In the Cellinese Lab we investigate the evolution, systematics and biogeography of angiosperms (flowering plants). In addition, we are interested in semantic data integration and interoperability and are developing tools that serve the biodiversity and phyloinformatics communities (e.g., TOLKIN, BiSciCol and RegNum).

Saturday, August 27, 2011

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 presentation on “Publishing re-usable phylogenetic trees, in theory and in practice” [2];
  3. lighting talk presentation and Birds-of-a-Feather gathering at 2011 iEvoBio, and
  4. 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
  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>
[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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