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SEEK Taxon Telecon Notes_17_Apr_2003

Notes from SEEK-Taxon WG Teleconference, 17 April 2003

Version History

  • DV, created 4-17-2003
  • MJ, edited 4-17-2003
  • JB, edited 4-18-2003
  • RP, edited 4-29-2003
  • JK, edited 5-2-2003


Be sure to delete your name and replace "NO ONE" when you are done.

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  • Jim Beach
  • Jessie Kennedy
  • Bob Peet
  • Matt Jones
  • Aimee Stewart
  • Dave Vieglais
  • Excused: Paula Huddleston, Susan Gauch

Next telecon May 6 2003, 10:00 CDT, Bob Peet will set up

To join the conference call dial: 919-962-2730 !

Beach reviewed status of planning of WG activities from Jan 30 WG meeting and Albuquerque PIs meeting (one breakout), also current HR plan. (As an aside discussed KU role in web site activities (Downie), Beach will coord with Michener about UNM SEEK webmaster and KU's role.)

In discussion of WG deliverables points made:

  • Instead of wholly new development, we might decide to focus on specifying and building interfaces between existing systems. JK
  • Several international projects working in this area, this WG has outreach responsibilities to be able to attain generality
  • We need to determine SEEK's priorities first, then decide how they map to other models and approaches that are out there
  • Interest in several existing projects, including Remsen's UBIO project, everyone should come to SD with basic understanding of some or all of these major projects. RP


Two types of deliverables from the Taxon working group:

  1. Software (formal requirements, models and services might also be deliverables)
  2. Publications


  • Determine the desirability of undertaking software development on several fronts simultaneously to take advantage of existing project expertise.
  • Should software development be staged, with deliverables (perhaps terminal) at the end of each stage. E.g. should we pursue an IR approach to dumb concepts as a first approximation, inferring concept and classification semantics and then, independently (and later) pursue a semantic approach?
  • Critical to know what is the target audience and use cases for each or other software approaches. Are we building an architecture for 10-20-30 scientist users in 2006? Are we trying to bring in and leverage the much broader global interest in classifications and taxonomy and provide services for disambiguating taxonomic concepts for other research uses besides data set retrieval from SEEK data providers? What are the global research needs? How do we make the SEEK architecture relevant to the broader research and conservation communities? JB

    • Matt: Prototype/s should interoperate between two information sources for generality.


  • Focus on developing a review paper on classification concept models -- instead of informal white paper style review, make it something more formal that can be published? What is the point of view? SEEK infrastructure perspective provides a different user view of the existing taxonomic resources.

Development Process

Initially a very short term view focussed on dermining which systems, approaches, tools, data structures, etc are most appropriate for the SEEK goals. Problem is determining what our goals are right now.

Potential paths:

  1. Software tools
  2. Schema mapping
  3. Interface tools

Action Items Before theSan Diego All Hands Meeting, May 2003

  • Candidate list of deliverables for SDO discussion
  • Modify list of deliverables in the MeetingJan30_2003 January meeting page? page
  • Flesh out the use cases MeetingJan30_2003 January meeting page?
  • Identify targets (tools, systems, databases, data structures) for review
  • Retrieve hardcopies of relevant literature for the review targets
  • Review some of the tools and systems
  • Jim: agenda for meeting (UNDERWAY See Below)
  • Bob: create and circulate job ads for 2 postdocs

Draft description:

Postdoctoral opportunities in Biological Classification and Nomenclature.

We seek two postdoctoral fellows to participate in a large, NSF and Mellon-funded ITR Project directed at development of a technology framework for data discovery, integration, and visualization for biodiversity research. The persons in these positions will be involved specifically in development of standards, methods, and tools for representing biological nomenclature and classification information. Even though the rules of taxonomy are quite specific, taxonomic understanding is dynamic, leading to constant changes in the taxonomic entities, the names applied to those entities, and their phylogenetic relationships. Consequently, taxonomic concepts and the application of names to those concepts vary through time and with the authority employed. Effective integration of data from diverse sources requires that the multiple and overlaping taxonomic concepts be tracked, as well as the multiple names that have been applied to them. We envision that the need for data integration will reshape the way organisms are reported in biodiversity and ecological data and publications, and the way biological taxonomists and ecologists conduct, report, and disseminate their research. Developing this link between ecology, systematics, and informatics is crucial to developing effective and useful ecological informatics tools. The postdocs will work directly with researchers at NCEAS and the University of North Carolina, and will be expected to locate at one of these institutions. Strong background in both biological systematics and computer and database skills is desirable. Send applications and at least two letters of recommendations by May 26 to Robert K. Peet, Dept. of Biology, CB#3280, University of North Carolina, Chapel Hill, NC 27599-3280, 919-962-6942,

SDO Meeting Agenda

Outline of agenda for SDO meeting

  1. Review the use cases -> MeetingJan30_2003 January meeting page? generate a finalized list that can be distributed to others in the SEEK project
  2. Go through publications etc for the review paper
  3. Revisit the functional requirements
  4. Decide on staging of deliverables
  5. What are overall objectives/priorities, use to help set short-term goals
  6. Have 1/2 hr discussion on scope of each of our deliverables

Tuesday May 13


  • Review Draft Use Cases from Jan 30 notes, WITH ADDS from WG members before the meeting.
  • Quickly review current approaches and literature on classification concept mapping and retreival
    • Everyone Please indicate here now, which classification concept model/system/software review materials you will bring to the meeting.
      • Beach: Beach, Pramanik and Beaman model for classification concepts (Taxon), James Ytow's paper
      • Kennedy: Prometheus, Perobase, Spice model, contribute to Behrendsohn's and Ytow's models.
      • who wants to do Other GBIF name approaches?
      • Peet: VegBank model and relatioinship to NatureServe's Biotics model and Berendsohn's model
  • Overview of functional requirements of SEEK taxon architecture, five year vision, what SEEK needs, what everyone else needs, how much overlap?

Wednesday May 14


  • Go through literature, mini-reviews (continued, if needed)
  • From UPDATED Use Case list, identify FR and primary deliverables (PD) for Year 1 objectives
  • Identify FR and PD for Year 3 objectives
  • Identify FR and PD for Year 5 objectives


  • Collaboration relationships with other projects:
    • Our own
      • software overlap, e.g. Prometheus, ITIS, Vegbank, BIOTICS
      • requirements overlap for services, data, objectives, etc.
      • data overlap e.g. ITIS, Specify Project will be a DIGIR source of multiple classifications of collection catalogs
    • Other commuity projects, e.g.
      • GBIF
    • Octopus
  • Human resources
    • What can we realistically going to accomplish with:
      • 1 professional programmer KU
      • 2 biological postdocs UNC (and a kidnapped basketball coach)
      • 1 informatics postdoc KU
      • 2-3 part time beginning graduate students
      • 1 part time developer/grad student Napier
      • 1/12 - 1/4 year allocations from co-PIs
      • Where can we beg, borrow, steal additional resources? Should we 'merge' some/all activities with other projects? Where are the actual connections?

Thursday May 15


  • Briefly review any unresolved issues with Use Cases, Functional Requirements, Primary Delieverables, Staging, Staffing
  • Begin development of project deliverables, software and publications


  • Development activities continued
  • future planning, meetings (Seek, side and outreach), new hires, next steps

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This page last changed on 28-Jun-2004 10:04:44 PDT by LTER.stekell.