation
name = "ensembl"
displayName = "ensembl"
host = "www.biomart.org"
port = "80"
visible = "1"
default = ""
includeDatasets = "hsapiens_gene_ensembl"
martUser = ""
/>
I get a time out error . I understand that this may be due to the fact the
my query is very big ,I have a few thousand proteins that I want to query. I
read that one solution would be to connect to the Database directly and not
via the URL.
I tried the following registry
<MartDBLocation
name = "ensembl"
displayName = "ensembl"
databaseType = "mysql"
host = "martdb.ensembl.org"
port = "3306"
database = "ensembl"
schema = "ensembl"
user = "anonymous"
password = ""
visible = "1"
default = ""
includeDatasets = "hsapiens_gene_ensembl"
martUser = ""
/>
but was unsuccessful to connect , in order to connect to the ensembl
database and use the human gene dataset. what am I doing wrong?
--
Sivan Ophir Goren
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