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- Taxon group
- Question has arisen about how linking is modeled in the Taxonomic Exchange Standard
- Reworking protype implementation fo name service
- Thau creating user authentication module (need to discuss with Tekell and EcoGrid ASAP)
- Peer review module being developed
- Kepler group
- UI design discussions ramping up
- Presenting Kepler and SMS stuff at SSDBM in Greece (Berkley/Bowers)
- New nightly build/test system in development
- EOT group
- New website authentication working, just about ready to deploy
- Organizing training workshops for Fall
- SMS/KR group
- New Java API being developed for accessing Sparrow from Kepler
- Working on Growl UI and capabilities
- Working on ontology for biodiversity indices
- Working on paper regarding the ant data prototype
- EcoGrid group
- New resultset implemented for Metacat, DiGIR, SRB
- Working on data query design and interfaces
- BEAM group
- Putting data in SRB for later access through EcoGrid
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
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
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
Completed tasks/bugs fixed
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.
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
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.
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
Completed Tasks/ Bugs Fixed:
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.
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)
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
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.
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
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
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:
You can see the status reports for other time periods as well.
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