[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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