Science Environment for Ecological Knowledge
Ecoinformatics site parent site of Partnership for Biodiversity Informatics site parent site of SEEK - Home
Science Environment for Ecological Knowledge









 

 

 



Taxon Meeting Feb 2005

This is version 77. It is not the current version, and thus it cannot be edited.
[Back to current version]   [Restore this version]


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

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  • Way to filter for UNPUBLISHED data in the TOS for particular user/editor community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



Go to top   More info...   Attach file...
This particular version was published on 16-Feb-2005 15:26:33 PST by KU.stewart.