Rise of the machinesRutger A. Vos, Hilmar Lapp, William H.

Piel, Val Tannen

What is TreeBASE?

A repository of user-submitted phylogenies and source data.

Accepts all types of comparative data for all taxa. Data are public once published in a peer-reviewed medium.

Data in preparation are available to the editors or reviewers using a special access code.

Web app 

The machine-readable web

Locations on the web are increasingly visited by machines

instead of human eyes.

Programmable interfaces with structured return values

The TreeBASE web APIObjects can be found using

CQL

Permanent, simple, URLs

Every object a resolvable resource

Serialized in various formats

Searching using CQLContextual Query Language –

standard for queries to information retrieval systems

Hides database schema

Instead, search on predicates

Search results as RSS

PhyloWS Resource URI

PURL domain

Phylogenetics

TreeBASE

PhyloWS

Object ID

http://purl.org/phylo/treebase/phylows/study/TB2:S1787

Same data, different formats

?format=NEXUSFlat file standard for

phylogenetics

?format=NeXMLXML redesign of NEXUS

?format=RDFCDAO/RDF mapping of NeXML

?format=HTMLWeb page describing the

resource

?format=RSS1RSS1.0 feed for search results

?format=NEXUSFlat file standard for

phylogenetics

?format=NeXMLXML redesign of NEXUS

?format=RDFCDAO/RDF mapping of NeXML

?format=HTMLWeb page describing the

resource

?format=RSS1RSS1.0 feed for search results

Data and metadataTreeBASE holds a lot of metadata, for example:

•Lat/long coordinates for specimen samples•Literature metadata•Identifiers

Using the newer serialization formats (NeXML and RDF) we can embed all of them using predicates from a variety of ontologies.

External links

TaxonTaxon

Taxonvariant

Taxonvariant

StudyStudy

Example: Journal feedsprism.publicationName==Evolution

Example: UniProt sequences

TreeBASE stores NCBI taxonomy identifiers

Standard tools can

rewrite these linkout URLs

Result is a corresponding list of UniProt

records

Example: ToLWeb pages

TreeBASE maps to uBio using skos:closeMatch...

…and uBio to ToL using gla:mapping

Example: geocoding

TreeBASE uses DarwinCore for lat/lon annotations

What's next?Make TreeBASE LinkedData

compliant

Make TreeBASE extensible with additional annotations using external triple store

Acknowledgements