Format: Parallel/Working Group

Title: TDWG Phylogenetics Standards Programming Workshop

Authors: Hilmar Lapp (US National Evolutionary Synthesis Center, Durham, North Carolina) & Nico Cellinese (University of Florida, Gainesville, Florida).

Abstract:

Since 2009 several of the emerging standards for accessing and exchanging phylogenetic data have been used or implemented in applications ranging from research-level interoperability studies to production community resources. For example, the programmatic data access interface of the newly released version of TreeBASE now supports the PhyloWS web-service standard, returns records in the NeXML exchange standard (among others), and uses the Comparative Data Analysis Ontology (CDAO) (as well as the Dublin Core and Darwin Core vocabularies) to express the semantics of metadata elements. Other efforts include converting the contents of TreeBASE into a format used by generic machine reasoners and building visual data browsers on top of it. Initiatives such as these are pivotal in establishing proof-of-principle for interoperability through standards application, and in identifying gaps requiring further standards development. This one-day, hands-on working meeting aims to support these on-going initiatives by providing an opportunity for developers to work together on issues ranging from gaps in phylogenetics standard compliance, to improving the existing standards, to increasing the depth and coverage of their documentation, all with a specific perspective on biodiversity informatics needs. Several potential targets have already been identified by members of the Phylogenetics Standards Interest Group, including increasing the support for the emerging data standards (e.g., NeXML) among  tree visualization tools; exposing the taxonomic data in online biodiversity data resources (such as EOL and Scratchpads) through a standard data access interface (e.g., PhyloWS); and defining for commonly used exchange formats how the leaf nodes of trees can be linked to those metadata that best facilitate integration of phylogenetic data (such as species names in a taxonomy, and geo-coordinates of the corresponding specimens in a museum collection). Another target is further developing the Phyloreferencing standard that was initiated in 2009, and which forms the basis of the topological query support in PhyloWS.  The targets will be further narrowed down to a feasible scope prior to the conference through online discussion on the tdwg-phylo mailing list, and everyone interested in participating should either join the discussion there, or contact the Interest Group conveners directly. We anticipate that the tasks eventually selected will need metadata and documentation experts as much as developers.

URLs:

Phylogenetics Standards Interest Group: http://www.tdwg.org/activities/phylogenetics/

TDWG-Phylo (the Interest Group’s mailing list): tdwg-phylo@tdwg.org

NeXML: http://nexml.org

PhyloWS: http://evoinfo.nescent.org/PhyloWS

CDAO: http://www.evolutionaryontology.org

Phyloreferencing: http://evoio.org/wiki/Phyloreferencing_subgroup