[Tdwg-phylo] MIAPA Workshop at the TDWG 2011 meeting, New Orleans, LA

[maryam panahiazar]

Hi Arlin,
I am going to attend to this workshop. We can talk about that more on
tomorrow meeting.
Bests,
Mary

On Tue, Sep 20, 2011 at 9:18 AM, Arlin Stoltzfus <arlin at umd.edu> wrote:

> With the workshop less than a month away, it might be a good time to start
> getting organized.  Do we have any way of knowing who is going to attend,
> other than the usual suspects?
>
> Arlin
>
> Begin forwarded message:
>
> *From: *Nico Cellinese <ncellinese at flmnh.ufl.edu>
> *Date: *August 15, 2011 10:36:10 AM EDT
> *To: *Phylogenetics Standards Interest Group <tdwg-phylo at lists.tdwg.org>
> *Subject: **[Tdwg-phylo] MIAPA Workshop at the TDWG 2011 meeting, New
> Orleans, LA*
>
> TDWG MIAPA Workshop
> Call For Participation:
> Steps towards a Minimum Information About a Phylogenetic Analysis (MIAPA)
> Standard
> Synopsis
> Many phylogenetic analysis results are published in ways that present
> serious barriers to their reuse in numerous research applications that would
> stand to benefit from them. While some of these barriers are well
> understood, such as issues with adherence to standard exchange formats,
> those centering on the associated metadata necessary for researchers to
> evaluate or reuse a published phylogeny have only recently begun to be
> articulated. One of the critical next steps towards formalizing these
> metadata requirements as a minimum reporting standard is to convene meetings
> of key stakeholder communities with the goal to identify information
> attributes  necessary and desirable for facilitating reuse, and to build
> consensus on their priority. To this end, we are holding a workshop at the
> 2011 Biodiversity Information Standards (TDWG) Conference to determine how a
> future reporting standard for phylogenetic analyses can best serve
> biodiversity science and related research applications.  We invite all
> interested colleagues to participate.
> Background
> The workshop of the Biodiversity Information Standards (TDWG) Phylogenetics
> Standards Interest Group held at the 2010 TDWG conference included a project
> focused on how to publish re-usable trees that can be linked into an
> emerging global web of data.  Through follow-up work, this led to the
> following tangible results:
>
>    1. An online draft report of the 2010 TDWG workshop [1], and a corresponding
>    manuscript on best practices for publishing phylogenetic trees (Stoltzfus et
>    al. in preparation);
>    2. An 2011 iEvoBio <http://ievobio.org/> presentation on “Publishing
>    re-usable phylogenetic trees, in theory and in practice” [2];
>    3. A lighting talk presentation and Birds-of-a-Feather gathering at
>    2011 iEvoBio <http://ievobio.org/>, and
>    4. A survey group that explored barriers to re-use and developed plans
>    for a survey <http://www.evoio.org/wiki/MIAPA>
>
> These activities have considerably clarified our understanding of the
> theory and practice of publishing re-usable phylogenetic trees: how many
> phylogenies are published each year, the (low) frequency of archiving, what
> archives and tools are available, what policies are in force, etc.  We have
> identified a number of barriers to re-use<http://www.evoio.org/wiki/BarriersToReUse> involving
> such aspects as technology, standards, culture, and access.
>
> Many of these barriers can be interpreted as a consequence of the lack of a
> community-agreed standard for what constitutes a well documented
> phylogenetic record.  In the absence of such a standard, trees are often
> archived as image files rather than in appropriate data exchange formats,
> and lack important accompanying information (metadata), such as externally
> meaningful identifiers, that would be needed to make them useful to others.
> The idea of a Minimum Information About a Phylogenetic Analysis (MIAPA) standard
> has been suggested [3], but so far there has not been a deliberate process
> to develop and disseminate a community standard.  Meanwhile, a number of
> systematics and evolution journals have begun to require archiving of the
> data underlying published research findings [4].  The emerging cultural
> shift in data archiving and sharing promoted by this policy change offers a
> unique window of opportunity to move ahead with the development and actual
> specification of a MIAPA standard.
>
> Similar to other minimum reporting standards [5], the primary focus of a
> future MIAPA standard would be on defining a “checklist” of metadata
> information attributes that, at a minimum, needs to accompany an archived
> phylogenetic analysis, and to which standards values for these attributes
> would need to adhere. The key step in developing community consensus on
> these elements of the standard is to convene a series of meetings that
> collectively involve participants from all major groups of stakeholders who
> would be affected by such a standard, such as users, producers, publishers,
> or archivists of phylogenetic analyses.  To aid this process, the
> Phylogenetics Standards Interest Group is holding a workshop at the 2011
> TDWG conference, with the goal to obtain consensus requirements and
> priorities for a MIAPA checklist for the purposes of biodiversity science,
> taxonomy, museum collections, and related research applications.
> Goals and deliverables
> The main goal of the workshop is to develop a shared understanding of the
> role that a MIAPA standard could play in facilitating re-use of phylogenetic
> analyses for the biodiversity science and related communities, and what the
> standard would need to specify in order to  best fill that role. Possible
> deliverables include
>
>    1. A draft set of information attributes that should or could be
>    included in a provisional MIAPA checklist, with a level of consensus for
>    each of them.
>    2. A database with use-cases based on exemplifying publications, that
>    report phylogenies to elucidate a broad spectrum of questions relating to
>    biodiversity science.
>    3. A refined MIAPA survey to be informed by biodiversity science cases
>    for reuse.
>    4. A plan for further community engagement and consensus-building among
>    biodiversity science stakeholders.
>
> Workshop format
> The workshop will start with a few presentations focused on (i) introducing
> MIAPA and its potential in facilitating reuse (J. Leebens-Mack); (ii)
> summarizing recent developments and current status of MIAPA-related efforts
> (A. Stoltzfus); and (iii) past experiences and resulting best practice
> recommendations on developing a minimum reporting checklist standard (D.
> Field). The rest of the workshop will be hands-on.  Participants in the
> workshop will break out into groups to address separate issues according to
> the anticipated deliverables and best practice recommendations.
>
> The workshop will be 1.5 days in duration, and be held during the 2011
> Biodiversity Information Standards (TDWG) conference, to take place Oct 17
> to 21, 2011 in New Orleans, USA. (http://www.tdwg.org/conference2011/).
>  The workshop will start in the afternoon of Monday, Oct 17, and end on
> Tuesday. Oct 18.
> How to participate
> Participation in the workshop is open to everyone interested. However,
> space is limited, and we therefore ask that, if you are interested in
> attending, to please communicate your interest through the MIAPA discussion
> group [6]. This will also allow us to include you in pre-workshop planning.
> Since the workshop is part of the TDWG conference, participants will need to
> register either for the full conference, or for the days of the workshop.
>
> The organizers will provide an electronic venue for participants to share
> ideas and develop plans in advance of the workshop.  After the initial
> presentations, participants will self-organize into task groups.
>
> Organizers
>
>    1. Nico Celinese, University of Florida
>    2. Hilmar Lapp, NESCent
>    3. Jim Leebens-Mack, University of Georgia
>    4. Enrico Pontelli, New Mexico State University
>    5. Arlin Stoltzfus, NIST & University of Maryland
>
> References
> [1] Whitacre et al. (2010). Current Best Practices for Publishing Trees
> Electronically.
> http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010
> [2] O’Meara et al. (2011). Publishing re-usable phylogenetic trees, in
> theory and practice. Available from Nature Precedings
> <http://dx.doi.org/10.1038/npre.2011.6048.1><https://docs.google.com/document/pub?id=1DiuMEK7g_DJSLzT9ElAwEtJiKRXuQAvoc0JtfoX0sqE>
> [3] Leebens-Mack, J., T. Vision, et al. (2006). "Taking the first steps
> towards a standard for reporting on phylogenies: Minimum Information About a
> Phylogenetic Analysis (MIAPA)." Omics 10(2): 231-7.
> [4] Whitlock, M., M. McPeek, M. Rausher, L. Rieseberg, and A. Moore (2010).
> Data Archiving (Editorial). The American Naturalist 175(2): 145.
> [5] Taylor, C.F., D. Field, S. Sansone, J. Aerts, R. Apweiler, M.
> Ashburner, C.A. Ball, et al. (2008). Promoting coherent minimum reporting
> guidelines for biological and biomedical investigations: the MIBBI project.
> Nature Biotechnology 26(8): 889-96. doi:10.1038/nbt.1411
> [6] MIAPA discussion group: http://groups.google.com/group/miapa-discuss
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>
>
>
> -------
> 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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