Re: [Treebase-devel] ABI proposal for phyloinformatics

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

Regarding ToLWeb, two comments.  I think this proposal is not going to  
do as well if it focuses on updating specific resources and bringing  
them closer to meeting user needs, as opposed to starting with the  
user needs and bringing to bear whatever tools or resources solve the  
problem most easily.   But we can wait to see what the program  
officers tell us.

Having said that, I'm pretty sure from the analysis of literature  
(that Brian and I are doing) that re-use of large species trees is an  
important use-case.  In a sample of 40 recent papers that hit  
"phylogen*" in the title or topic (obviously not a random sample, but  
we wanted to find the folks who focus on trees), we found 5 that use  
phylomatic or APG trees, and 1 that uses the animal supertree from  
Bininda-Emonds.

APG and phylomatic appear to be leaving ToLWeb and TreeBASE in the  
dust, in terms of scientific re-use.  Whatever they are doing to bring  
trees to users, we should be doing.

Arlin

On Jun 7, 2011, at 3:20 PM, William Piel wrote:

>
> Yeah, since ToLWeb provides an XML dump of the whole tree, from the  
> TreeBASE side a cross-walk with ToLWeb (or mechanisms to benefit  
> from the ToLWeb skeleton for enhancing the searching of TreeBASE)  
> could be done without *any* modifications of ToLWeb (or at least we  
> could provide ToLWeb with clade-level query links that they can add  
> to each clade page if they choose to).  Likewise, we will no-doubt  
> want to provide higher-name-sensitive queries using NCBI and ITS  
> (etc) without requiring permission to change their code (to say the  
> least!).
>
> But clearly we want something tighter than just consuming ToLWeb's  
> XML -- and we want ToLWeb to benefit as much as TreeBASE. But in  
> that case, I think some sort of tap on David Maddison and Andrew  
> Lenards's shoulder is needed (David is on the phylorf mailing list,  
> but is he following this?).  I gather that ToLWeb code is not yet  
> Open Source...
>
> bp
>
>
> On Jun 7, 2011, at 1:48 PM, Hilmar Lapp wrote:
>
>> Jim:
>>
>> On Jun 7, 2011, at 1:30 PM, Jim Leebens-Mack wrote:
>>
>>> I am a bit concerned about the tight connection between TB and  
>>> ToLWeb that is outlined in the pitch.  Are folks intending to re- 
>>> engineer BOTH TB and ToLWeb?  In my mind, ToLWeb would be just one  
>>> of many platforms from which folks may want to delve into the  
>>> phylogenetic knowledge that could be accessed in TreeBASE.
>>
>>
>> Good points, and indeed what I had in mind technically(*). The way  
>> I am envisioning this to be implemented is indeed using  
>> technologies (HTTP/REST APIs, canonical resolvable identifiers,  
>> RDF) that allow very loose coupling. I left that out as I thought  
>> the tech soup shouldn't be in there, but I agree what's missing now  
>> is the notion that this will be achieved through loose coupling.
>>
>> So as for reengineering, the idea is to engineer (or reengineer  
>> where that's necessary) components for *both* systems that allow  
>> that loose coupling in a way that achieves the stated goals.  
>> Components that need not change to achieve this would not be touched.
>>
>> 	-hilmar
>>
>> (*)  Socially (as opposed to technically), I think ToLWeb can, and  
>> should, play a much more important role in enhancing TreeBASE  
>> content in the sense of turning data into knowledge than other  
>> platforms that we would enable here. Perhaps a useful analogy to  
>> think about is Genbank as the the raw sequence data repository and  
>> NCBI Gene (and its predecessor LocusLink) as well as RefSeq as  
>> resources that attempt to turn this into curated knowledge.
>
>
>
>
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-------
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