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%META:TOPICINFO{author="HilmarLapp" date="1225425380" format="1.1" version="1.1"}%
%META:TOPICPARENT{name="WebHome"}%
---+!! %MAKETEXT{"TDWG Phylogenetics Standards Workshop"}%
The workshop took place on Oct 19, 2008, at the 2008 TDWG Annual Meeting in Fremantle (Perth),
*Table of Contents:*
%TOC%
---++ %MAKETEXT{"Agenda"}%
[[http://docs.google.com/Doc?id=dhdjhbvd_47ccsrndg6][Workshop objectives, agenda, and initial participant list]] were published in advance and disseminated to all TDWG conference attendees 1 week prior to the event.
---++ %MAKETEXT{"Workshop Notes"}%
Attendees: 18 in total
---+++ Introductions
* Stan Blum: TDWG process
* Foster sharing of standards, data, and biodiversity informatics developments
* Process is fairly lightweight
* Put up (social) interfaces for other people to discover you and find out how to contribute
* Interest group is a group of people that have a shared set of problems that they would like to address.
* Key piece for a group to "declare itself" is a charter: what is it that the group aims to do.
* Then create Task Groups, each of which will also have a charter that says what the Task Group will do.
* Standards are essentially documents, specifications.
* Infrastructure in the form of mailing lists and wikis are provided.
* Ratification is initiated by the convener of the Task Group
* Submits the specification document to the Executive Committee
* Review manager is assigned and arranges review of the specification
* Public review follows after review recommendations are taken care of
* There is no voting process.
* Q: TDWG is reported to be very slow.
* Key to keep pushing on the committees, communication is key
* Process being in place helps in comparison to previously annual pace
* Q: how is participating in TDWG better than just putting stuff up in SourceForge?
* There's a lot of experience among TDWG that is related to many of data and types of data and problems we would be dealing with.
* Can take advantage of the participants/experts in other groups.
* Interface and communication between biologists and information technologists, which is what TDWG is well set up for
* Q: what is a good (or a bad) charter?
* Charters and process have only been instituted since 2 years. The experience and lessons learned from this are limited at this point.
* Charters ideally are updated at least once annually.
---+++ Session I
* David Kidd:
* proper representation of geographical areas
* position of observed and inferred nodes, branch paths
* vicariance-related metadata
* branches can be segmented, using different methods, representing for example time, or shortest distance (which in projections isn't necessarily a straight line)
* paleocontinental reconstruction methods and/or parameters and simulation metadata needed
* data from stratigraphy can have (dating) errors associated with it
* Pyramid of standards: space (geographic, GML), place (ecological, EML), time (stratigraphic), form (taxonomic): shouldn't phylogenetic standard be in the middle of all of this
* Rick Ree:
* where does X (extant, or ancestral taxon) live?
* where has it been found or collected?
* expert opinion (monographs, floras)
* describing the geographic range
* quantitative: lat/long, grid cell values
* qualitative: geopolitical units
* predictive: ecological niche, model?
* inspiration from use cases: historical biogeography, ancestral range estimation
* take advantage of analogy from standards and ontologies developed for characters?
* geographic range as an emergent trait of a taxon
* take standards that have already been developed (OGS geospatial standards) and look at them through the lens of phylogenetics)
* TDWG work can consist of recommending certain ways to applies an external standard
* One of the first questions could be to determine whether we can exchange the biogeographical data and reconstructions (e.g. from DIVA and LAGRANGE) that we already have
* Greg Riccardi
* 230,000 images at present, several TBs of space
* Capture and track the data that support phylogenetic inference based on characters
* Morphbank objects (images, collections, etc) have external links: specimen, sequence
* Chain of evidence
* Morphbank is being used by external tools, for example MX, as the underlying image store
* Character state annotation: "sort a bale of plants" metaphor for images
* Character definitions in trees data files are typically much to short and limited to search databases such as Morphbank
* Linking images to anatomy ontology terms: ideally have an outline of the part linked, not just the whole image or a pointer within the image
* Defining characters and states by using ontology terms: capturing, and linking from states
* would also enable the ability to infer the relatedness of characters
* Q: Can we have ontologies that are based in phylogeny. It is impossible otherwise to simply combine different morphological ontologies.
* Q: what is the role of ontologies to informatics standards? -> metadata (property) meaning standardization
* There is no good way currently to link various annotations in various media about a digital or collection object
---+++ Session II
* Rutger Vos: <nop>NeXML format
* Chris Zmasek: <nop>PhyloXML, phylogenomics
* using phylogenies for functional inference
* Q: library support? -> Forester, <nop>BioPerl
* Hilmar Lapp: <nop>PhyloDB, <nop>BioSQL, <nop>PhyloWS
* Nico Cellinese: Phylogenetic nomenclature
* Define names not based on organismal traits but based on phylogenetic relationships
---+++ Breakout Groups:
The breakout groups were determined from a 45min group discussion and whiteboarding of suggestions, following by self-assignments to groups.
1. Phyloinformatic Web services (Bill P., Rutger, Cindy)
* data services. which data or metadata are needed from providers
* data demands that ask for portals (such as GBIF, EOL)
* crosstalk & provenance between providers
* scope recommendations, workflows, use cases
1. Metadata standardization & Ontology (David, Chris, Peter, Aaron, Bill, James)
* metadata uses, properties, semantics
* reuse possibilities for other TDWG standards
* expressing the domain model independent of technology
1. Deposition to repositories
* incentives and standards to increase deposition rates
* reporting requirements to enable repurposing
---++++ Report-out from the groups
*Group 1)* Bill P.
* divided tasks between "tree decoration" and "tree delivery"
* tree decoration:
* coevolution (food web, pollinator, host-parasite): for a given set of hosts, give me the tree of parasites
* computational: calculate divergence times or ages
* use the tree as input, get it out decorated with certain metadata
* tree delivery
* types are parameter query and computational query
* results in ID list
* given an ID, the desired view (what elements are to be returned) and format, return the object(s)
* ability to say, give me all trees that contain human, but only those that are about apes
* ability to give a scope of the desired trees
* ability to dump data, be alerted to updates (e.g., RSS feed)
* different levels of hierarchy of objects: analyses, matrices, trees
*Group 2+3)* David
* attributes about what makes up a phylogeny, provenance, where data came from and what type, papers possibly associated, parameters used, when and where was it done
* branch length, support values, need multiple of these
* tree to tree relationships
* breaking branches into segments
* sets of nodes, within and between trees, and sets of trees, relationship between nodes (e.g., homologs, host-parasite)
* attributes of nodes (type of node, species or gene, taxon concept, area, more than object per node)
* gene trees are a big application of trees
* talk to geospatial group to learn about their objects and standards
* talk to technical architecture group to learn more about ontologies
* started with an exercise that needs to be followed up with
* there seems to be a taskgroup developing ontologies for this area
* formulating the elements and use cases would create momentum
---++++ Interest Group charter
* Keep it simple
* encouragement to list core members
* implementation is the proof, further those efforts
* intersection, don't over-think, what are the core elements
-- Main.HilmarLapp - 31 Oct 2008
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