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