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

[Arlin S. <ar...@um...>]

I'd like to get some feedback on an idea for a workshop project.  This  
came up earlier today in a discussion with Jim Leebens-Mack, Enrico  
Pontelli & Maryam Panahiazar.   We are interested in annotating a set  
of phylogenetic studies (one of the suggested deliverables below).   
The process of annotation would help us to work out the metadata  
attributes needed to describe a study-- in particular, describing  
phylogenetic methods and workflows is a thorny problem--, and the  
resulting set of annotated studies could serve as a benchmark or  
training set for automated methods.

We talked about using random samples of phylogeny publications, or  
some set of canonical or exemplary publications.

Then the thought occurred to us: if ultimately we are trying to  
facilitate data-sharing, why waste our time annotating publications  
for which we are not offering the supporting data for public re-use  
via some searchable interface?  Instead, why not annotate some studies  
that are already poised for re-use, with the data available via a  
searchable interface?  An example would be the ~300 studies that were  
deposited last year in TreeBASE.   If we work with the TreeBASE  
providers, perhaps we could provide an search interface that takes  
advantage of the extra annotations.  Another important set of re- 
useable trees is the set of trees agglomerated into the APG tree, or  
the ToLWeb tree.

Any thoughts on this?  Would this compromise our other goals of  
working out problems in annotation while creating a benchmark set of  
publications?   What is the best set of publications to annotate?

Arlin

On Aug 15, 2011, at 10:36 AM, Nico Cellinese wrote:

> 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 (ar...@um...)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org