Interfaces for databases: TreeBASE, Dryad, DataONE

Next Steps

Treebase

  • (See Sunday’s post) - Phylo-ws implemented, but a few extra functions would strengthen the interface a bit: limit the number of trees returned, querying trees for branch lengths,

  • RaXML pipeline for returning rough branch lengths conditioned on the given topology, user documentation, more test examples.

  • Implement OAI-PMH test cases for treebase: For instance, query all records after a given date (or all possible other queries), i.e.

https://treebase.org/treebase-web/top/oai?verb=ListRecords&metadataPrefix=oai_dc&after=1996-11-04T00:00:00Z

And return treebase ids that can then be handed to search_treebase to pull the phylogenies. DONE 2011-05-11

  • Pull treebase ID from phylo-ws query and return the corresponding OAI-PMH metadata information. DONE 2011-05-11

Interfacing with Dryad:

  • Currently neither repository seems to always provide the key identifiers to point to the other one.  For instance, William Piel points out the same study in TreeBASE and in Dryad, where neither links to the other.   Not sure why this study doesn’t get listed in Dryad’s search returns.  Discussing with members of both teams (William, Rutger, and Harry with TreeBASE, Kevin and Ryan with Dryad) about addressing this.

  • Sometimes Dryad does provide the treebase url, but would have to identify from the url directly (after parsing all dc:idenfier terms), as it isn’t more clearly specified.

  • GOAL: From a TreeBASE query (for trees/phylo-ws or metadata/OAI-PMH): be able to return Dryad data and metadata associated with the study.

  • GOAL: From Dryad-query: return trees associated with a Dryad study by querying TreeBASE.

Dryad Implementation GOALS:

  • Extend OAI-PMH interface to the Dryad API

  • Current Dryad returnsdon’t include clear identifiers to the data files urls.

  • Work with Dryad to figure out how to access data files as well as meta-data from the API.

  • Extend toDataONE API?  Presumably will also have OAI-PMH based access to metadata?

BACKGROUND (NOTES IN PROGRESS)

A few further development goals

Define the databases, API, goal.

Define teams, discussions, wikis, lists.

Development goals listed/tracked as Issues on the Github repository