Re: [Treebase-devel] application-to-TreeBASE direct submission?

[Hilmar L. <hl...@ne...>]

Hi Arlin,

I spoke with Sudhir earlier this year at the ISMB conference about  
pretty much the same thing. The Dryad-TreeBASE interface isn't secret  
in any way [1,2], and as Bill points out is quite limited in what it  
achieves.

In the ABI grant proposal we submitted in July [3], we actually  
propose to create precisely such a submission API that 3rd party  
applications can use to submit richly annotated data to TreeBASE  
directly, and indeed we propose to build on the Dryad/TreeBASE hand- 
shaking interface to accomplish this. If Sudhir has resources  
available to prototype this now, at the end of TreeBASE or MEGA or  
both, that'd be terrific, and I'd be happy to help as far as I can to  
facilitate that better.

BTW I also spoke with Sudhir about possibly supporting NeXML from  
within MEGA, and he appeared very open to that - he said that  
essentially all he needs is someone who can help by providing the  
guidance on NeXML implementation. MEGA supporting NeXML wouldn't help  
with TreeBASE submission right now, but I imagine that the envisioned  
programmable submission API would certainly rely on NeXML.

	-hilmar

[1] https://datadryad.org/wiki/TreeBASE_Submission_Integration
[2] https://datadryad.org/wiki/BagIt_Handshaking
[3] http://www.evoio.org/wiki/ABI_2011_proposal

On Nov 4, 2011, at 7:53 AM, Arlin Stoltzfus wrote:

> Hello all.  Yesterday I had a talk with Sudhir Kumar, author of MEGA,
> which probably is responsible for more published trees than any other
> phylogeny inference package (not necessarily the most trees among the
> phylogeny elite represented in TreeBASE).   I discovered that MEGA has
> a graphical name-reconciling interface for users to align mismatched
> OTU names between tree and alignment files-- this is a common problem
> and a barrier to re-use that I have encountered personally multiple
> times.
>
> He suggested the idea that, to facilitate effective archiving, it
> might be useful to have a way for phylogeny applications to generate a
> submission in TreeBASE, providing metadata such as software version
> and run conditions.
>
> Probably you have heard this suggestion before (I heard it earlier
> this week from Joseph Hughes in regard to BEAST).
>
> I mentioned that TreeBASE has a top-secret interface that Dryad uses
> to submit NEXUS files, and that this could be the basis for a
> submission interface for other applications.  My understanding is that
> this is done via web-services, and that the user gets a link to a
> temporary submission that must be completed interactively.  I hope I
> didn't give the wrong impression.
>
> Anyway, Sudhir was very interested in this.  He said that he has
> programmers with time to work on this kind of thing.   If the MEGA
> team prototyped a direct-submission interface, they could write a
> brief paper about it, and maybe we could get other developers together
> to hash out the metadata terms to support,  based on the recent MIAPA
> exercise at TDWG.   If we could get MEGA and the top 3 TreeBASE
> programs (PAUP, MB, RAXML-- right?), that would cover a very large
> segment of users.
>
> I realize that this approach might not be the best way to promote
> archiving in the long-term.  However, it might be more effective in
> the short term, and we might learn a lot from it.
>
> I'd like to hear any thoughts you have on this.  Would this be a
> useful exercise?  What are the disadvantages?  How could it fit into a
> larger strategy?
>
> 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
>
>
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-- 
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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