[tdwg-phylo] Upcoming TDWG meeting
arlin at umd.edu
Fri Aug 27 22:24:59 CEST 2010
Is anyone else interested? If there is interest, I'll start a
planning document (TDWG phylo twiki?).
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.
> From: tdwg-phylo-bounces at lists.tdwg.org [mailto:tdwg-phylo-bounces at lists.tdwg.org
> ] On Behalf Of Arlin Stoltzfus
> Sent: Friday, August 27, 2010 11:27 AM
> To: tdwg-phylo at 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:
> 1. 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).
> 2. 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.
> 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.
> 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
> Arlin Stoltzfus (arlin at 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
Arlin Stoltzfus (arlin at 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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