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PhyloSharingWorkshop2013.txt
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PhyloSharingWorkshop2013.txt
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%META:TOPICINFO{author="RutgerVos" date="1383835789" format="1.1" version="1.15"}%
%META:TOPICPARENT{name="WebHome"}%
---+!! <center>Sharing and delivery of reusable phylogenetic knowledge</center>
%TOC%
---++ Synopsis and Goal
This combined symposium and workshop event aims to present and put to the test recent community progress towards effective sharing and reuse of expert phylogenetic knowledge, a key ingredient to addressing comparative research questions across biology. Even though many researchers would rather reuse a quality phylogeny than try to build it themselves, in practice it is difficult and often enough impossible to find suitable phylogenies, to evaluate their fitness for purpose, and to access them in a format suitable for analysis. To mitigate these obstacles, an interdisciplinary grassroots network has begun to develop solutions that include data standards, metadata ontologies, a decoupled architecture, and community-building hackathons. Aside from presenting the results of these efforts and showcasing diverse applications for phylogeny reuse, the event will allow participants to inform these efforts so they respond to biodiversity science needs. Finally, the event is designed to catalyze new collaborations by providing ample room for interactive demonstrations using participant-contributed research problems.
---++ Background
Phylogenies are fundamental to understanding how our planet’s biodiversity evolved, and to predicting how it might respond to accelerating environmental change. They are crucial to data analysis in many biological fields, including ecology and biodiversity science, to identify patterns in data while accounting for the non-independence of observations due to their shared ancestry. As a consequence, an increasing number of researchers require access to accurate and reliable phylogenetic knowledge, but lack the expertise in systematics to create it themselves. Even though a tremendous amount of phylogenetic knowledge is created and published by experts, and despite the existence of long-standing community resources such as the Tree of Life Web Project and !TreeBASE, reuse of phylogenetic knowledge is surprisingly low ([[http://doi.org/10.1186/1756-0500-5-574][Stoltzfus et al, 2012]]).
Several reasons for this have been suggested, including that suitable phylogenies can be hard to discover; their exact provenance necessary to judge their fitness for reuse is often unclear; they may have missing or non-standard taxon labels; they may be available only as figures in journals; and their size, format, or some other property may make them difficult to use in the desired analysis program. To mitigate these obstacles, a grassroots network of information scientists, software developers, and biologists from a variety of fields has begun to develop sociological and technological solutions that will facilitate easy sharing, discovery, and reuse of expert phylogenetic knowledge. These solutions include metadata-friendly data standards, metadata ontologies, and an architecture proposal for a how a set of decoupled and distributed components can interoperate to support the predominant use-cases for sharing and reusing phylogenies. They also include community-building activities, in particular hackathons, that have successfully engaged practicing scientists and informatics experts from a wide diversity of backgrounds.
---++ Agenda
The event will consist of two parts of about 90 minutes each, with a short coffee break between them. The first part is in the form of a symposium, and features six speakers from community efforts on phylogenetic knowledge interoperability and from phylogenetic knowledge synthesis collaboratives presenting short talks (10 minutes each), followed by 30 minutes of discussion with the panel of speakers.
After a short coffee break, the second part, in the form of a workshop, consists of individual software demonstrations to which attendees are invited to bring their own data problems (such as taxonomic name resolution and how to obtain the best phylogeny for a list of species) to evaluate hands-on the potential of the presented solutions for their research and data integration problems.
*Venue: Theatre I "America del Nord"* _(tentative, still subject to change)_
*Symposium: Thursday, October 31, 9am*
* 9:00am: Opening Keynote: Ross Mounce, University of Bath, UK: [[https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/495][Sharing phylogenetic data: even more vital for morphological data]]
* 9:15am:
* Jonathan Rees, National Evolutionary Synthesis Center (NESCent), USA: [[https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/492][Assembling a draft overall tree of life from phylogenetic trees and taxonomic databases]]
* Rutger Vos, NCB Museum Naturalis, Netherlands: [[https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/525][PhyloTastic - names-based phyloinformatic data integration]]
* Saverio Vicario, Institute for Biomedical Technologies, Italy: [[https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/366][Numerical tree representations and their application to MCMC phylogenetic inference, phylogenetic signal, and ... database query]]
* Alexandre Antonelli, University of Gothenburg, Sweden: [[https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/363][SUPERSMART: Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa]]
* Suzanna Lewis, Lawrence Berkeley National Laboratory, USA: [[https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/444][Quest for Orthologs: anchoring comparative biology research]]
* 10:05am: Panel discussion with all speakers
* 10:30am: _Coffee Break_
*Workshop: Thursday, October 31, 11am*
[[https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/548][Hands-on demonstrations of the following resources]]: _(Note: The list is tentative and may still change prior to the workshop.)_
* [[http://opentreeoflife.org/][Open Tree of Life]] (Jonathan Rees)
* [[http://phylotastic.org][Phylotastic]] (Rutger Vos)
* [[http://biovel.eu][BioVeL]] (Saverio Vicario)
* [[http://www.supersmart-project.org/][Supersmart]] (Alexandre Antonelli)
* [[http://questfororthologs.org/][Quest for Orthologs]] (Suzi Lewis)
*Adjourn at 12.30pm.
---++ Participants
_The participant list is developing, and will initially only contain the speakers. Symposium as well as workshop are open to anyone attending the TDWG conference, and drop-ins are welcome at any time._
| *Name* | *Affiliation* |
| [[http://antonelli-lab.net/][Alexandre Antonelli]] | University of Gothenburg, Sweden |
| [[http://cellinese.blogspot.com/][Nico Cellinese]] *#* | University of Florida, USA |
| [[http://www.mendeley.com/profiles/hilmar-lapp/][Hilmar Lapp]] *#* | National Evolutionary Synthesis Center (NESCent), USA |
| [[http://www.lbl.gov/lsd/People_&_Organization/Scientific_Staff_Directory/Lewis_Lab.html][Suzi Lewis]] | Lawrence Berkeley National Laboratory (LBL), USA |
| [[http://rossmounce.co.uk/][Ross Mounce]] | University of Bath, UK |
| [[http://mumble.net/~jar/][Jonathan Rees]] | National Evolutionary Synthesis Center (NESCent), USA |
| [[http://www.mendeley.com/profiles/saverio-vicario/][Saverio Vicario]] | Institute for Biomedical Technologies, Italy |
| [[http://rutgervos.blogspot.com/][Rutger Vos]] *#* | Naturalis Biodiversity Center, Netherlands |
*#* Co-conveners of this event.
---++ Links and Resources
*Links:*
* [[https://docs.google.com/document/d/1Kmy-fywV36Knxyl7PNUWVmXvCj9tW5Pznr4X9-3F5cc/pub][Original proposal]]
*Relevant publications:*
* Stoltzfus, Arlin, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, et al. 2013. “Phylotastic! Making Tree-of-life Knowledge Accessible, Reusable and Convenient.” BMC Bioinformatics 14 (1): 158. doi:[[http://doi.org/10.1186/1471-2105-14-158][10.1186/1471-2105-14-158]].
* Stoltzfus, Arlin, Brian O’Meara, Jamie Whitacre, Ross Mounce, Emily L Gillespie, Sudhir Kumar, Dan F Rosauer, and Rutger A Vos. 2012. “Sharing and Re-use of Phylogenetic Trees (and Associated Data) to Facilitate Synthesis.” BMC Research Notes 5 (1) (October 22): 574. doi:[[http://doi.org/10.1186/1756-0500-5-574][10.1186/1756-0500-5-574]].
* Vos, Rutger A, James P Balhoff, Jason A Caravas, Mark T Holder, Hilmar Lapp, Wayne P Maddison, Peter E Midford, et al. 2012. “NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata.” Systematic Biology 61 (4) (July 22): 675–89. doi:[[http://doi.org/10.1093/sysbio/sys025][10.1093/sysbio/sys025]].
* Prosdocimi, Francisco, Brandon Chisham, Enrico Pontelli, J.D. Thompson, and Arlin Stoltzfus. 2009. “[[http://www.la-press.com/initial-implementation-of-a-comparative-data-analysis-ontology-article-a1526][Initial Implementation of a Comparative Data Analysis Ontology]].” Evolutionary Bioinformatics Online (5): 47–66.
*Slides*
* [[http://www.slideshare.net/rossmounce/sharing-reusable-phylogenetic-data-were-not-there-yet][Ross Mounce - Sharing re-usable phylogenetic data: we're not there yet]]
* [[http://www.slideshare.net/rvosa/tdwg-2013vos][Rutger Vos - PhyloTastic: Names-based phyloinformatic data integration]]
* [[http://figshare.com/articles/SUPERSMART_Self_Updating_Platform_for_Estimating_Rates_of_Speciation_and_Migration_Ages_and_Relationships_of_Taxa/840544][Alexandre Antonelli - SUPERSMART: Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages and Relationships of Taxa]]
* [[http://figshare.com/articles/numerical_representation_of_phylogenetic_tree/841733][Saverio Vicario - Numerical tree representations: their application to MCMC phylogenetic inference, phylogenetic signal, - and database query?]]
* [[http://www.slideshare.net/jar375/jar-tdwg2013][Jonathan Rees - Assembling a draft overall tree of life from phylogenetic trees and taxonomic databases]]
* [[http://www.slideshare.net/suzi.lewis/q4-o-at-tdwg-2013][Suzi Lewis - Quest for orthologs: anchoring comparative biology research]]
---++ Acknowledgements
<img src="%ATTACHURLPATH%/Naturalis_Biodiversity_Center_logo_2012.png" alt="Naturalis_Biodiversity_Center_logo_2012.png" width='82' height='122' style='float:left'/>
The symposium was made possible thanks to additional sponsorship provided by [[http://www.naturalis.nl][Naturalis Biodiversity Center, Leiden, the Netherlands.]]
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