[Treebase-devel] NeXML submissions to TreeBASE as GSOC project?

[Arlin S. <ar...@um...>]

I'd like to suggest-- to anyone who might be interested in serving as  
a mentor-- implementing NeMXL submissions to TreeBASE as a possible  
GSOC project.   The idea would be to reduce the amount of user  
interaction with TreeBASE, supporting direct submission of critical  
information represented in the NeXML file, including the usual matrix  
and trees, as well as
* GenBank accessions
* links from OTUs to taxon concepts
* methodological links from a matrix to a tree
* authors and contact information

This would open the door for the development of third-party annotation  
tools or phylogeny inference tools that generate submission-ready  
NeXML files that meet a minimal standard (like MIAPA if it exists).  A  
bioinformatics grad student in Jim Leebens-Mack's lab is gearing up to  
develop such a submission tool this spring.

A further project might be to develop and implement a web services  
protocol so that annotation clients can submit to TreeBASE.

Arlin

Begin forwarded message:

> From: Rutger Vos <rut...@gm...>
> Date: March 3, 2011 5:38:55 AM EST
> To: Arlin Stoltzfus <ar...@um...>
> Cc: William Piel <wil...@ya...>, Enrico Pontelli <epo...@cs... 
> >, Jim Leebens-Mack <jle...@pl...>, "mar...@gm... 
>  panahiazar" <mar...@gm...>
> Subject: Re: MIAPA demo & GSOC projects: TreeBASE, NeXML coordination
>
> It would be great if NeXML submissions to TreeBASE could be a GSoC
> project, but that does mean that whoever (else) wants to mentor that
> should sign themselves up to the PhyloSoC wiki in rather short order:
> http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011
>
> On Wed, Mar 2, 2011 at 3:43 PM, Arlin Stoltzfus <ar...@um...> wrote:
>> Enrico, Bill--
>>
>> Some of us (Jim, Maryam, Rutger and I) have been having a  
>> discussion about a
>> MIAPA demo project this spring that may lead to GSOC projects and to
>> long-term funding.
>>
>> A likely target is a submission tool that would facilitate the  
>> annotation of
>> methods and the creation of an archive-ready record.  I did a
>> proof-of-concept of this a few years ago
>> (https://www.nescent.org/wg_evoinfo/Supporting_MIAPA#Proof-of-concept_.28annotation_software.29) 
>> .
>>  We would use external vocabularies (many useful sources have been
>> identified) and represent annotations using meta statements in NeXML.
>>
>> Maryam (PhD student in bioinformatics, CS background) has some  
>> months to
>> devote to this project while working with Jim.  So, this (or  
>> something like
>> it) is really going to happen over the next few months.
>>
>> We agreed it would be good to get Enrico and Bill involved to talk  
>> about
>> possible GSOC projects, and how to leverage this into other, larger  
>> plans.
>> For instance, a GSOC project to modify TreeBASE to allow NeXML  
>> submissions
>> would be timely.  More generally, it would be nice to demo a web  
>> services
>> architecture for submission, so that various clients could submit  
>> records.
>>  For several years, Enrico has wanted to apply computational  
>> intelligence to
>> workflow description and execution.
>>
>> Here is one vision for an overall strategy:
>>
>>  http://www.evoio.org/wiki/DemonstrationProject#An_overall_strategy
>>
>> If you are interested, please join us for a teleconference on  
>> Friday at
>> 10:00 am.  Enrico already has expressed interest.  Bill, let me  
>> know if you
>> are interested.  Regards,
>>
>> Arlin
>> -------
>> Arlin Stoltzfus (ar...@um...)
>> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
>> IBBR, 9600 Gudelsky Drive, Rockville, MD
>> tel: 240 314 6208; web: www.molevol.org
>>
>>
>
>
>
> -- 
> Dr. Rutger A. Vos
> School of Biological Sciences
> Philip Lyle Building, Level 4
> University of Reading
> Reading
> RG6 6BX
> United Kingdom
> Tel: +44 (0) 118 378 7535
> http://www.nexml.org
> http://rutgervos.blogspot.com

-------
Arlin Stoltzfus (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org