[Tdwg-phylo] MIAPA Workshop at the TDWG 2011 meeting, New Orleans, LA
Hilmar Lapp
hlapp at nescent.org
Tue Sep 20 15:22:28 CEST 2011
We asked those interested in participating to say "hello" on the MIAPA
list. So far one person did (Son Tran from NMSU).
-hilmar
On Sep 20, 2011, at 9:18 AM, Arlin Stoltzfus 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:
>> 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
> <ATT00001.txt>
>
> -------
> 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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--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
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