533 lines
20 KiB
Plaintext
533 lines
20 KiB
Plaintext
head 1.17;
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access;
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symbols;
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locks; strict;
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comment @# @;
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1.17
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date 2010.10.03.16.22.45; author NicoCellinese; state Exp;
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branches;
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next 1.16;
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1.16
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date 2010.10.01.20.06.45; author HilmarLapp; state Exp;
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date 2010.10.01.18.09.40; author HilmarLapp; state Exp;
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date 2010.10.01.16.09.20; author HilmarLapp; state Exp;
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date 2010.10.01.12.51.38; author ArlinStoltzfus; state Exp;
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date 2010.09.30.05.11.52; author ChristopherGoddard; state Exp;
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date 2010.09.30.03.01.14; author TorstenEriksson; state Exp;
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date 2010.09.29.21.59.30; author ArlinStoltzfus; state Exp;
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date 2010.09.29.21.19.01; author DanRosauer; state Exp;
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date 2010.09.29.21.16.20; author ArlinStoltzfus; state Exp;
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date 2010.09.29.15.53.09; author NicoCellinese; state Exp;
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date 2010.09.29.14.44.02; author HilmarLapp; state Exp;
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date 2010.09.28.13.16.14; author NicoCellinese; state Exp;
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date 2010.09.27.22.01.33; author HilmarLapp; state Exp;
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next ;
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desc
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1.17
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@%META:TOPICINFO{author="NicoCellinese" date="1286122965" format="1.1" version="1.17"}%
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%META:TOPICPARENT{name="WebHome"}%
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---+ Working Meeting at TDWG 2010
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We held a full-day hands-on working meeting at the 2010 TDWG Conference in Woods Hole, MA, on Wednesday, Sep 29. The meeting took place in room MRC #310 (in the [[http://www.tdwg.org/fileadmin/2010conference/graphics/WHMapv2.pdf][building marked with 8 in the MBL building map]]).
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We started with short introductions around the room, and then decided on development targets according to participants' interests.
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---++ Participants
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<div style="float: right; width: 305px; margin-left: 5px;"><img src="%ATTACHURLPATH%/TDWG_Phylo_2010-1.jpg" alt="TDWG_Phylo_2010-1.jpg" width="300px" />
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<span style="font-size: x-small;">Elena Herzog, Dan Rosauer, Kate Rachwal, and Chris Goddard are unfortunately missing from this photo.</span>
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</div>
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| *Name* | *Institution* |
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| Nico Cellinese | Florida Museum of Natural History, University of Florida |
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| Torsten Eriksson | Swedish Museum of Natural History, Stockholm |
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| Chris Goddard | Florida Museum of Natural History, University of Florida |
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| Elena Herzog | Bik-F - Biodiversity and Climate Research Center |
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| Hilmar Lapp | NESCent |
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| Kate Rachwal | Florida Museum of Natural History, University of Florida |
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| Dan Rosauer | Yale University |
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| Arlin Stoltzfus | NIST, University of Maryland |
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---++ Development targets
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The [[https://docs.google.com/document/pub?id=1ihH6MGKBCpH10sqvDK5ahLgvz6P_qP-TaN-vLt6O9j8][meeting abstract]], which incorporated the input obtained from interest group members through the mailing list, suggested several targets. These were further narrowed down at the meeting to the list below.
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1. LinkingTrees2010 (Dan, Jamie, Arlin, Torsten, Elena)
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* Work out *best practices for publishing a tree electronically*, via an archive such as [[http://www.treebase.org TreeBase]] or [[http://datadryad.org Dryad]], or via the semantic web (presumably using [[http://www.evolutionaryontology.org/cdao CDAO]]). At minimum, get some actual trees (+/- matrices) ready to submit. At best, draft a how-to guide for publication.
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* Make it easy for users to put species name (or other taxonomic identifier), specimen or source identifier, and geographic coordinates into their trees.
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1. Further develop the [[http://www.evoio.org/wiki/Phyloreferencing_subgroup][Phyloreferencing standard]]. _Hilmar Lapp_, _Nico Cellinese_
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* Compare with Mike Keesey's [[http://namesonnodes.org/][Names on Nodes]].
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* [[https://spreadsheets.google.com/pub?key=0AmUeHhtnDeCZdGRFMHQ5U2RVSG9CNFBRanpKZlJHYVE&hl=en&output=html][Phyloreferencing vocabulary draft]] started at the 2009 !VoCamp.
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* [[http://sourceforge.net/apps/mediawiki/treebase/index.php?title=API][TreeBASE API]] and the full [[https://spreadsheets.google.com/pub?key=0Av8UW3JvZsgcckwtLU83cHloUjhGY25uRzUtb2ZBbHc&hl=en&single=true&gid=0&output=html][Metadata query vocabulary used by TreeBASE]]
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1. Increase the support for the emerging data standards (e.g., !NeXML) among tree visualization tools (Kate)
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* For example, [[http://jsphylosg.com][jsPhyloSVG]] supports !phyloXML, but not !NeXML. Same with [[http://code.google.com/p/phylobox][Phylobox]].
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* Or, write an XSLT to translate [[http://www.phyloxml.org][phyloXML]] to [[http://www.nexml.org][NeXML]], and vice versa. The good news is that XML is emerging as a standard for serializing trees and associated data. The bad news is that there are 2 different schemas.
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1. Ruby-on-Rails / Web-application version of Phenex functionality (Chris)
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---++ Outcomes
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---+++ LinkingTrees2010
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_Dan, Jamie, Arlin, Torsten, Elena_
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Best practices for publishing a tree so that it is reusable and can be linked to other data.
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Outcomes
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* Identified key features that maximize potential for reuse or integration (accn, lsid or other taxo ref, geo coord)
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* identified resources available (file formats, data archives, tools)
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* !TreeBASE supports archiving with capacity to add key features (NCBI or UBio name matching)
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* Tested with reasonable success using files from Mesquite and Bio::NEXUS
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* !TreeBASE steps one through the process.
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* found out how !NeXML and !PhyloXML can represent key features
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* (partly) created set of matching test files in different formats
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* Planned follow-up (Dan, Arlin)
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* Report for TDWG
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* request comments from a larger group of stakeholders
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* possible manuscript for publication.
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---+++ Further develop the [[http://www.evoio.org/wiki/Phyloreferencing_subgroup][Phyloreferencing standard]]
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_Hilmar, Nico_
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Outcomes
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1. Trying to understand what [[http://namesonnodes.org][Names on Nodes]] (Keesey) might contribute
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* Relative to previous effort, doesn't add biologically significant use cases (except perhaps to remind us that crown and stem clade modifiers are not yet included in the phyloreference specification).
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* The tool has a very nice UI, and the code (Macromedia Flash) could possibly be modified to accept phyloreference expressions, in addition to !MathML, which it was written for. (It does apparently already support !NeXML.)
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1. [[https://spreadsheets.google.com/pub?key=0AmUeHhtnDeCZdGRFMHQ5U2RVSG9CNFBRanpKZlJHYVE&hl=en&output=html][Standard vocabulary]] for pinning down the semantics of specifiers in phyloreferences (such as denoting taxon identifier, scientific name, specimen identifier, sequence accession numbers, etc. This was left hanging from the !VoCamp.
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* Determined that this significantly overlaps with, and hence should be merged into the !PhyloWS query predicate vocabulary, for which !TreeBASE currently publishes the de-facto draft (see [[http://treebase.svn.sourceforge.net/viewvc/treebase/trunk/treebase-core/src/main/resources/treebase.owl][treebase-core/src/main/resources/treebase.owl]] in the !TreeBASE codebase).
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* *Follow-up step:* Need to create a draft master query predicate vocabulary as part of the !PhyloWS standard specification, then merge in terms needed for phyloreferencing but currently lacking from the vocabulary.
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* *Follow-up step:* Need to initiate a discussion whether the !PhyloWS query predicate should stand on its own, or should in the long run better be merged into Darwin Core or CDAO.
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1. Taxonomy broker: This was tabled at the 2009 !VoCamp. A taxonomy broker returns species names (tip labels) in exchange for higher-level taxon names, !PhyloCode names, type specimen identifiers, and other "canonical" metadata that not every phylogenetic data provider might have for every tree.
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* Determined that this is a key piece of infrastructure, and a current gap. Without it, some of the most intuitive use-cases will not work, such as querying for all trees containing _some_ "Aves" when most trees won't have internal node labels.
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* We thought that a limited, yet still useful implementation could be scoped such that it is feasible as a Summer of Code project, so that the benefits could be demonstrated. The implementation would work on top of an existing taxonomy or nomenclatural authority, such as the NCBI taxonomy, and !RegNum.
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* Based on a conversation with Rich Pyle, it also appears that GNA (Global Names Architecture) may have many of the necessary pieces and services.
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* *Follow-up steps:* Check the GNA codebase for relevant pieces (once published?). Write Summer of Code project idea (Feb 2011).
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---+++ !PhyloXML to !NeXML interconversion
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_Kate_
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Using XSLT to convert between two emerging XML standards for phylogenetics:
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* Started with a stylesheet that takes as input a !phyloXML document and converts to !NeXML.
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* Planned follow-up:
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* Kate commits for another week
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* expects to finish XSLT that converts at least the trees !phyloXML to !NeXML.
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* finishing the job might be doable within a month.
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---+++ Web interface to phenex functionality
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_Chris_
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Web-based ontology annotation of phylogenetic data: porting Phenex to the web
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* Preliminary work is on !GitHub: [[http://github.com/c1sgo/rjs_phenex]]
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* Started with the basic framework classes and windows.
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* Might take only around 2-3 weeks to make an initially functional version.
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* Chris is committed to at least a few weeks more work on this
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%META:FILEATTACHMENT{name="TDWG_Phylo_2010-1.jpg" attachment="TDWG_Phylo_2010-1.jpg" attr="" comment="" date="1285949256" path="TDWG Phylo 2010-1.jpg" size="1257206" stream="TDWG Phylo 2010-1.jpg" user="Main.HilmarLapp" version="1"}%
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@
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<span style="font-size: x-small;">Elena Herzog, Kate Rachwal, and Chris Goddard are unfortunately missing from this photo.</span>
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%META:TOPICINFO{author="HilmarLapp" date="1285956580" format="1.1" reprev="1.15" version="1.15"}%
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---+++ LinkingTrees2010
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Dan, Jamie, Arlin, Torsten, Elena
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Hilmar, Nico
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* implementation could be adapted to compute phyloreferences via !phyloWS
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* relative to previous effort, doesn't add biologically significant use case
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1. Left hanging from !VoCamp
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* vocabulary that can be used to pin down semantics of specifiers in phyloreferences
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* taxonomy broker (allows people to query resources)
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* e.g., query "aves" in tb even thhough tb entries don't have "aves" labels on nodes
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* query authority with voucher specimen
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---+++ !PhyloXML to !NeXML interconversion (Kate)
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---+++ Web interface to phenex functionality (Chris)
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@
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%META:TOPICINFO{author="HilmarLapp" date="1285949360" format="1.1" reprev="1.14" version="1.14"}%
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We are holding a full-day hands-on working meeting at the 2010 TDWG Conference in Woods Hole, MA, on Wednesday, Sep 29. The meeting is currently scheduled for room MRC #310 (in the [[http://www.tdwg.org/fileadmin/2010conference/graphics/WHMapv2.pdf][building marked with 8 in the MBL building map]]).
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The meeting is open to all. We will start with short introductions around the room for any participants that are new, and then decide on development targets according to participants' interests. We do intend to break into working subgroups or teams relatively quickly, and so we are currently not planning on overview or other introductory presentations. (However, a subgroup may choose to first update itself on research and tool resources that pertain to their chosen target.)
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<img src="%ATTACHURLPATH%/TDWG_Phylo_2010-1.jpg" alt="TDWG_Phylo_2010-1.jpg" width="300px" />
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The [[https://docs.google.com/document/pub?id=1ihH6MGKBCpH10sqvDK5ahLgvz6P_qP-TaN-vLt6O9j8][abstract of the meeting]] (generated from input solicited from interest group members through the mailing list) suggests several targets. The list below is tentative at this stage. Please add either more specifics to a listed target, or a completely new target. Also, add your name to those targets that you are most interested in working on. (Putting your name down is an expression of interest, not a commitment yet. Hence, you can put your name down for more than one target.) Also, there is the mailing list (see Gettting Involved) for discussion prior to Wed, or post on Twitter using the #TDWG hashtag.
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* [[https://spreadsheets.google.com/pub?key=0AmUeHhtnDeCZdGRFMHQ5U2RVSG9CNFBRanpKZlJHYVE&hl=en&output=html][Phyloreferencing vocabulary draft]] started at the 2009 VoCamp.
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1. Increase the support for the emerging data standards (e.g., NeXML) among tree visualization tools (Kate)
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* For example, [[http://jsphylosg.com][jsPhyloSVG]] supports phyloXML, but not NeXML. Same with [[http://code.google.com/p/phylobox][Phylobox]].
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* Or, write an XSLT to translate [[http://www.phyloxml.org phyloXML]] to [[http://www.nexml.org NeXML]], and vice versa. The good news is that XML is emerging as a standard for serializing trees and associated data. The bad news is that there are 2 different schemas.
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1. web interface to phenex functionality (Chris)
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* TreeBASE supports archiving with capacity to add key features (NCBI or UBio name matching)
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* TreeBASE steps one through the process.
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* found out how NeXML and PhyloXML can represent key features
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* first: trying to understand what Names on Nodes (Keesey) might contribute
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* implementation could be adapted to compute phyloreferences via phyloWS
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* second: left hanging from vocamp
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---+++ PhyloXML to NeXML interconversion (Kate)
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* Started with a stylesheet that takes as input a phyloXML document and converts to NeXML.
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* expects to finish XSLT that converts at least the trees phyloXML to NeXML.
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* Preliminary work is on GitHub: [[http://github.com/c1sgo/rjs_phenex]]
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%META:TOPICINFO{author="ChristopherGoddard" date="1285823512" format="1.1" version="1.12"}%
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* Preliminary work is on GitHub: [[http://github.com/c1sgo/rjs_phenex]]
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---++ Participants
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| *Name* | *Institution* |
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| Nico Cellinese | Florida Museum of Natural History, University of Florida |
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| Hilmar Lapp | NESCent |
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| Arlin Stoltzfus | NIST, University of Maryland |
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| Dan Rosauer | Yale University |
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| Chris Goddard | Florida Museum of Natural History, University of Florida |
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| Elena Herzog | Bik-F - Biodiversity and Climate Research Center |
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| Kate Rachwal | Florida Museum of Natural History, University of Florida |
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| Torsten Eriksson | Swedish Museum of Natural History, Stockholm |@
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| Torsten Eriksson | Swedish Museum of Natural History, Stockholm |
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* Or, write an XSLT to translate [[http://www.phyloxml.org phyloXML]] to [[http://www.nexml.org NeXML]], and vice versa. The good news is that XML is emerging as a standard for serializing trees and associated data. The bad news is that there are 2 different schemas.
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| Kate Rachwal | Florida Museum of Natural History, University of Florida |@
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@none
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text
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@d1 1
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a1 1
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%META:TOPICINFO{author="NicoCellinese" date="1285775589" format="1.1" version="1.7"}%
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d14 2
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a15 2
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* Make it easy for users to put species name (or other taxonomic identifier), specimen or source identifier, and geographic coordinates into their trees. _Arlin Stoltzfus_, _Dan Rosauer_
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* Work out *best practices for publishing a tree electronically*, via an archive such as [[http://www.treebase.org TreeBase]] or [[http://datadryad.org Dryad]], or via the semantic web (presumably using [[http://www.evolutionaryontology.org/cdao CDAO]]). At minimum, get some actual trees (+/- matrices) ready to submit. At best, draft a how-to guide for publication. _Arlin Stoltzfus_
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a22 2
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1. Expose the taxonomic data in online biodiversity data resources (such as EOL and Scratchpads) through a standard data access interface (e.g., PhyloWS).
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* One of the possible targets here might be to create an application that uses the EOL API to expose its data according to the PhyloWS standard. This would probably use mostly the classification API to EOL.
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@
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1.6
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@none
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@d1 1
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a1 1
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%META:TOPICINFO{author="HilmarLapp" date="1285771442" format="1.1" reprev="1.6" version="1.6"}%
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d35 1
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@
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1.5
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@none
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@d1 1
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a1 1
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%META:TOPICINFO{author="ArlinStoltzfus" date="1285769527" format="1.1" reprev="1.5" version="1.5"}%
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d16 4
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a19 1
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1. Further develop the [[http://www.evoio.org/wiki/Phyloreferencing_subgroup][Phyloreferencing standard]]. (compare with Mike Keesey's [[http://namesonnodes.org/ Names on Nodes]]. _Hilmar Lapp_, _Nico Cellinese_
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d26 1
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a26 1
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---++ Participants
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@
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1.4
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@none
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@d1 1
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a1 1
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%META:TOPICINFO{author="HilmarLapp" date="1285766250" format="1.1" version="1.4"}%
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d13 4
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a16 2
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1. LinkingTrees2010: Make it easy for users to put species name (or other taxonomic identifier), specimen or source identifier, and geographic coordinates into their trees. _Arlin Stoltzfus_, _Dan Rosauer_
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1. Further develop the [[http://www.evoio.org/wiki/Phyloreferencing_subgroup][Phyloreferencing standard]]. _Hilmar Lapp_, _Nico Cellinese_
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d19 1
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d22 2
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a23 4
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1. Work out *best practices for publishing a tree electronically*, via an archive such as [[http://www.treebase.org TreeBase]] or [[http://datadryad.org Dryad]], or via the semantic web (presumably using [[http://www.evolutionaryontology.org/cdao CDAO]]). At minimum, get some actual trees (+/- matrices) ready to submit. At best, draft a how-to guide for publication. _Arlin Stoltzfus_
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1. Write an XSLT to translate [[http://www.phyloxml.org phyloXML]] to [[http://www.nexml.org NeXML]], and vice versa. The good news is that XML is emerging as a standard for serializing trees and associated data. The bad news is that there are 2 different schemas.
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1. Develop a plan to integrate [[http://search.cpan.org/dist/Bio-NEXUS Bio::NEXUS]] with BioPerl or Bio::Phylo. Bio::NEXUS is a Perl API for NEXUS files with a sophisticated parser and a toolbox full of goodies. But the NEXUS IO is a limiting factor in its use. _Arlin Stoltzfus_
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---++ Participants
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d31 1
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a31 1
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| Elena Herzog | Bik-F - Biodiversity and Climate Research Center |@
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1.3
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@d1 1
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a1 1
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%META:TOPICINFO{author="ArlinStoltzfus" date="1285690069" format="1.1" reprev="1.3" version="1.3"}%
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a28 1
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| Bill Piel | Yale |
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d30 1
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@
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1.2
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@none
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@
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@d1 1
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a1 1
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%META:TOPICINFO{author="NicoCellinese" date="1285679774" format="1.1" version="1.2"}%
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d19 3
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a21 1
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d30 1
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a30 1
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| Chris Goddard | Florida Museum of Natural History, University of Florida |@
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1.1
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@none
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@
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@d1 1
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a1 1
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%META:TOPICINFO{author="HilmarLapp" date="1285624893" format="1.1" reprev="1.1" version="1.1"}%
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d28 1
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@
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