Data Access

Web Browser User Interface

Primary access to the database is through its web interface, where users most commonly search on authors, citations, and taxa. Datasets are downloadable in NEXUS and NeXML formats for further analysis.

Programmatic Data Access

In addition to the web interface, TreeBASE can be accessed programmatically through a stateless web service interface and URL architecture. This interface can deliver data in several different formats, including NEWICK, NEXUS, JSON, NeXML.

• a PhyloWS RESTful API. A detailed description of TreeBASE's PhyloWS implementation is on the TreeBASE wiki.
• OAI-PMH metadata harvesting interface is available, though under development. A description of the available operations is on the TreeBASE wiki.
• SQL data dumps, coming soon.

Links to external objects

TreeBASE stores references to and provides outlinks to external objects including DOIs (for publications), NameBankIDs and NCBI taxids (for taxa), and Genbank accession numbers (for sequences).

Links to objects within TreeBASE

TreeBASE issues persistent and resolvable uniform resource identifiers (URIs) to studies, matrices, trees, and nodes in trees. These allow external data services to link directly into TreeBASE resources. For example:

URI to a study

http://purl.org/phylo/treebase/phylows/study/TB2:S1925

URI to a matrix

http://purl.org/phylo/treebase/phylows/matrix/TB2:M2610

URI to a tree

http://purl.org/phylo/treebase/phylows/tree/TB2:Tr2026

RSS Feeds

When TreeBASE's API delivers a list of results in RDF/XML, it expresses this in RSS 1.0. This delivery allows programmatic capture of these results as well as human perusal using a RSS client reader or browser. For example, a user interested in a certain taxon could express a query as a PhyloWS URL and enter it into his or her favorite RSS reader. As a result, any new submissions to TreeBASE that includes this taxon of interest will alert the user with a new RSS article.

Data Dumps

In the future, users who wish to perform queries and analyses beyond the scope and performance of TreeBASE will be able to acquire entire periodic data dumps that comply with a standard data model, such as BioSQL.