Skip to content
master
Switch branches/tags
Code
This branch is 29 commits ahead of kcranston:master.
Contribute

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

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

About

Phylotastic TreeStore

Resources

License

Releases

No releases published

Packages

No packages published