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









 

 

 



Status Report 14 June 2004

This is version 8. It is not the current version, and thus it cannot be edited.
[Back to current version]   [Restore this version]


Summary

Collecting individual reports, will summarize on 15 June

Individual reports

Rod Spears

Completed Tasks/ Bugs Fixed:

  • Bug 1594 - Impl revised Resultset XSD for all 3 platforms
  • Spent time thinking about the registry and DiGIR and how DiGIR will need to register multiple times. Each time for a different type of data, thus specifying the portal URL and the Consecptual schema namespace

Current Work and Bugs:

  • Start on Bug 1595 - Create Advance Query Builder UI
    • Initial prototyping to understand what parts of Swing can be used directly and what part may need to be extended. Next I should have a detailed summary

Significant Issues

  • None

Xianhua Liu

Completed Tasks/ Bugs Fixed:

  • Finished design of Auto-Manager: auto-email, auto-assignment and auto-decision
  • Implemented auto-email function

Current Work and Bugs:

  • developing Auto-Manager for Concept Review System to automatically complete some system administration tasks, such as sending emails,assigning proposals to peer-viewers.

Significant Issues

  • None

Sergui Krivov

Completed tasks/bugs fixed

  • developed toolbox pane (no icons yet) and enabled raw visual editing of simple owl constructs
  • wrote a small section of growl paper

Current Work and Bug

  • functions for editing relations and links
    • owl-dl compliance resolution for graphic primitives
  • enable node property editing
  • one more section for growl paper
Significant issues
  • Should we support owl-full? All who responded seems favor support for owl-dl only

Rich WIlliams

Completed tasks/bugs fixed

  • None

Current Work and Bugs

  • Developing an ontology for biodiversity indices, extending existing ontologies to accommodate this, and adding instances for the biodiversity indices and related concepts. This includes a general model for properties computed in terms of other properties.
  • Review/comment on paper that Shawn is lead author on, about the inter-ant parasitism semantic mediation prototype.
  • GrOWL editor: updating of the OWL model when the user edits the displayed graph

3) Significant issues

  • I looked into existing work on the semantics of mathematics, potentially for use when defining quantities in terms of other measured quantities. A useful initiative is www.openmath.org, an emerging standard for representing the semantics of mathematical objects.

Jing Tao

Completed Tasks/ Bugs Fixed:
  • Finished the collaboration and class diagram draft design for bug 1584 and 1586
  • Installed and evaluated both windows and linux SAS as sql engine
  • Resinstalled and tested Metacat ecogrid server in my local machine after Rod changed the code according to the change of resultset

Current Work and Bugs:

  • Continue to find a good sql engine for data query
  • Probably start to code after finding a good sql engine
  • Fix some bugs in ecogrid client after the resultset change

Significant Issues

  • None

Aimee Stewart

Completed tasks/bugs fixed
  • Bug 1602 - Moved the Taxonomic Object Service SOAP service to http://seek.ittc.ku.edu:9080/TaxObjServ . The WSDL is available from the link there (http://seek.ittc.ku.edu:9080/TaxObjServ/services/TaxonomicObjectService?wsdl).

Current Work and Bugs

  • Working on Bug 1576 - Implement EnterProviderData. This includes modifying the architecture somewhat to separate database modification methods from database query methods into separate classes. Also adding a database connection class which will be used by both DB classes.
  • Described (in an email to Seek-Taxon) the difficulties we are encountering with the assumption that a GUID-bearing Taxonomic Concept is defined by the current Taxon Exchange Schema.

Significant issues

  • Taxon Exchange Schema and GUIDs described in seek-taxon email. This may warrant a Seek-Taxon teleconference, preferably by polycom.

Chad Berkley

Completed tasks/bugs fixed
  • Worked on the Kepler poster for SSDBM
  • Worked on nightly build systems for kepler (bug 1588)
  • Began preperation to go to SSDBM

Current Work and Bugs

  • Hopefully get a nightly build system working
  • Leave for Greece

Significant issues

  • none

Nico Franz

Completed Tasks/ Bugs Fixed:

  • None, really.

Current Work and Bugs:

  • Since SEEK Edinburgh, has been writing on a substantial manuscript (with R. Peet as co-author) for the journal Taxon, which deals with concepts and relationships among them.
  • The manuscript is about half-way completed; will take another 2-4 weeks to be ready for internal review.
  • This work is seen as a precursor to the GUID development, i.e. it's trying to answer the question when/what (something) should get a GUID.

Significant Issues

  • There's been a bit of a quiet in SEEK Taxon after the Edinburgh meetings, but apparently that just ended today, with KU sending out an update/request.
  • As the TDWG New Zealand planning is moving ahead, would like to make sure that the concept/relation paper is part of our SEEK Taxon presentation package there.

Deana Pennington

Completed tasks/bugs fixed
  • completed specs for IPCC climate data processing as kepler design workflow and accompanying document
  • completed specs for sampling actor
  • sent notes on Kepler (user feedback) to Rod
  • sent GARP output schema to Shawn

Current Work and Bugs

  • planning for new BEAM working group on diversity/productivity
  • getting all relevant data for ecological niche modeling project into the SRB
  • thinking about user interface design and testing approaches

Significant issues

  • will have to create EML for all of the IPCC data
  • need a decision on the useability engineer slot (LOTS of discussion on the lists about the UI & testing)

Samantha Romanello

Completed tasks and Bugs fixed

  • Finalized agenda for upcoming Data Management Tools Workshop
  • Finalized GIS agenda for RCN training

Current Work and Bugs

  • Website
    • Working on copy for education section of website; attaching links to presentations of former and current trainings.
  • Trainings
    • Need to finalize ecoinformatics agenda for RCN training October 18- 30:
    • Composing email for Monthly SEEK Seminar

  • Conferences and Events
    • In contact with Sandy re moprho tutorial for upcoming ESA August 1 - 7: Workshop; Evening Session
    • Working on poster presentation for ESA

Significant issues

  • Finalize participant and trainer numbers for September KNB Data Management Tools training -- conference call scheduled for June 22.
  • Finalize ecoinformatics agenda and logistics for RCN training October 18- 30

Jenny Wang

Completed Tasks/ Bugs Fixed:
  • Analyzed our schema matching tool user interface design
  • Fixed one of the bugs for improving its UI: the windows for 2 schema trees were changed to be individually scrollable in order to be able to visually handle the mappings between very large schemas

Current Work and Bugs:

  • Work on 2 paper drafts
  • Fix more bugs of the tool:
    • make details of nodes accessible from the GUI,
    • look for solutions for the conflicted requirements on java version from running multiple threads on windows and the XQuery engine with Kepler.

Significant Issues

  • The second bug is related to making easier connection of our tool with Kepler.

Dave Thau

Completed tasks/bugs fixed

  • Got local version of the taxon server set up in my IDE and running on my home machine.

Current Work and Bugs

  • Working on bug #1597 - the intial user management for the taxon server. Wrote initial tests and some of the code for logging in / logging out and editing user information. Probably will finish this part by Wednesday.
  • Working on paper with Shawn Bowers for the Semantic Web and Databases conference.

Significant issues

  • None.

Shawn Bowers

Completed tasks/bugs fixed
  • Worked mainly on Bug 1592 "describe Sparrow toolkit interface". In particular, defined a preliminary draft of a Java API for accessing ontological information via Sparrow to support Bug 1546 "dynamic data and actor views using ontologies". I also defined a simple extension to the API (set of derived classes) for Bug 1546, which would take a single concept from an ontology and return a tree-structure representing the appropriate Kepler tree-view for browsing (that is, the result is a data structure that could be used to populate a tree-view, however that would work). Still need to add to the API to fully support bug 1546, since it requires access to information about actors.I'll "release" a stable version of the APIs soon, as Javadocs and UML diagrams. Want to prototype it first.
  • Worked on a paper with Dave Thau and Rich Williams to describe the Ant Parasitism SMS prototype. It is due on the 21st.

Current Work and Bugs

  • Need to start working on implementing the API, which means writing the java code and connecting it to the Sparrow code (this work is situated in bug 1592 and 1546).
  • Extend API (see 1 above).
  • Need to finish writing the paper
  • Need to prepare slides for SSDBM paper -- I leave Friday.

Significant issues

  • none

Robert Gales

Completed Tasks/ Bugs Fixed:

  • Split the taxonomic object service into two interfaces, ITOSQueryable for handling queries to the Taxon cache and ITOSModifiable for adding information to the Taxon cache
  • Created a facade object CTOSFacade that implements both interfaces and
exposes the taxonomic object service through SOAP.
  • Moved the previous CMainTOS to CTOSQueryEngine implementing the ITOSQueryable interface and created the stub class CTOSModEngine implementing the ITOSModifiable interface.
  • Implemented the CDetailedName class for handling the complex atomized names
  • Moved all classes that are parts of a concept from the tree package to the concept package.

Current Work and Bugs

  • Bug 1577 - Implement AddRelationship
  • Bug 1603 - Implement AddConcept
  • Bug 1604 - Convert ITIS database dump to TES

Significant Issues:

  • None

Other Status Reports

You can see the status reports for other time periods as well.



Go to top   More info...   Attach file...
This particular version was published on 14-Jun-2004 18:29:22 PDT by NCEAS.jones.