Re: Priority list / graphs.

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Re: Priority list / graphs.

Benjamin Hitz

I think the datamodel for interactions/pathways needs to change to be more graph-like.  
I am not sure exactly how to do this - it does seem that the ontology data definition handles this pretty well, but it's quite hard to read in the "tree model" browser.

For example, the "default" pathway model only allows assignment of genes to pathways, when actually a pathway is a (directed) graph between genes/substrates/products.
Similarly - the issue of interaction lists being redundant is because you have:
gene a has a collection of interactions with genes [b, c, d, f]
and
gene b has a collection of interactions with genes [a, d, f, q, z]

But the a->b interaction in both collections is actually the "same" interaction (sometimes with a different directionality).  It's also a graph structure (directed, with some undirected edges)

Ben
On Apr 7, 2011, at 8:20 AM, Richard Smith wrote:

> Hi all,
> We've made an attempt at ordering the list of developments by priority.
> Let us know if you have any comments/objections:
>
> http://mods.intermine.org/wiki/DevelopmentPriorities2011
>
> I only have 30 minutes for the call today as there is a modENCODE
> webinar.
>
> Cheers,
> Richard.

--
Ben Hitz
Senior Scientific Programmer
Saccharomyces Genome Project
Stanford University
[hidden email]




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Re: Priority list / graphs.

Richard Smith
Yes, we need to do something about interactions.  We've tried a couple
of iterations and haven't got it right yet.  We can also store more
information about structure of pathways.

How about we make our May 5th Mines for MODs call about this?  We can
all share any bright ideas we have.

Richard.


On 07/04/2011 18:24, Benjamin Hitz wrote:

>
> I think the datamodel for interactions/pathways needs to change to be more graph-like.
> I am not sure exactly how to do this - it does seem that the ontology data definition handles this pretty well, but it's quite hard to read in the "tree model" browser.
>
> For example, the "default" pathway model only allows assignment of genes to pathways, when actually a pathway is a (directed) graph between genes/substrates/products.
> Similarly - the issue of interaction lists being redundant is because you have:
> gene a has a collection of interactions with genes [b, c, d, f]
> and
> gene b has a collection of interactions with genes [a, d, f, q, z]
>
> But the a->b interaction in both collections is actually the "same" interaction (sometimes with a different directionality).  It's also a graph structure (directed, with some undirected edges)
>
> Ben
> On Apr 7, 2011, at 8:20 AM, Richard Smith wrote:
>
>> Hi all,
>> We've made an attempt at ordering the list of developments by priority.
>> Let us know if you have any comments/objections:
>>
>> http://mods.intermine.org/wiki/DevelopmentPriorities2011
>>
>> I only have 30 minutes for the call today as there is a modENCODE
>> webinar.
>>
>> Cheers,
>> Richard.
>
> --
> Ben Hitz
> Senior Scientific Programmer
> Saccharomyces Genome Project
> Stanford University
> [hidden email]
>
>
>
>


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Re: Priority list / graphs.

Benjamin Hitz
Agreed...  I find some time to look into the data models further.

Ben
On Apr 8, 2011, at 6:39 AM, Richard Smith wrote:

> Yes, we need to do something about interactions.  We've tried a couple
> of iterations and haven't got it right yet.  We can also store more
> information about structure of pathways.
>
> How about we make our May 5th Mines for MODs call about this?  We can
> all share any bright ideas we have.
>
> Richard.
>
>
> On 07/04/2011 18:24, Benjamin Hitz wrote:
>>
>> I think the datamodel for interactions/pathways needs to change to be more graph-like.
>> I am not sure exactly how to do this - it does seem that the ontology data definition handles this pretty well, but it's quite hard to read in the "tree model" browser.
>>
>> For example, the "default" pathway model only allows assignment of genes to pathways, when actually a pathway is a (directed) graph between genes/substrates/products.
>> Similarly - the issue of interaction lists being redundant is because you have:
>> gene a has a collection of interactions with genes [b, c, d, f]
>> and
>> gene b has a collection of interactions with genes [a, d, f, q, z]
>>
>> But the a->b interaction in both collections is actually the "same" interaction (sometimes with a different directionality).  It's also a graph structure (directed, with some undirected edges)
>>
>> Ben
>> On Apr 7, 2011, at 8:20 AM, Richard Smith wrote:
>>
>>> Hi all,
>>> We've made an attempt at ordering the list of developments by priority.
>>> Let us know if you have any comments/objections:
>>>
>>> http://mods.intermine.org/wiki/DevelopmentPriorities2011
>>>
>>> I only have 30 minutes for the call today as there is a modENCODE
>>> webinar.
>>>
>>> Cheers,
>>> Richard.
>>
>> --
>> Ben Hitz
>> Senior Scientific Programmer
>> Saccharomyces Genome Project
>> Stanford University
>> [hidden email]
>>
>>
>>
>>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO Consortium
Stanford University ** [hidden email]




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