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
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@flmnh.ufl.edu Date: August 15, 2011 10:36:10 AM EDT To: Phylogenetics Standards Interest Group tdwg-phylo@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@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
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@flmnh.ufl.edu Date: August 15, 2011 10:36:10 AM EDT To: Phylogenetics Standards Interest Group <tdwg- phylo@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@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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Chuck Bell (Nola), Susan Perkins (amnh), Bill Piel will attend. I may have missed someone too, needs to check my past emails.
Nico
Sent from my iPad
On Sep 20, 2011, at 9:22 AM, Hilmar Lapp hlapp@nescent.org wrote:
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@flmnh.ufl.edu Date: August 15, 2011 10:36:10 AM EDT To: Phylogenetics Standards Interest Group tdwg-phylo@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@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 :
tdwg-phylo mailing list tdwg-phylo@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-phylo
Hello all,
I won't be at the TDWG meeting, but I will be at the Genome Standards Consortium meeting next week in Bremen (http://gensc.org/gc_wiki/index.php/GSC_12). Will anyone else from these lists be in attendance, and in particular does anyone already plan to represent/present an update on MIAPA? If not, I'd be happy to do so, with some help from those closer to the action.
Todd
On 20 Sep 2011, at 15:22, Hilmar Lapp wrote:
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@flmnh.ufl.edu Date: August 15, 2011 10:36:10 AM EDT To: Phylogenetics Standards Interest Group tdwg-phylo@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
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Arlin Stoltzfus (arlin@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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Hi Arlin, I am going to attend to this workshop. We can talk about that more on tomorrow meeting. Bests, Mary
On Tue, Sep 20, 2011 at 9:18 AM, Arlin Stoltzfus arlin@umd.edu 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@flmnh.ufl.edu *Date: *August 15, 2011 10:36:10 AM EDT *To: *Phylogenetics Standards Interest Group tdwg-phylo@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); 2. An 2011 iEvoBio http://ievobio.org/ presentation on “Publishing re-usable phylogenetic trees, in theory and in practice” [2]; 3. A lighting talk presentation and Birds-of-a-Feather gathering at 2011 iEvoBio http://ievobio.org/, and 4. A survey group that explored barriers to re-use and developed plans for a survey http://www.evoio.org/wiki/MIAPA
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-usehttp://www.evoio.org/wiki/BarriersToReUse 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. 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
- 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.2011.6048.1https://docs.google.com/document/pub?id=1DiuMEK7g_DJSLzT9ElAwEtJiKRXuQAvoc0JtfoX0sqE [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 https://docs.google.com/–Report Abusehttps://docs.google.com/abuse?id=1DiuMEK7g_DJSLzT9ElAwEtJiKRXuQAvoc0JtfoX0sqE –Updated automatically every 5 minutes
Arlin Stoltzfus (arlin@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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participants (6)
-
Arlin Stoltzfus -
FLMNH -
Hilmar Lapp -
maryam panahiazar -
Nico Cellinese
-
Vision, Todd J