FW: cytoscape "ontology-troubled network" reply

[Alexander Pico]

Justin,

I turned your example text file into a SIF (attached), imported it into Cytoscape and then used the Ontology and Annotation importer to get GO slim terms for Mus musculus.  The keys matched between your file and the annotation. I confirmed this by previewing the first 12,000 rows of the annotation file, which includes ‘Apobec1’ and shows 18 matches for that particular ID. But, when I click ‘Import’, nothing but empty fields are loaded. I think this is what you were seeing as well.

Not sure why this isn’t working...

 -Alex


On 6/14/09 5:37 AM, "Justin Sharps" <tr0p...@gmail.com> wrote:

> Hi Alex,
>
> Actually, the ID's for the nodes are the NCBI EntrezGene IDs. That's why I
> used the name mapping files - to add the MGI ID and symbols as attributes, and
> then I tried to use those as the linking attribute for the ontology data. I've
> attached a portion of the file I was using, and I'm attaching another file in
> which I've gone through and renamed the EntrezGene IDs to the Symbol, as
> according to MGI. It's a text file table with positive and negative
> interactions. (---> is positive, --| is negative) I hope this is useful for
> troubleshooting, thanks for your help.
>
> Thanks,
> Justin
>

On 6/12/09 1:52 PM, "Alexander Pico" <ap...@gladstone.ucsf.edu> wrote:

>
> Justin,
>
> 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" <tr0p...@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.
>>
>> Thanks,
>> Justin
>>
>>>
>
>
>
> >