draft survey about metadata on trees

[Karen Cranston]

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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[Arlin Stoltzfus]

Karen--

I don't think we need the explanatory text (although it wouldn't hurt), but what I really would like to see is a question like this:

> Please indicate the journal of your most recent phylogeny publication (if in the past 3 years)


with a pull-down list of the top tree-publishing journals, plus a blank option to fill in a journal not listed, plus the option "I haven't published a tree in the past 3 years".

This will allow us to cross-reference our sample of respondents with other populations, because we can generate a list of all phylogeny pubs in the past 3 years. This will reveal biases in our sample, e.g., if our respondents never publish in "International Journal Of Systematic And Evolutionary Microbiology" then we are missing the microbiologists, because its a very popular tree-publishing venue.

Below is a list of the top 20 tree-publishing journals for 2010, with the number of articles matching "phylogen*". This distribution has a very long tail.

Arlin
-------

Molecular Phylogenetics And Evolution (399)
International Journal Of Systematic And Evolutionary Microbiology (389)
PLOS One (273)
Zootaxa (219)
BMC Evolutionary Biology (216)
Molecular Biology And Evolution (116)
Proceedings Of The National Academy Of Sciences Of The United States Of America (106)
Taxon (97)
Applied And Environmental Microbiology (96)
BMC Genomics (88)
Journal Of Clinical Microbiology (84)
Archives Of Virology (83)
Molecular Ecology (81)
Cladistics (81)
Biological Journal Of The Linnean Society (75)
Journal Of Vertebrate Paleontology (75)
Journal Of Biogeography (72)
Zoological Journal Of The Linnean Society (66)
Mycologia (64)
Plant Systematics And Evolution (62)

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-------
Arlin Stoltzfus (ar...@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

[Hilmar Lapp]

One thing I just came across that might be useful in terms of tallying preference votes for MIAPA attributes:

http://www.cs.cornell.edu/andru/civs.html

It implements the Condorcet election method, also called preference voting:

http://en.wikipedia.org/wiki/Condorcet_method

Perhaps it will be too complicated to integrate this with a Google or online survey software form for the other question. However. the software seems to allow uploading a table of votes, so it could still be used for tallying if can get the table out of the online survey or Google forms spreadsheet.

-hilmar

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

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: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
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