TDWG Interest Group on Phylogenetics Standards: Charter

Convenor

Nico Cellinese
University of Florida
354 Dickinson Hall
Gainesville, FL 32611, U.S.A.
ncellinese(at)flmnh.ufl.edu

Hilmar Lapp
National Evolutionary Synthesis Center (NESCent)
2024 W Main St., Ste# A200
Durham, NC 27705, U.S.A.
hlapp(at)nescent.org

Core Members

We welcome and encourage participation from everyone interested in the objectives the group. We therefore take an inclusive view on membership, and consider all subscribers of the group's mailing list (tdwg-phylo(at)tdwg.org) as members of this interest group. Thus, membership does not imply agreement with the standards or approaches the group might choose to promote. 

Purpose

To draft and ratify a set of standards that facilitate integration and interoperable exchange of phylogenetic data and their semantics.

Motivation

Phylogenetic trees and data play a central role in modern biology by organizing data and knowledge by lines of descent, including the large and constantly increasing information about the past and present diversity of life on earth. Trees also provide the foundation for comparative analyses of the evolution of molecular, phenotypic, functional, and other traits of species. Thus, knowledge about phylogenetic relationships is key to understanding the patterns and processes underlying past and present biodiversity, and how diversity might change in the future in response to changes in climate, habitat, and community composition.

To achieve the necessary ability to repurpose phylogenies across research communities and disciplines, phylogenetic data must be broadly accessible online, interoperable between data providers, and its meaning must be interpretable by machines.  More specifically, the integrative power of a tree depends on its data and metadata decorations. A tree topology alone with no discernible annotation cannot be repurposed or integrated. The kinds of data and metadata that the elements of a tree can be associated with are increasingly diverse and include, but are not limited to, biological (e.g., molecular sequences, specimen identifiers, morphological characteristics), taxonomic (names, identifiers, and other properties used for taxon identification), geographic (specimen locations, distribution ranges), environmental (climate data, geochemical data), ecological (habitat and community characteristics), epidemiological (clinical symptoms, treatment regimen, patient data), paleontological (fossil characters, locations and dates), and computational (e.g., branch lengths, node support) information.

The major obstacle hindering broad availability and repurposing of phylogenetic data and their metadata is the lack of effective standards and a community-driven process for adopting and extending them. There are no widely accepted standards for annotating tips, internal nodes or branches. Instead, existing formats have been modified in incompatible ways, such that annotations from one program or data provider fail to be read, or are misinterpreted or lost when imported into another program. The objective of this interest group is to address this obstacle.

History and Context

This group originated from a 2008 whitepaper by N. Cellinese, based on which N. Cellinese and H. Lapp organized a full-day workshop and a symposium on Phylogenetics Standards at the 2008 TDWG Annual Conference.  These kick-off activities were jointly funded by the Biodiversity Synthesis Center (BioSynC, a component of EOL) and the National Evolutionary Synthesis Center (NESCent).  Since then, leaders and members of the group have been involved in a variety of activities, ranging from improving and applying relevant emerging standards, to holding a hackathon on database interoperability, to seeking funding for building a larger community network.

Summary

The Phylogenetics Standards Interest Group aims to develop, consolidate, inform, promote, and adopt effective standards that foster the broad availability and repurposing of phylogenetic data and their metadata. To achieve this, and to make sure that the standards meet actual needs, the group emphasizes a community-driven process and grass-roots participation.  By doing so, the Interest Group yields a platform that helps in broadly promulgating standards and in furthering adoption among stakeholders. 

This group interacts with other interest groups, within and outside of TDWG, to facilitate re-use of already existing efforts and standards, and allows harnessing the expertise and experience within the TDWG organization in developing standards and communicating those to the public.

This group interacts with other interest groups, within and outside of TDWG, to facilitate re-use of already existing efforts and standards, and allows harnessing the expertise and experience within the TDWG organization in developing standards and communicating those to the public.

The standardization efforts of the group include phylogenetic data exchange formats, metadata vocabularies and ontologies defining semantics in a computable manner, documentation of provenance, and programmable access to online phylogenetic data resources. The group also identifies and recommends data or metadata areas in need of service providers or portals, and suggests relationships between providers. 

Finally, the group plans to suggest incentives and mechanisms for increasing the rate and consistency of data deposition in repositories, including a minimum reporting standard that maximizes the chance of repurposing.

Becoming Involved

To become involved in the Phylogenetics Standards Interest Group, simply sign up on the group's mailing list. New participants are welcome to join at any time, ask questions, engage in discussions, or simply lurk and observe.

Resources

• Phylogenetics Standards Interest Group
• Phylogenetics Standards group wiki
• Phylogenetics Standards mailing list
• Evolutionary Database Interoperability Hackathon
• Phyloinformatics VoCamp
• EvoIO grant application to the US National Science Foundation

Clients

• Taxonomists/Systematists
• Librarians
• Publishers
• Conservationists
• Ecologists and other biologists who need information about taxa, for example, what they are, where they occur and observations about them.
• Collections cataloguers