[Gmod-help] cosmoss.org Physcomitrella mod

Tue Apr 20 03:56:03 EDT 2010

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Hi Dave,

thank you very much!
That's excellent news!

I'll definitely will look into Phenote as I have not seen or used it so
far. If the overlap is too big, we don't mind on focusing on other
useful GMOD-additions. Anything that works is fine;-)

If you want, I can also send a draft for the letter. We need to submit
the grant on April 26th.

Looking forward to working with you.

All the best,
Daniel

All the best
Dave Clements wrote:
> 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
>>
> 
> 
> 

- --
Dr. Daniel Lang
University of Freiburg, Plant Biotechnology
Schaenzlestr. 1, D-79104 Freiburg
fax:        +49 761 203 6945
phone:      +49 761 203 6989
homepage:   http://www.plant-biotech.net/
            http://www.cosmoss.org/
e-mail:     daniel.lang at biologie.uni-freiburg.de

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Explore the moss genome
at the 3rd cosmoss.org Physcomitrella Genome Workshop from
September 13th-15th 2010 in Freiburg
https://www.cosmoss.org/physcome_project/wiki/Cosmoss_workshop
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