Re: [Treebase-devel] viz problem with trees for S11267

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On Apr 14, 2011, at 9:39 AM, Richard Ree wrote:

> Hi folks,
> 
> Just joined the list, as I am interested in using TB to develop collaborative methods for synthesizing plant phylogeny, e.g., by grafting clades together and other kinds of agglomeration.  So, I am particularly interested in the API and harvesting, especially with respect to taxonomic names and classifications, and GenBank identifiers of sequences.
> 
> Speaking of which, how would I go about harvesting the GenBank numbers for a given study and associating them with their alignments?  Its that possible with the current API?
> 
> I like Rutger's plug-in ideas.  In general, it's easier for someone like me to provide a simple web service, rather than contribute directly to TB development.
> 
> -Rick

I guess there are various options for this. 

For example, you could start by finding studies published by a guy named "Ree":

http://purl.org/phylo/treebase/phylows/study/find?query=dcterms.contributor=Ree&format=rss1

Out of that list, pick the first item (S10145), and you could ask for a list of matrices:

http://purl.org/phylo/treebase/phylows/study/find?query=tb.identifier.study=S10145&format=rss1&recordSchema=matrix

And then if you pick one matrix (e.g. M4388), you could ask for the NeXML serialization of it:

http://purl.org/phylo/treebase/phylows/matrix/TB2:M4388?format=nexml

And in the OTU section, you'll find a mapping between "Ruta graveolens" and NCBI's taxid 37565:

<otu about="#otu21609" id="otu21609" label="Ruta graveolens">
<meta href="http://purl.uniprot.org/taxonomy/37565" id="meta21613" rel="skos:closeMatch" xsi:type="nex:ResourceMeta"/>

Alternatively, you could ask for a list of trees:

http://purl.org/phylo/treebase/phylows/study/find?query=tb.identifier.study=S10145&format=rss1&recordSchema=tree

And then serialize one of the trees:

http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6161?format=nexml

.... with the same annotation in for Ruta graveolens. 

bp