Is anyone else interested? If there is interest, I'll start a planning document (TDWG phylo twiki?).
Arlin
On Aug 27, 2010, at 2:45 PM, Dan Rosauer wrote:
Hi Arlin and others
I think that idea 1 below is a really valuable topic to address. The ability to link tree tips to other sources of data by taxon name or identifier is a threshold step for automating a whole range of analyses and displays. For example, the software I work on, Biodiverse, links phylogenies to species location data for visualisation and analysis. It would be great to have it running automatically online, linking (for example) trees from treebase to distributions from GBIF. To do this (and many other things) however we need a better solution to the taxon matching problem you describe.
cheers Dan
From: tdwg-phylo-bounces@lists.tdwg.org [mailto:tdwg-phylo-bounces@lists.tdwg.org ] On Behalf Of Arlin Stoltzfus Sent: Friday, August 27, 2010 11:27 AM To: tdwg-phylo@lists.tdwg.org Subject: Re: [tdwg-phylo] Upcoming TDWG meeting
I'm sending this reply to only the tdwg-phylo list (sending to everyone seems like overkill).
Here are two ideas based on the use of phylogenies:
- For various reasons, its important to be able to associate
valid species sources or other universal identifiers (e.g., NCBI gis) with the human-readable OTU identifiers used in tree files, but this typically isn't done and it's not always easy. The goal of this project is to enable ordinary phylogenetics & systematics users to use current standards (Newick, NHX, phyloxml, ...) to associate species names (possibly other tax ids) with phylogenies in their usual workflows. The focus is on developing short-term tools and strategies that might lead to better long-term solutions. In some cases, its just a matter of knowing how to use the file format properly, possibly aided by better tools for data input. For users whose workflows rely on Newick, we would need a way to keep a separate mapping of OTU ids and tax ids, along with tools to interconvert or translate to one of the other formats (this could be as simple as an Excel spreadsheet or as complex as a web service that maintains your mapping and does the translation for you).
- There is a huge variety of tree viewers. To some extent, users
need this variety due to their having different feature sets. But users shouldn't have to choose the viewer based on data format restrictions. The goal of this project is to improve the usability of tree viewers. Assess the interoperability (standards compatibility) of tree viewing software, develop strategies to improve it, and get started on any strategies that can be implemented. Its not possible to modify viewers whose source code is unavailable, but there may be ways to work around this with scripts and translation tools.
Arlin
On Aug 26, 2010, at 9:40 PM, Nico Cellinese wrote:
Hi all,
we have reserved one full day for a Phylogenetics Standards hands-on activity at the upcoming TDWG conference. We asked for power strips and wireless network and tables that we can sit around and work together. The only thing that's missing right now is what exactly we should target. The options are wide open right now, with the two only major constraints being that (a) we have no funding this year to bring people in who wouldn't otherwise be there, and (b) abstract submission deadline is next Wednesday.
Any feedback or ideas, wild or not, that you have would be welcome - send those our way.
And BTW currently this workshops seems to be placed on the Wednesday of the conference week, so those of you blitzing the local biosphere will unfortunately have a conflict.
Cheers, Nico & Hilmar
<><><><><><><><><><><><><><><><><><><><> Nico Cellinese, Ph.D. Assistant Curator, Herbarium & Informatics Adjunct Assistant Professor, Department of Biology
Florida Museum of Natural History University of Florida 354 Dickinson Hall, PO Box 117800 Gainesville, FL 32611-7800, U.S.A. Tel. 352-273-1979 Fax 352-846-1861 http://www.flmnh.ufl.edu
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Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org
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------- Arlin Stoltzfus (arlin@umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org