Fwd: [opentreeoflife] draft survey about metadata on trees

[Laura A Katz]

Begin forwarded message:

From: Laura A Katz <lk...@smith.edu>

Date: June 30, 2012 1:46:21 PM EDT

To: opentre...@googlegroups.com

Cc: MIAPA <miapa-...@googlegroups.com>

Subject: Re: [opentreeoflife] draft survey about metadata on trees

Karen,

This looks great.  A couple of very minor things:

- 'data' is plural (i.e. "how useful are the data?")

- these two questions seem redundant

Type of tree estimate: maximum-likelihood, majority-rule consensus, etc.

What method was used to infer the tree (likelihood, parsimony, distance, bayesian, etc)

- how about something like:

' method for orthology determination, if relevant'

' approach for masking ambiguous sites'

' availability of vouchers (i.e. museum specimen, tissue sample, photodocumentation)

I don't think more explanation is needed -- less may be more here.

Laura

On Jun 22, 2012, at 11:50 AM, Karen Cranston wrote:

Hi folks,
Following up on the message from a few weeks ago about metadata on
trees, a few of us [1] have drafted a survey that we hope to send out
soon for community input. Here is the draft invitation letter and link
to the survey. I'd like comments on 1) the letter and 2) the design of
the survey. The list of metadata elements come from the draft MIAPA
survey [2] from last year's TDWG meeting. I welcome comments on
metadata elements you think are glaringly absent from the list, but
please no discussion here about items on the list (i.e. don't respond
to this email by answering the survey questions!).

One specific question: should there be a section at the bottom that
explains each element in detail? Hover text is not possible with
software I am using.

Cheers,
Karen

=================
What data makes a phylogenetic tree useful?

When publishing a phylogenetic tree, or evaluating a tree, we
generally want more than simply the tree structure - for example, who
inferred the tree? using what data and what methods? what are the
organisms at the tips? what are the support values?

Of course, those who use / evaluate trees want as much data as
possible about a tree. Those who publish / database trees want a quick
and simple submission system. How do we balance these sometimes
conflicting viewpoints?

The following survey asks you to categorize various data elements
about trees in terms of 1) how useful is the data? and 2) how
difficult is it to collect? It should take about 10 minutes.

https://duke.qualtrics.com/SE/?SID=SV_b2upIMII4fxJkAA&Preview=Survey&BrandID=duke

This survey is brought to you by MIAPA and Open Tree of Life. MIAPA
(http://www.evoio.org/wiki/MIAPA) aims to develop a formal spec for
Minimum Information About a Phylogenetic Analysis. The Open Tree of
Life (http://opentreeoflife.org) is collecting input phylogenies for
synthesis into a comprehensive tree of life. We will share the results
via the MIAPA and Open Tree of Life websites, and results will inform
the MIAPA standard as well as the collection of information for
OpenTree.

If you have any questions about this project, please contact Karen
Cranston (karen.c...@nescent.org).

Thank you!
Karen (on behalf of MIAPA and Open Tree of Life)
=================

[1] Arlin Stolzfus, Jim Leebens-Mack, Jamie Estill and Karen Cranston
[2] http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Community_survey

--
~~~~~~~~~~~~~~~~~~~~~~~
karen.c...@gmail.com
~~~~~~~~~~~~~~~~~~~~~~~

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+++++++++++++++++++++++++++++++++++++++++++++
Laura A. Katz, Elsie Damon Simonds Professor
Department of Biological Sciences
lk...@smith.edu
44 College Lane
Smith College
Northampton, MA 01063
Phone:  413-585-3825 (office)
        413-585-3750 (lab)
Fax:  413-585-3786
http://www.science.smith.edu/departments/Biology/lkatz/
+++++++++++++++++++++++++++++++++++++++++++++

+++++++++++++++++++++++++++++++++++++++++++++
Laura A. Katz, Elsie Damon Simonds Professor
Department of Biological Sciences
lk...@smith.edu
44 College Lane
Smith College
Northampton, MA 01063
Phone:  413-585-3825 (office)
        413-585-3750 (lab)
Fax:  413-585-3786
http://www.science.smith.edu/departments/Biology/lkatz/
+++++++++++++++++++++++++++++++++++++++++++++