[Tdwg-phylo] Fwd: MIAPA Workshop at the TDWG 2011 meeting, New Orleans, LA
Arlin Stoltzfus
arlin at umd.edu
Tue Sep 20 15:18:18 CEST 2011
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:
> 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);
> An 2011 iEvoBio presentation on “Publishing re-usable phylogenetic
> trees, in theory and in practice” [2];
> A lighting talk presentation and Birds-of-a-Feather gathering at
> 2011 iEvoBio, and
> A survey group that explored barriers to re-use and developed plans
> for a survey
> 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
> 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
> 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.
> A database with use-cases based on exemplifying publications, that
> report phylogenies to elucidate a broad spectrum of questions
> relating to biodiversity science.
> A refined MIAPA survey to be informed by biodiversity science cases
> for reuse.
> 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
> Nico Celinese, University of Florida
> Hilmar Lapp, NESCent
> Jim Leebens-Mack, University of Georgia
> Enrico Pontelli, New Mexico State University
> 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
> >
> [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
> Published by Google Docs–Report Abuse–Updated automatically every 5
> minutes
-------
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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