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.
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.
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).
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:
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.
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.