PhyloWS FAQ

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Frequently Asked Questions about PhyloWS.

Who do I ask about PhyloWS?

Start with Himlar Lapp.

Who is the lead for PhyloWS?

Start with Himlar Lapp.

Where do I find out more about PhyloWS?

What is the process for updating/changing the PhyloWS standard?

Is PhyloWS implemented?

PhyloWS is partially implemented. There is a prototype for Tree of Life; that is you can, through PhyloWS and a REST interface, obtain ToL trees. However, there are pieces of the specification that still need to be fleshed out.

Does PhyloWS provide operations on data?

No. PhyloWS is focused on providing data.

Does PhyloWS work with PURLs?

Yes.

Does PhyloWS include authentication?

No. This should be handled by the data provider. Authentication is not specific to phylogenetics or even biologicals web service providers. Thus, it should be handled independently of PhyloWS.

Is PhyloWS based on SRU protocol?

Yes and no. The only thing dependent on SRU is....

How do I parse the query urls used by PhyloWS?

There are numerous parsers listed on the SRU Tools page.

What is the return format of PhyloWS?

The return format, by default, is NeXML. The data provider can provide different formats but they have to support NeXML.

How do you discover the capabilities of the provider?

This is discussed in the PhyloWS/REST wiki.

Are there basic functionalities that must be implemented by the data provider?

At a minimum, a data provider should provide the ability to retrieve tress and data. Additionally, they should also provide the ability to find tress by metadata.

Is there an envelope for the return?

No, errors are returned as standard httpd status codes (link), which is handled by REST.

Are multiple trees returned in one file or in separate files?

According to SRU standards, one tree is returned per NeXML file for resource URIs.

What do the IDs mean that are found in the returned NeXML file?

The IDs found in the file are local to the file. Do not assume that the data provider will be able to do anything with ids in the file.

How do I use the data returned from PhyloWS? What is the meaning?

CDAO represents a solution to this aspect.

How do I use PhyloWS to access data holdings, search data holdings, query interfaces?

The full question was:

How do I use PhyloWS to access individual items and resources (e.g., one tree in TreeBASE, one alignment in an Alignment database) and how are these data returned?

NeXML provides a solution to some of these issues by offering a standard interchange format.