Who we are
The EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities that focused on software and data interoperability for evolutionary analysis, including the Evolutionary Informatics working group (2006-2009), and the Evolutionary Database Interoperability hackathon (2009). EvoIO aims to be a nucleating center for developing, applying and disseminating interoperability technology that connects and coordinates between stakeholders, developers, and standards bodies.
Members of the EvoIO group, which include biologists and computer scientists, have over the past 3 years harnessed a variety of collaborative events to successfully build an initial stack of interoperability technologies that is owned by the community and open to participation:
- NeXML, a NEXUS-inspired XML format that is validatable yet extensible
- CDAO, an ontology of comparative data analysis formalizing the semantics of evolutionary data and metadata; and
- PhyloWS, a web-services interface standard for querying, retrieving, and referencing phylogenetic data on the web.
For more information about how to get involved, read on.
- A grant proposal to NSF's Advances in Biological Informatics (ABI) program titled "An Ontology-Based System for Querying Life in a Post-Taxonomic Age" (PIs: Cellinese and Lapp) has now been funded. The proposal and public abstract are available on Figshare (doi:10.6084/m9.figshare.1401984). The project picks up some ideas from the Phyloreferencing subgroup of the Phyloinformatics VoCamp.
- Many of us are PIs or Leadership Team members of a NESCent working group called Hackathons, Interoperability, Phylogenies (HIP). HIP is the current locus of most of our activity . So far we have had two Phylotastic hackathons focused on a web-services implementation of the pruning, grafting, name-reconciliation and other functionalities necessary for researchers to take advantage of emerging megatrees. HIP is planning a third hackathon to develop a socially networked phyloinformatics community of practice.
- We organized a workshop on "Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA) Standard" at the 2011 TDWG Conference in New Orleans, LS. The workshop took place on Monday, Oct 17, and Tuesday, Oct 18. The goal of the workshop was to determine how a future reporting standard for phylogenetic analyses can best serve biodiversity science and related research applications.
- We submitted an NSF ABI proposal on development and (finally!) linking TreeBASE and ToLWeb, entitled "Towards a comprehensive, community- owned and sustainable repository of reusable phylogenetic knowledge" (Lapp, Bietz, Cranston, Piel, Donoghue, Westneat). The proposal was not funded.
- At iEvoBio 2011 in Norman, OK, Arlin Stoltzfus gave a talk on "Publishing re-usable phylogenetic trees, in theory and practice"
- In December 2010, EvoIO participants submitted a proposal to NESCent for a working group entitled HIP: Hackathons, Interoperability, Phylogenies (Vos, Stoltzfus). The proposal is for a series of hackathons partly supported by outside partners. NESCent recently announced that this proposal will be funded. Woo hoo!
- A proposal for a new NESCent course titled "Phyloinformatics: linking with online data and services" was submitted by EvoIO participants (Stoltzfus, Vos, Cranston, Lapp) in July 2010 and subsequently selected for funding, but had since to be canceled due to conflicting obligations of the PIs. Instead, Vos and Piel co-taught a Computational Phyloinformatics course modeled after previous instances of this course, but supplemented with programming exercises using PhyloWS wrappers for ToLWeb and uBio. The course was held in Kyoto in August 2011, and supported by the Bioinformatics Center of Kyoto University and DBCLS/JST, with co-sponsorship by NESCent.
- EvoIO participants in various ways participated in the iEvoBio satellite conference at Evolution 2010 in Portland, OR:
- Rutger Vos gave a talk on "TreeBase2: Rise of the machines" (Rutger Vos, Hilmar Lapp, Bill Piel, Val Tannen)
- Brandon Chisham presented "CDAO-Store: A New Vision for Data Integration" (Brandon Chisham, Trung Le, Enrico Pontelli, Tran Son, Ben Wright)
- Arlin Stoltzfus presented "EvoIO: Community-driven standards for sustainable interoperability" (Arlin Stoltzfus, Nico Cellinese, Karen Cranston, Hilmar Lapp, Sheldon McKay, Enrico Pontelli, Rutger Vos)
- The EvoIO group staged a successful Phyloinformatics VoCamp November 7-11, 2009 in Montpellier, France, co-located with the annual meeting of the . A VoCamp is a hands-on meeting for investigators to create and develop ontologies and lightweight vocabularies in support of data integration and re-use-- in this case, the integration and re-use of phylogenetic trees and associated data and metadata. More information at VoCamp1.
- We submitted a proposal to the NSF INTEROP panel in 2009 for "A network for enabling community-driven standards to link evolution to the global web of data (EvoIO)". More information at NSF INTEROP 2009. This proposal was not funded.
How to get involved
How to get involved? Each stack component has an open community of developers and a mailing list. Click on the links below to find out more. You can sign up for the mailing list and start to contribute.
- NeXML's mailing list is firstname.lastname@example.org (contact Rutger Vos, <firstname>email@example.com)
- PhyloWS's group is firstname.lastname@example.org (contact Hilmar Lapp, <firstinitial>email@example.com)
- CDAO's mailing list is firstname.lastname@example.org (contact Arlin Stoltzfus, <firstname>@umd.edu)
- RSS feed of relevant projects
Also EvoIO folks are looking for interoperability “targets”, which can be either single projects that want to make resources more interoperable, or pairs of resources that want to integrate. Contact any of us if you have an idea.