Frequently Asked Questions



What is CDAO?

CDAO is a standard for describing comparative data in a semantically rigorous way.


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What is PhyloWS?

PhyloWS is a standard for exposing phylogeny data using a REST-ful API.

CDAO-store uses PhyloWS to allow clients to access information in the store about trees, taxonomic identifiers, minimum-spanning clade, and nearest common-ancestor of a set of nodes.


/tree/

To access a TreeBASE tree (like Tree3099) in phylows, the following is used:
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/tree/Tree3099
To get Tree3099 into a certain format, append one of these: (remove the [])
"?format=[nexml,html,phyloxml,rdf,cdao,prolog,graphml]"

By default, phylows returns trees in the RDF/CDAO format.


/matrix/

Matrices are similarly accessed:
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/matrix/M4307


/nca/

The nearest common ancestor of a set of nodes can be found using:
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/nca/TreeBASE_Tree_ID/TU1/TU2/.../TU_N
NOTE: Taxon names are all 'one word', use '_' to join words together. (i.e. Ilex_anomala)


/msc/

The minimum spanning clade of a set of nodes can also be found using:
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/msc/TreeBASE_Tree_ID/TU1/TU2/.../TU_N


/size/

A list of trees by some size criterion, such as the number of nodes, leaves, or internal nodee, and the direction of the relation (ie trees larger than or smaller than the specified amount).
The options avaible are size/[node|leaf|internal]/[smaller|greater|equal]/[0..N]
curl http://www.cs.nmsu.edu/~cdaostrore/cgi-bin/phylows/size/node/greater/50


/listing/

We also support searching for available tree and matrix id"s as follows.
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/listing/trees[?key=SUB_STRING]
or
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/listing/matrices[?key=SUB_STRING]
The key parameter is optional and allows one to filter the id"s based on some those containing some string.


/algorithm/

This is used to return a list of all the Trees generated by a particular algorithm. For instance:
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/algorithm/parsimony
This would return all the trees that used the Parsimony algorithm.


/program/

This works much like /algorithm/ except that is uses Software instead.
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/program/paup
This would return all the Trees made using the PAUP software


/author/

This returns Trees linked to particular authors.
curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/author/last/Piel
This url would return a list of Trees associated with Piel.
First names can also be queried in a manner. For instance "/last/Doe/first/John", would look for trees associated with John Doe.


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SPARQL queries

We currently have an implementation that allows for very basic SPARQL queries through our phylows service...

/sparql/

curl http://www.cs.nmsu.edu/~cdaostore/cgi-bin/phylows/sparql/select/N/where/line1/line2
This creates the query:
SELECT N WHERE{
line1.
line2.}

Only 1 variable is allowed for now, in the future we will try to allow a more friendly version.


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Importing files to CDAO store

CDAO store currently supports importing RDF files into the triple store. In addition, we can currently translate NEXUS, MEGA, PHYLIP, and NeXML formats to our format.


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CDAO explorer

Here are a few screenshots and a brief walkthrough of CDAO Explorer: Walkthrough


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Tree/Matrix Naming Convention

Names are currently based on the TreeBASE accession names they were given.


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Getting RDF/XML file of my tree/matrix

See:PhyloWS


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Exporting to non-CDAO file format

CDAO store supports exporting files to the following formats:

  • RDF/XML (using CDAO)
  • NeXML
  • PhyloXML
  • Nexus
  • Newick
  • GraphML
  • Prolog
You can access these by the Phylows service for each tree (i.e. "?format=nexml" at the end for nexml output) or by clicking the link on the individual tree html search pages.


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There appears to be an error...

CDAO Explorer has its own error reporting system, however if something is wrong with the PhyloWS services, please Email Us


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Other questions? Email:us