I'm using cytoscape 2.6.2 on Mac OSX 10.5.7 (leopard) with recenly
updated Java. I'm working with a predicted network of mouse genes -
transcription factors and their putative target genes. I want to
import the ontology data to the network so I can filter and select
nodes by ontology data...
The problem is that when I use the "File --> Import --> Ontology and
Annotation..." function in cytocape, the full GO is loaded into the
session, but won't associate with the nodes. They remain as completely
separate networks, however the nodes gain attributes such as
ontology.name and ontology.is_obsolete, but all these attributes are
empty. I used the name mapping files, so I've tried associating
DB_Object_Symbol with Official Symbol, and DB_Object_ID with MGI (with
and without prefixes), but nothing seems to work. Any help would be
greatly appreciated.
> I'm using cytoscape 2.6.2 on Mac OSX 10.5.7 (leopard) with recenly
> updated Java. I'm working with a predicted network of mouse genes -
> transcription factors and their putative target genes. I want to
> import the ontology data to the network so I can filter and select
> nodes by ontology data...
> The problem is that when I use the "File --> Import --> Ontology and
> Annotation..." function in cytocape, the full GO is loaded into the
> session, but won't associate with the nodes. They remain as completely
> separate networks, however the nodes gain attributes such as
> ontology.name and ontology.is_obsolete, but all these attributes are
> empty. I used the name mapping files, so I've tried associating
> DB_Object_Symbol with Official Symbol, and DB_Object_ID with MGI (with
> and without prefixes), but nothing seems to work. Any help would be
> greatly appreciated.
I've come up with something of a work-around, but it's still not
working completely and I'm wondering if anyone has insight into the
new situation. I downloaded the mouse gene ontology file manually
from MGI, and then imported using the "file --> import ---> ontology
and annotation" option. I chose the local mouse ontology file and
associated column 3 with the Official Symbols in my network and column
5 with the GO. It seemed to work to a degree, importing the name and a
couple other columns correctly, but column 5 gets imported as an array
of GO ID's to each node, instead of actually mapping to those GO's.
Has anyone encountered this before or know how to fix it?
Thanks,
Justin
On Jun 13, 5:52 am, Alexander Pico <ap...@gladstone.ucsf.edu> wrote:
> What IDs are used for the nodes in your network? MGI or symbols, I presume.
> Could you send the file or a sample of the file for troubleshooting?
> -Alex
> On 6/11/09 10:25 PM, "JustinS" <tr0ph...@gmail.com> wrote:
> > Hi,
> > I'm using cytoscape 2.6.2 on Mac OSX 10.5.7 (leopard) with recenly
> > updated Java. I'm working with a predicted network of mouse genes -
> > transcription factors and their putative target genes. I want to
> > import the ontology data to the network so I can filter and select
> > nodes by ontology data...
> > The problem is that when I use the "File --> Import --> Ontology and
> > Annotation..." function in cytocape, the full GO is loaded into the
> > session, but won't associate with the nodes. They remain as completely
> > separate networks, however the nodes gain attributes such as
> > ontology.name and ontology.is_obsolete, but all these attributes are
> > empty. I used the name mapping files, so I've tried associating
> > DB_Object_Symbol with Official Symbol, and DB_Object_ID with MGI (with
> > and without prefixes), but nothing seems to work. Any help would be
> > greatly appreciated.
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