TreeBASE2: Rise of the Machines
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Transcript of TreeBASE2: Rise of the Machines
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Rise of the machinesRutger A. Vos, Hilmar Lapp, William H.
Piel, Val Tannen
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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.
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Web app
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The machine-readable web
Locations on the web are increasingly visited by machines
instead of human eyes.
Programmable interfaces with structured return values
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The TreeBASE web APIObjects can be found using
CQL
Permanent, simple, URLs
Every object a resolvable resource
Serialized in various formats
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Searching using CQLContextual Query Language –
standard for queries to information retrieval systems
Hides database schema
Instead, search on predicates
Search results as RSS
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PhyloWS Resource URI
PURL domain
Phylogenetics
TreeBASE
PhyloWS
Object ID
http://purl.org/phylo/treebase/phylows/study/TB2:S1787
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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
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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.
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External links
TaxonTaxon
Taxonvariant
Taxonvariant
StudyStudy
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Example: Journal feedsprism.publicationName==Evolution
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Example: UniProt sequences
TreeBASE stores NCBI taxonomy identifiers
Standard tools can
rewrite these linkout URLs
Result is a corresponding list of UniProt
records
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Example: ToLWeb pages
TreeBASE maps to uBio using skos:closeMatch...
…and uBio to ToL using gla:mapping
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Example: geocoding
TreeBASE uses DarwinCore for lat/lon annotations
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What's next?Make TreeBASE LinkedData
compliant
Make TreeBASE extensible with additional annotations using external triple store
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Acknowledgements