wiki-archive/twiki/data/Phylogenetics/MIAPAWorkshop2011Ideas.txt

%META:TOPICINFO{author="ArlinStoltzfus" date="1320240464" format="1.1" version="1.19"}%
%META:TOPICPARENT{name="MIAPAWorkshop2011"}%
---+++ Scoping questions 

The scoping questions originally listed here were addressed at the TDWG workshop in 2011, with results available at [[http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Scope_discussion][http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/MIAPADraft#Scope_discussion]].  

---+++  Exploring the Role of OBI in MIAPA
We would like MIAPA to develop as a set of concepts and relations that are formalized within an ontology. In this regard, we need to recognized that a significant amount of work has already been done in the context of three ontologies
   * PhylOnt created by Leebens-Mack's team
   * CDAO (including the v2 version that includes a classification of methods)
   * the Ontology for Biomedical Investigations ([[http://obi-ontology.org/page/Main_Page][OBI]])
In particular, it appears that OBI already provides the a rich infrastructure for the general description of experiments and protocols; we believe that much can be achieved by simply integrating these three ontologies. Our proposal is to integrate in the use-cases and benchmark activities discussed below exercises aimed at using the three ontologies to create sample reports.

Interested parties: Son Cao Tran

---+++  Annotation Phylogeny Papers with PhylOnt  Ontology and other NCBO ontologies
We implemented a tools to annotate concepts in Phylogeny related documents with concepts from ontology such as PhylOnt ontology and other related ontologies.
after annotation user can publish the annotations and retrieve annotation for re-use.

Interested parties: Jim Leebens-Mack and Maryam Panahiazar

---+++ Actual examples of MIAPA-compliant reports

People have been talking about MIAPA for 5 years now, but there is not a single example of a MIAPA-compliant report.  Why don't we make a few?  We could use the [[http://www.evoio.org/wiki/MIAPA_Draft_RFC][strawman draft of MIAPA]].  Like most MIBBI standards, it does not specify a format.  Therefore, we could use currently available formats, perhaps supplemented with metadata files.  Or we could use a NEXUS file with comments (square-bracketed strings) to contain the MIAPA-relevant annotations.  

Because the point of this project is just to create sample records, we can avoid complexities (e.g., highly complex workflows due to iteration or reuse) and start with some reports that are easy to characterize.  The rough outline for the project would be: 
   * identify a few (3 to 6) simple studies for which we can obtain trees, matrix, and PDF of publication 
   * create a record for each study that complies with the strawman draft of MIAPA
   * for one of the studies, create different versions of the same record using different formats (e.g., NEXUS-with-comments vs. NeXML vs. treefile+alignmentfile+metadatafile) 

The MIAPA page has [[http://www.evoio.org/wiki/MIAPA/PhyloWays#some_candidate_cases][a short list of examples, some simple]], but I don't know how many we can get PDFs for.  

---+++ Create benchmark of annotated pubs relating phylogenies and biodiversity

The notion of annotating a set of phylogenetic studies was suggested in the workshop announcement.   The process of annotation would help us to work out the metadata attributes needed to describe a study, e.g., describing phylogenetic methods and workflows is a thorny problem.  The resulting set of annotated studies could serve as a benchmark or training set for automated methods.   

The publications could be a random sample from the relevant literature, or some set of canonical or exemplary publications. 

Alternatively, given that our larger goal is 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 with 2010 publication dates 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.     

Interested parties: 

---+++ Sharing the tree of life: What can we learn from mega-phylogeny resources & use-cases?  

Trees with large numbers of species have many uses in community ecology, bioinformatics, biodiversity studies, etc.  NSF has poured a large amount of money into "assembling the tree of life" for the benefit of the scientific community, but there is no comprehensive tree-of-life resource for scientists to use.  How can this situation be improved, and in particular, how does improvement depend on information standards?  

One way to understand this situation is to study which resources promote re-use, and why.  ToLWeb has hundreds of curators and a huge code-base, but it seems to be rarely used for research.  By comparison, Phylomatic rocks, even though it is an extremely small project and is limited to plants.  The NCBI taxonomy hierarchy provides the organizing framework for a number of projects (e.g., Rod Page's iPhylo; Ross Mounce has started [[http://www.citeulike.org/user/rossmounce/tag/ncbitaxonomy][a short list of citations for such projects]]), in spite of the fact that it is not properly a phylogeny, and it is distributed in a form (SQL database dump) that most users would find intimidating.  

Another way to understand this situation is to look at what users are doing when they make use of a tree of life.  The studies listed below rely on a large tree to accomplish research objectives such as computing measures of phylogenetic diversity, or studying trait correlations among a large set of species.  

   * [[http://www.ncbi.nlm.nih.gov/pubmed/21402914][Burns JH, Strauss SY: More closely related species are more ecologically similar in an experimental test. Proc Natl Acad Sci U S A 2011, 108(13):5302-5307.]]
   * [[http://dx.doi.org/10.1111/j.1600-0706.2010.18898.x][Duarte LdS: Phylogenetic habitat filtering influences forest nucleation in grasslands. 2011, 120(2):208-215.]]
   * [[http://www.amjbot.org/content/early/2011/01/25/ajb.1000154.abstract][Walls RL: Angiosperm leaf vein patterns are linked to leaf functions in a global-scale data set. American journal of botany 2011.]]
   * [[http://dx.doi.org/10.1111/j.1466-8238.2010.00582.x][Zhang S-B, Ferry Slik JW, Zhang J-L, Cao K-F: Spatial patterns of wood traits in China are controlled by phylogeny and the environment. Global Ecology and Biogeography 2011, 20(2):241-250.]]
   * [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21166972][Morlon H, Schwilk DW, Bryant JA, Marquet PA, Rebelo AG, Tauss C, Bohannan BJ, Green JL: Spatial patterns of phylogenetic diversity. Ecology letters 2011, 14(2):141-149.]]
   * [[http://dx.doi.org/10.1016/j.mambio.2010.03.004][Riek A: Allometry of milk intake at peak lactation. Mammalian Biology Zeitschrift fur Saugetierkunde 2011, 76(1):3-11.]]

Interested parties:  

-- Main.ArlinStoltzfus - 07 Oct 2011