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Taxon Meeting Feb 2005

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15-17 February 2005, Santa Barbara, California, USA

Participants:

Taxonomists/Users:

  • Carl Ferrarres (all catfish species project, systematist)
  • Dan Graf (Philadelphia) bivalves, systematics
  • Mike Catarino (SB, California beetles) (Ronald persona)
    • nomenclature, phylogeographic,
  • Paul Valence Scott (Santa Barbara, marine bivalves)

SEEK Taxon Group

  • Jim Beach, Laura Downey, Nico Franz, Xianhua Liu, Bob Peet, Jessie Kennedy, Martin Graham, Robert Gales, Susan Gauch, Aimee Stewart

TaxonFunctionsAndUsability

Functions to implement (SeekTaxonTools)

Current Focus

1. TCS creation function
  • create TCS from user input data

2. Viewing in multiple ways (for scientists/policy makers too)

  • Interactive function for viewing existing matching concepts and decision making

3. Visualization Function (Small scale)

  • Filter by different attributes, View and edit info in TOS in different manners

4. Multi-classification Visualization function (Large scale down to small)

  • Several trees - see multiple matching concepts from a query within their classification trees

Backend or later

5. EML taxonomic data creation - function to create whatever EML group decides upon (EML group)
  • plugin to Morpho

6. Other Schema to TCS mapping (behind the scenes)

  • XSLT transform?

7. Merge datasets (later)

  • need input from SEEK
  • unified concepts for 2 datasets containing taxa that can be analyzed together
  • important, but later, many issues

8. Peer Review function (low priority)

  • Way to filter for UNPUBLISHED data in the TOS for particular user/editor community
  • Use visualization function

Misc Discussion

  • Only one concept for a group of similar concepts with different forms of author string, etc, should have an LSID. Algorithms should resolve concepts to longest form.

Personas

Ronald

  • Community ecologist
  • Taxonomic expertise in particular taxa in geographic region
  • keep track of community
  • use taxonomic data available to improve classification of community
  • capture info
  • datasets persist over time for monitoring and consistency in treatment
  • data compatible with similar efforts in other geo areas

User information

  • ITIS is not useful, concept and how it was developed is wrong
    • currently looking at data just at face value, names only
    • looking at old data, changes over tiime
  • Sharing, integration of data, names, is that a problem? - yes, it's our job
    • If can determine relationships b/w different uses of a name, will correct
  • Distinguish between nomenclature and usage
  • JK - how do you separate names vs meaning?
    • lots of times concepts introduced in papers, with no name attached
    • a name with no author string can be assumed to be the original concept
    • poorly annotated names cannot be resolved - won't bother
  • Need a collaborative tool to look at differences of opinion over time - literature, images, type specimens
  • Don't care to document geographic and typological? changes of concepts over time - provide the references for those who are interested in this. Perhaps JK is overestimating the importance of this historical information
  • Paradox - want all the info, synonymies, etc available, but also want a single, simple list
  • Who is going to populate this database?
    • Bob - start fresh, with new info (ask about his point here)
  • don't give too much authority to "online", this data is transient, don't confuse with archived data
  • Dan - revisions of his species are just reshuffling, table of valid species, maintain separate family, genus, species, Fritz Haas and Simpson, http://mussel-project.net, valid species assoc with an author, attached to nomen,
  • Paul would like our tools to not only handle quagmire of legacy data, but help us go forward
  • Brian Fisher - ants in Madagascar - several kilos of ants every month for 7 years - very few identifications completed. Now can objectively identify from DNA overnight.

Target users

Wed 16 Feb 2005

Providers of Data

  • P1 Taxonomists
  • P2 Aggregators
  • P3 Publishers

Users of Data

  • Amateur taxonomists
  • Scientists/ecologists
    • E1 Ecologists creating datasets
    • E2 Ecologists trying to answer broad-scale global questions
    • E3 Scientists trying to help policy makers make decisions
  • Public
  • Government decision makers

Our tasks

1. Populate database
    • harvest
    • P1/E2 help relate concepts
      • First 4 functions above
      • Tasks
        • add known concepts
        • create new concepts
        • relate existing concepts

BEAM Use Case (Call with Kate Jones)

  • Want old datasets, old treatments/classifications of bats
  • Has mappings (digital format) b/w names as in Wilson/Reeder with valid names 1993
  • some geographic ranges - difficult with past names
  • will find out what others do wrt identifying species from old data
  • Nico: want to track species naming for a group back to Linneaus (she laughs)
  • Interesting: Pipistrellus genus, red bat, Molossidae
  • Our plan:
    • Get data from Kate
    • See what is missing
    • How can we make it easy for her to enter missing links

Bats chosen as group

  • different type of migration
  • insectivors
  • ecological issues

SMS/Taxon interaction (Call with Matt)

  • Minimal interaction - SMS is client of TOS - Shawn & Thau's ant demo showed problems
    • They were modeling for ants - species is an instance of a class in OWL
    • Info to be resolved can be done with database approach, difficult to scale up
    • observations spread over thousands of species - in their approach load everything into memory
    • If they contact server for each species, lots of overhead
  • Matt thinks lots of overlap - Taxon is special case of SMS
    • Susan - Overhead dealt with by resolving datasets ahead of time and stored/indexed
    • Data integration - can't easily be done ahead of time
    • We are further along with working system than SMS, so that may hamper integration
  • Email SMS asking for OWL format for Taxon info
    • did EML to OWL
  • JK: Where do we fit in?
    • Niche modeling - search ecogrid for species occurrence data with name/species/concept overlaps
    • Looking for name - may look for something precise or loosely defined
    • Look for any number of taxa and return clustered groups of consistent taxa
    • Want non-overlapping list of concepts for modeling?
    • N-way mapping of concepts
      • for mammals of NA, mammals w/in bounding box - list
      • every item should represent single concept
      • drag each item on canvas and user decides whether to use for analysis
    • BEAM proposal that Nico sent out is good description of SEEK needs from Taxon
  • Digir data - may need private aggreement to use collector/date though not expose

Action item

  • BEAM think about scenarios useful to Taxon
      • Niche modeling case study (mostly museum data)
      • Biodiversity case study (more ecological data) - is there documentation? Not yet
      • Domain experts?
      • Maybe Rob or Aimee go to KR/SMS/BEAM mtg - 7-10 March at UC Davis
  • Engage SMS group before May
    • ex: OWL output for Taxon info - get someone with more ecological background involved as well - Mark, Deana, Matt
    • Next time we contact Shawn, ask Matt to join us
  • EML - taxonomic metadata needs to be present, but usually in the data itself
    • now, 3 distinct locations in EML, entire thing should be revisited
    • relationship b/w EML and Biological Data Profile (BDP) FGDC data standards


Other proposed topics

Tools

Tools

Tools

!

  • what? who? when?

TUESDAY (Feb 15)

  • Brief progress reports
    • Kansas – Beach
    • Napier – Kennedy
    • Kansas – Stewart
    • Chapel Hill – Peet
    • Kansas – Gauch

  • Discussion of usability and design - Downey

  • Overview of proposed tools; we have done this before, but only over the phone and not with our usability expert present.
  • III. Concept/Relationship/Status Exploration Tool
  • IV. Multi-Classification Visualization Tool (optional)

  • Proposals for Revision in the TCS/TES – Peet & Kennedy
  • Interaction with TDWG & LC – Franz & Kennedy
  • V. Concept/Relationship/Status Creation Tool
  • II. Batch-Data Import Tool (optional)

  • Case studies & datasets – Schildhauer & Franz
    • North American Mammals in general
    • Bats
    • North American plants

  • SEEK perspective; wikipedia approach – Peet
  • VI. Taxonomic Proposal & Review Tool
  • VIII. Concept Mark-Up Tool (optional)

  • Publications – Kennedy
    • QRB
    • BioScience
    • Others

  • Institutionalization – Beach
    • KU & NCEAS
    • ITIS
    • USDA
    • GBIF
    • Euro-Med

  • Future Meetings – Beach
    • Estes Park
    • TDWG
    • SEEK – November

  • Schedule and timelines



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This particular version was published on 16-Feb-2005 15:30:59 PST by KU.stewart.