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Phylotastic TreeStore
Python JavaScript
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README.markdown

Phylotastic TreeStore

This is not quite working yet.

This web app provides an adaptor that exposes some aspects of the SPARQL endpoint (powered by Virtuoso) running at: http://phylotastic.nescent.org/sparql via the PhyloWS API https://www.nescent.org/wg_evoinfo/PhyloWS/REST

An example instance is running at: http://phylotastic.nescent.org/PhylotasticTreeStore/phylows/

Installation

If you have installed pip ( http://pypi.python.org/packages/source/p/pip/pip-1.1.tar.gz#md5=62a9f08dd5dc69d76734568a6c040508 ), which may require setuptools ( http://pypi.python.org/pypi/setuptools ).

Then, from bash prompt, you should be able to:

wget http://www.web2py.com/examples/static/web2py_src.zip
unzip web2py_src.zip
virtualenv vdev
source vdev/bin/activate
pip install rdflib
pip install requests
pip install dendropy
git clone git://github.com/phylotastic/PhylotasticTreeStore.git
ln -s "$PWD/PhylotasticTreeStore" web2py/applications/PhylotasticTreeStore
python web2py/web2py.py --nogui

Enter an admin's password for web2py and then visit: http://127.0.0.1:8000/PhylotasticTreeStore/phylows in your browser.

You'll need version 0.13.0 or greater of requests and 3.2.1 or greater of rdflib

Notes

To see the RDF representation of a tree enter the following query at http://phylotastic.nescent.org/sparql

prefix obo: 
prefix cdao: 
construct 
{
?node obo:CDAO_0000179 ?parent_node . 
?node obo:CDAO_0000187 ?otu .
?otu rdfs:label ?otu_label .
}
 where 
{
 obo:CDAO_0000148 ?root .
?node obo:CDAO_0000179 ?parent_node . 
?node obo:CDAO_0000179 ?root option(transitive) . 
OPTIONAL { 
    ?node obo:CDAO_0000187 ?otu . 
    ?otu rdfs:label ?otu_label .
}
OPTIONAL { 
    ?root obo:CDAO_0000187 ?otu . 
    ?otu rdfs:label ?otu_label .
}
}

Or see the N-triples at http://phylotastic.nescent.org/sparql?default-graph-uri=&query=prefix+obo%3A+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2F%3E%0D%0Aprefix+cdao%3A+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fcdao.owl%23%3E%0D%0Aconstruct+%0D%0A%7B%0D%0A%3Fnode+obo%3ACDAO_0000179+%3Fparent_node+.+%0D%0A%3Fnode+obo%3ACDAO_0000187+%3Fotu+.%0D%0A%3Fotu+rdfs%3Alabel+%3Fotu_label+.%0D%0A%7D%0D%0A+where+%0D%0A%7B%0D%0A%3Chttp%3A%2F%2Fphylotastic.nescent.org%2Ftrees%2FTreemytree3%3E+obo%3ACDAO_0000148+%3Froot+.%0D%0A%3Fnode+obo%3ACDAO_0000179+%3Fparent_node+.+%0D%0A%3Fnode+obo%3ACDAO_0000179+%3Froot+option%28transitive%29+.+%0D%0AOPTIONAL+%7B+%0D%0A++++%3Fnode+obo%3ACDAO_0000187+%3Fotu+.+%0D%0A++++%3Fotu+rdfs%3Alabel+%3Fotu_label+.%0D%0A%7D%0D%0AOPTIONAL+%7B+%0D%0A++++%3Froot+obo%3ACDAO_0000187+%3Fotu+.+%0D%0A++++%3Fotu+rdfs%3Alabel+%3Fotu_label+.%0D%0A%7D%0D%0A%7D%0D%0A&format=text%2Fplain&timeout=0&debug=on

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