[Gmod-help] cosmoss.org Physcomitrella mod

Mon Apr 19 17:31:49 EDT 2010

Hi Daniel,

Thanks for the detailed response and additional information.  I'm going to
try to cover all the points.

First, I will talk to Scott and unless he sees a problem, we'll get you a
letter of support, on GMOD letterhead, within the next week.

GMOD has not traditionally been strong at microarrays or proteomics.  Chado
does have a MAGE module, but its used by only a subset of users and neither
Scott nor I have personal experience with it.  Java TreeView (cluster
visualization for microarrays) is also a part of GMOD, but it's connection
to GMOD is distant.  Java TreeView is widely used outside of the GMOD
community.  We do support RNA-Seq data as genomic/sequence data, but I
hadn't really given it any thought yet on how to represent the data as
expression data (in the Chado expression module).  I'm sure it can be done,
though.  Patrick Lemaire may also have already given this some thought.

My expectation is that NISEED could be used to curate and display
anatomy-based annotation.  I'm not so sure about the other ontology types.
For general ontology annotation, GMOD has an ongoing conversation with the
Phenote team about integrating it into GMOD.  Phenote (
http://gmod.org/wiki/Phenote) does ontology based phenotype annotation.
Phenote is also used by several groups to curate other, non-phenotype,
annotations, and the Phenote group has submitted a grant proposal to adapt
it to better support any type of ontology-based annotation.  That grant also
includes integrating Phenote into GMOD.  The Phenote group is led by Nicole
Washington <nlwashington at lbl.gov>, who works for, you guessed it, Suzi
Lewis.

Phenote (in its future version) may overlap, but not entirely, with genonaut
(nice name!).  For example, I don't believe that Phenote has plans to
support interaction data.  Nicole could shed some light on how much overlap
she thinks there is.  However, GMOD is not opposed to having more than one
solution to a problem, especially when the solutions don't entirely
overlap.  We also don't know that the Phenote proposal will get funded.

I'll defintely send you a few more questions while writing the letter.

Thanks for contacting us!

Dave C

On Sat, Apr 17, 2010 at 3:25 AM, Daniel Lang <
daniel.lang at biologie.uni-freiburg.de> wrote:

> Hi Dave,
>
> thank you for your answer!
>
> Dave Clements schrieb:
>
>  Suzi Lewis confirmed that the new Apollo grant has been definitively
>> funded and that work start on 1 May.  (Now you've heard it second and third
>> hand. :-) I also urge you to contact Ed and Suzi.
>>
> I'll definitely will contact them once I have finished the proposal. We are
> very much interested in contributing to GMOD, because we have benefited so
> much from it so far.
> To clarify: Of course, we will only release any of the modified code if
> they want us to. I do not want to go into competition or so. If Suzi Lewis
> and colleagues think it is a good idea to include our changes, it would be
> excellent. If not, we have no intention to release it elsewhere.
>
>
>  Patrick Leamaire's group in Marseilles (Patrick <
>> lemaire at ibdml.univ-mrs.fr <mailto:lemaire at ibdml.univ-mrs.fr>>, ANISEED
>> Group <aniseed at ibdm.univ-mrs.fr <mailto:aniseed at ibdm.univ-mrs.fr>>), is
>> fairly far along in porting the NISEED platform to use Chado.  That will
>> include a web front end for viewing and curation.  NISEED supports atlases
>> for expression, phenotypes and cell fates.  Patrick is also very interested
>> in interaction networks.  I strongly urge you to contact Patrick to let find
>> out if what his group is doing will work for you.  I'm hoping to make the
>> NISEED platform a part of GMOD.
>>
> I have not seen ANISEED so far. Wow, they're really far a long! Really
> impressive! It would be excellent if this would become part of the GMOD
> tools!
>
> The project we plan is a bit different, though. Sadly, for Physcomitrella
> so far in situ is not established.
> We need a ontology-driven gene- and gene-set-wise visualization for
> microarray, RNAseq, Proteomics and SAGE data.
>
> The query-tool I had in mind is similar to that at ANISEED or a mart. Would
> be cool if the ANISEED interfaces could be used for that.
>
> So far we have implemented a modperl/Ajax GO/Gene name/Reference Annotation
> tool (genonaut). If we can continue, we want to migrate that to Chado and
> transform it into a plugin architecture to visualize annotation like gene
> family, interaction, expression and other ontology annotation like PO, SO
> and GO.
> Moss development and tissues are only in part covered by PO, so we are
> developing bryophyte-extensions of PO. Either we'll end up committing it to
> PO or release it as Moss Ontology.
>
> Most of the interactions that are available for Physcomitrella are
> miRNA<->target. We want to model interactions as ontology terms as well.
>
> So basically what our community needs is a generic OA tool (GO, SO, PO,
> interaction, expression...). Multiple genes should be annotatable at the
> same time. The basic idea would be a webstartable Java app that reads
> multiple OBO/OWL defs from remote sources and allows to assign terms,
> evidence codes, dbxrefs and raw values for a given set of genes. IO should
> be possible with either Chado or the gene ontology schema or a plain text
> GOA like format.
>
> Does something like this exist? If not do you think it would be an
> interesting addition to GMOD?
>
>
>> GMOD does not (in my opinion) have an integrated solution for interaction
>> data.  We do have Pathway Tools (http://gmod.org/wiki/Pathway_Tools)
>> which covers this.  It has many GMOD users, but it does not integrate with
>> anything else in GMOD.  It is also not open source.  There's also been talk
>> of bringing NBrowse (http://gmod.org/wiki/NBrowse) into GMOD, but we have
>> no definitive plans.  Anything that would help us in this area would help
>> us.
>>
> Ah, I had the impression that NBrowse already was integrated... If you
> think it would be a good idea, we could e.g. work on a CHADO interface for
> Nbrowse, Cytoscape or other existing tools. Alternatively, a
> javascript/Bioperl-based web app in the tradition of gbrowse could also be
> something we could work on.
>
>
>     For our proposal to be successful, it would be crucial for us to know
>>    what you think of these ideas and if you would support us. As always,
>>    the deadline is close - the end of April.
>>
>>    What we could offer would be 3 dedicated developers for at least 3-6
>>    years.
>>
>>
>> That's absolutely great.  This is one of our requirements that people
>> often don't think about.  See http://gmod.org/wiki/GMOD_Membership for
>> what is needed to become a part of GMOD.
>>
> Yes, I read it and we would be very proud to become part of GMOD during the
> course of the project! It is something we have to earn.
>
> I know it is much to ask, especially on such a short notice and under the
> circumstance that we have not been working together yet.
> cosmoss.org is at a cross-roads: it was a side project to make the data
> from the genome project available - now we either continue and build a MOD
> the community can use to improve the annotation or we personally have to
> move on and follow up other projects.
> We and JGI are currently working on genome V2.0 to assemble WGS scaffolds
> into chromosomes and have a lower plant reference genome.
>
> If we get the grant, we three (Andreas (Postdoc), Karol (PhD student) and
> myself (Postdoc)) finally could focus on the development of the MOD...
>
> But the program we are submitting our proposal to is very competitive and I
> strongly believe that it is very important for the success of the proposal
> to have some sort of letter of support from you to show that you'd welcome
> our efforts.
>
> I hope, this is not too much to ask and would be very grateful. I
> definitely will use this discussion to further improve the work packages.
>
> All the best,
> Daniel
>

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