Status Report 12 July 2004

Summary

• KR/SMS Group
• Shawn is writing a new manual for the measurement ontology that Rich is building
• Shawn points out the need for us to really develop a well-thought out approach to handling identifiers throughout SEEK

• Kepler group
• Working on ontology-based browsing in Kepler to make it easier to find data and actors
• Some new actors for biodiversity calculations and running 'R' scripts are available in Kepler
• Working on data query UI design and implementing data query functions for EcoGrid

• EcoGrid group
• Loading new data into SRB, working on put interface for writing data
• Jing is working on data query and subsetting interface for EcoGrid
• Steve is starting to design and implement a web interface for EcoGrid for the website

• Annual Report
• The annual report to NSF is due. We will need a complete list of SEEK-sponsored publications from all participants. I will send a reminder email. Also, group leaders will be asked to write a summary of this year's progress (Beach, Jones, Michener, Rajasekar, Schildhauer, Ludaescher) for inclusion in the report using NSF's required format (see last year's report).

Individual reports

Chad Berkley

• fixed eml parser for eml 2.0.1 release (no bug number)
• reinstalled eml parser on ecoinfo
• tested eml 2.0.1 validity with parser

Current Work and Bugs

• working on bug 1546, integrating sparrow into kepler for use in organizing the actor library
• trying to determine what we need to do to moml to allow us to encapsulate this information.
• conference call with matt, shawn, mark and dan about this.
• created screen shots for discussion about the ontological interface in kepler
• working on getting eml 2.0.1 released. reviewed schemas. checked the eml parser for 2.0.1 compliance. found one bug and fixed it. also updated the parser so the namespaces are no longer hardcoded into the java code.

Significant issues

• None

Dan Higgins

• Checked in an interactive Command Line actor that allows one to interactively issues commands to systems like 'R' that can operate with command line I/O through standard streams.

Current Work and Bugs:

• Working on workflow example applets for addition to Kepler web site; also investigating use of WebStart for distribution of example workflows
• Continuing work on various R actor(s)
• Working on actor which calculates a variety of Biodiversity indices

Significant Issues

• None

Rod Spears

• Working on converting prototype to production code for Advanced version of the Query Builder
• Almost completed the "where" clause builder for the Advanced tab
• Last week I attended the GRIDs conference in Madison.
• Most significant thing was that they have finally gotten the message that your average scientist cannot easily deal with certificate based security.
• The Earth Web project wrote some code on top of Globus and MyProxy to enable scientist to sign up for a user name and password that behind the scenes translates into a certificate that is managed by MyProxy. Then whenever they submit jobs or makes requests, the certs are obtained and the everything happens seamlessly.
• This part of the project is being broken out and made "generic" for all consumers. This will be the perfect solution for us.
• Was out two days last week.

• Continued on Bug 1595 - Create Advance Query Builder UI
• Finish Trip Report for Madison

Significant Issues

• None

Shawn Bowers

• Didn't complete or fix anything.

Current Work and Bugs

• Started working on a manual for the main components of the ontology Rich has been developing. This involved trying to clearly understand what is in the ontology (one of my main goals of writing the manual), discussing the contents with Rich, and providing feedback, etc. I am writing the manual using the new wiki. I think in doing this, we have come up with a more robust notion of observations / measurement, which is at the heart of the ontology. My goal is to keep plugging away at this "on the side."
• We are also experimenting with the use of higher-level modeling constructs to make it easier for extending the ontology by, e.g., domain scientists or metadata experts; allowing them to move to a higher semantic level than direct owl syntax. The jury is still out on the approach, though.
• Worked on a tool to convert owl dl to sparrow. This tool is taking a bit longer than expected; mainly due to some problems/complexities in owl itself and the tools that exist for working with owl. Once this tool is finished, hopefully this week, the rest of the sparrow api should go very quickly.
• Helping to arrange a three day meeting in San Diego for the KR/SMS and BEAM group for September.
• Looking into the use of binding patterns to help specify common transformations between otherwise incompatible concepts within an ontology. For example, for converting between UTM and Lat/Lon coordinates and so on.
• Participated in a phone meeting concerning the interface design for ontology-based actor browsing in Kepler.
• Started looking closely at the biodiversity datasets and metadata.

Significant issues

• I think an issue that is surfacing is the need for identifiers in Kepler for actors, workflows, and datasets. Some questions that come up in this regard are: Who is responsible for assigning and maintaining identifiers? What identifier scheme should be used and how? Given an identifier, how do we locate the associated actor, workflow, or dataset? There are probably more issues than these.
• Another issue, that as far as I can tell has been shelved, is how to explicitly represent the input/output port types of actors used in Ptolemy/Kepler. Is someone working on this that is part of the Kepler group? What is the progress? (I think Efrat has been looking at somewhat similar issues, but more for understanding how actors are connected within a workflow.)

Nico Franz

• First draft of concept relationship paper sent to co-author (Peet).

• Still finishing up certain sections of the paper. Will inquire about placing it on the list of talks presented at TDWG 2004.

Significant Issues

• Manuscript will soon be distributed more widely. Issues that came up during a recent conference call (with KU/Napier, etc.) will be worked mostly into another paper (with Thau) about GUIDs, which I'll start once the current project is ready for submission.

Rich WIlliams

• None

Current Work and Bugs

• Continued ontology design discussion with Shawn, made some changes to MeasurementBase.owl
• Continued work debugging code to save OWL file from GrOWL

Significant issues

• None

Jenny Wang

• Correctly handle union types of matches from the GUI of our schema matching tool.
• Partially implemented the abstract schema interface and devoloped a translator that imports DTDs into the schema matching tool as Abstract Schemas. But the "OR" case in DTDs is not handled in an appropriate way yet. Also it may require changes to the abstract schema interface when going further on the design and implementation of schema morphisms.

Current Work and Bugs:

• Work on 2 paper drafts
• Fix more bugs of the tool:
• Modify the GUI to include an arrow panel for indicating where it is working on,
• correctly handle union types of matches identified during matching process,
• consistently highlight where user attention is needed
• Implement abstract schemas and abstract schema morphisms to make the tool more general: develope another translator for importing XML Schemas into the tool as Abstract Schemas, and design a schema morphism interface.

Significant Issues:

• The implementation of abstract schemas and schema morphisms will help the tool handle constraints to some extent.

Steve Tekell

• Fixed and in Prod. : Bug 1616 - RSS feed shows incorrect URL
• Converting old wiki content

• Eco Grid Web Interface - first, figure out what this is

Significant Issues

• None

Robert Gales

• None

Current Work and Bugs:

• Bug 1618 - Fix rank representation in DB to support the schema and entry of taxonomic concepts

Significant Issues

• None

Jing Tao

• None

Current Work and Bugs:

• Working on data access rules in ecogrid metacat.

Significant Issues

• None

Bing Zhu

• Developed a Perl script to upload 'whywhere' data along with their metadata into SRB. Whywhere data was successfully uploaded into SRB storage place. This completed the initial task for SEEK bug 1596.
• Developed an initial implementation within SRB for Niche Modeling to retrieve partial images. With this implementation, Niche Modeling applications successfully get partial images and Metadata in a distributed environment.

Current Work and Bugs:

• continue work on an Ecogrid solution for Niche Modeling. The prospective approach will have a generic approach which can be applied to other applications who request partial data transfer. (Bug 1596)

Significant Issues:

• The initial prototype designed by Raja and Bing for Ecogrid will extend the SRB capability into Ecogrid to allow partial data retrieval within Ecogrid.

Aimee Stewart

Completed tasks/bugs fixed

• Finished initial work on multi-threaded parser (bug 1617) for taxonomic exchange schema. This encompasses a reference parser for parsing Vouchers (bug 1620) and Publications (bug 1619). Testing still needs to be completed on these objects though, so the bugs are not resolved yet. Made other modifications to concept objects to handle additional fields in the schema.

Current Work and Bugs

• Working on the API for enterProviderData (bug 1576). The next step in this process will be to thoroughly test the parsers and handlers with our available data. Since the schema is not yet in final form, I will concentrate on testing elements of the TES parsing for which we have data.

Significant issues

• none

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