%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: NeXML format * Chris Zmasek: PhyloXML, phylogenomics * using phylogenies for functional inference * Q: library support? -> Forester, BioPerl * Hilmar Lapp: PhyloDB, BioSQL, 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