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









 

 

 



SMS Breakout Nov 2004

This is version 36. It is not the current version, and thus it cannot be edited.
[Back to current version]   [Restore this version]


Topics for SMS Breakout at SEEK AHM

Wednesday, November 3, 1:30 -- 5:00 (Walnut, 6th)

Moderator: Bertram Ludaescher

Agenda

  • Updates: Overview and Progress
    • Semantic Typing
  • General Discussion
    • Current issues
    • New ideas
    • Priorities
    • Goals (Short-term, 6-month, 1 year)

Notes

  • Bertram (overview)
    • requirements:
      • semantic (in addition to structural) annotation of:
        • services (actor) and
        • datasets
      • for ... discovery, WF design, ...
      • prerequisites: what does this annotation langauge have?
    • structural types
      • array of float; list of record of (int, float, string); etc.
      • e.g., relational schema type, ptolemy type
      • applies both to data and "functions" (actors)
      • essentially, useful for plumbing -- the level of the programmer, or data provider
    • semantic type
      • formal expression referencing concepts in an ontology
      • to provide a high-level, conceptual of data and services
    • data(set)
      • informal descriptions: eml style metadata, keywords, controlled vocabularly
      • formal description
        • dataset ~ concept
        • attribute (column) ~ concept
        • fine-grained:
          • query(X1, X2, ..., Xn) ~ concept expression(X1, ..., Xn)
          • Xi are "tags" or variables point to substructure
    • actors (services)
      • overall function
      • input/output signature (-> reuse framework from dataset annotation)
    • Questions
      • How do you require that certain things must be registered, e.g., that a lat lon point has an x and y coord
      • How do you handle null values in a table ... e.g., a row doesn't have an x value
      • What is the difference between an annotation langauge and a description logic
  • Shawn (details of semantic registration language)
    • simplified Antweb example
      • abundance datasets
      • d1,d2 have similar structure (geo-referenced data)
      • d3 is differently structured (co-occurence based)
      • d4 lists host/parasite relationships (inquilinism)
    • Measurement, parasitism ontology (from SWDB'04 paper)
      • Presentation
      • observation, TaxonID, Parasite, Host
      • Example: annotating d1 ...

d1(Ge,Sp,Co,Lt,Ln) ~
Observation(O), value(O,Co), context(O,S), location(S,P), LatLonPoint(P), latDeg(P,Lt), lonDeg(P,Ln), item(O,A), Abundance(A), property(A,N), SciName(N), genus(N,Ge), species(N,Se).
      • Who is creating these mappings?
      • Shawn: use of a tool

  • Discussion about interface ...
    • Can we use growl browser to do the semantic annotation mappings graphically
      • similar in style to xml mapping tools
      • what is missing:
        • multiple selection of nodes
        • difficult to get relevant stuff when you expand nodes ... many nodes you don't care about up the inheritence tree
        • just want subclass and derived properties
        • graph query language ... to filter ... decouple what you show and select
          • e.g., i am only interested in isa links, so you might want to have a power user language, to subset what you are currently showing
          • would generalize; think it would be a useful extension to these visual editors, ... "+ isa; - any"
          • expression language for power use to turn on and off certain things; incremental search that start from results
        • graphic frame logic
          • a fundamental problem with visualization formulas as opposed to logical _consequent_ of the formulas

  • Jessie: ProFormaVis -- based on Angiosperm ontology
    • structures, attributes-values
    • reads in ontology; divides the gui into structure hierarchy, selected structure description details
    • the ontology doesn't try to define what a plant is, but gives the set of things you might want to say about plants
    • trying to describe a specimen, e.g., leaf, with attribute veination pattern, and anastomosing and arcuate...
      • the veination patther is anastomosing and arcuate
    • the end to end application: the scientist refines the set of things and properties (attribute values) that are useful for a collection; a form is generated / configured based on those filters; for others to classify items to

  • follow-up list
    • growl extension selective viewing / filtered views based on some keywords / or in general queries / or just let user select nodes in the neighborhoods in the tree


Back to the Annual meeting agenda



Go to top   More info...   Attach file...
This particular version was published on 03-Nov-2004 14:00:00 PST by SDSC.bowers.