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Where: San Diego, CA
Venue: San Diego Supercomputer Center
When: Oct 24-28, 2005
Weather: Historical Current
The SEEK 2005 All Hands meeting will be a forum for discussing progress on the EcoGrid, SMS, KR, Kepler, BEAM, Taxon, and EOT activities. We expect that all funded SEEK participants will attend in order to stimulate communication and collaboration across the project. We will also be inviting colleagues from the CIPRES, NESCENT, and GEON projects to discuss opportunities for collaboration with allied disciplines. The basic agenda is presented below, although this will be adjusted as we near the meeting timeframe due to the rapid advances made by the SEEK project.
- Morning arrivals from airport
- 1:00pm Introductions (Jones)
- 1:05pm Welcome to SDSC (Vijay Samalam, Executive Director of SDSC)
- 1:15pm Plenary (Jones)
- Half hour update talks on:
- SEEK overall and Kepler (Jones)
- BEAM (Pennington)
- Taxon (Kennedy (TCS), Peet (ConceptMapper), Stewart (TOS))
- Semantic Mediation (Ludaescher)
- Knowledge Representation (Schildhauer)
- EcoGrid (Jones)
- EOT (Romanello)
- 8:00am Coffee
- 8:30 - 9:30 am Invited presentations from visiting projects
- CIPRES (30 minutes)
- NESCENT (30 minutes)
- 9:30 - 10:30 Questions and Discussion on synergy and collaboration with NESCENT and CIPRES
- 10:30 - 10:45 Break
- 10:45 - 12:00 Data Integration as 2006 goal
- Merging data sets tagged with taxonomic concepts (Peet, 15 minutes presentation)
- Discuss Taxon/SMS/Kepler Integration
- How can and should these subprojects work together to solve the data integration problem?
- 1:00 pm - 5:30pm
- Breakout: Data supporting case studies (Pennington)
- EcoGrid Breakout (Jones)
- Overview of incomplete tasks (Jones)
- Reorganization of EcoGrid code, refactoring clients
- Authentication via GAMA and GSI (report and discussion)
- EcoGrid portal
- Ontology-based searching in EcoGrid
- Downey, Going Forward slides from Estes Park DONE
- 3:00 Break
- Xianhua, Concept Mapping and authoring tool: review of prototype, next steps.
- Martin, Collections visualization tool: review of prototype, next steps
- 7:00pm Group Dinner, Location TBD
- 8:00am Coffee
- 8:30 am - 12:00 pm
- Kepler-Taxon work flow discussion including Higgins, Pennington, integration of DiGIR and Kepler in use case work flow, responsibilities, where is the user interaction? TOS Actor-how would it be used in workflows? What are the usage scenarios for TOS within Kepler? How else might the TOS be embedded in Kepler?
- High-level Taxon-Kepler Interaction Design and Engineering Issues with Dan Higgins
- The 'selection problem' How do users *find* and then *select* the focal concept for searching, parameterizing an actor, with the concept one wants to work with. 1st generation, little interactivity, fill in a Kepler parameter file.
Wrap Robs current work flow into a custom actor, interactivity would come later, and maybe then passing parameter files to the actor from an application outside of GARP.
- Problem with names being mapped to more than once concept for GARP work flow
- Merging data sets with concepts that overlap, how do we integrate them once they come back
- Looping issue in GARP usecase workflow: going through list of concepts to find synonyms to identify overlaps (names with 2 or more concepts), Gales & Jones, Action: make a custom TOS actor instead of modifying web services actor (which came from GEON)
- SEEK-Taxon would like to see more possibility for an interactive UI within Kepler for TOS query and selection tasks. Alternative is to stop, restart and repeat short workflows as the 'interactivity'
- Uber-discussion: next two year vision, deliverables, roadmap, engineering dependencies, end-user tasks to be supported, data acquisition for the prototypes, decomposing Kepler engineering steps to accomplish usage scenarios. How do all the SEEK-Taxon components fit together now?
- Broader TDWG and community issues for TCS and TOS. What are their expectations? Our responsibilities? Can SEEK demonstrate the utility of TCS and TOS within the next year? What tools do we need to complete and harden for the community to buy into TCS and TOS? What can we expect from the GBIF community? Short term versus ultimate objectives.
- SEEK Use Case #2 need a taxon concept merging tool. SMS is working on merging other types of parameters across site data sets. (Get a list of species from LTER data sets, assume they are in EML, input to TOS GetBestConcept?, output unique list of merged names,
- Must mark up taxon names as concepts with GUIDs in the EML data sets first, GUIDs would be the concept IDs. Need a tool to do that, Morpho is the likely app. If no GUID in the data set, a call to TOS could match on data set taxon name and a taxon reference.
- Kepler work flow scenario:
- if the GUIDs match between data sets, we merge
- if the names from two data sets match (derived from GUIDs in the date set) in TOS, we combine them
- if concepts match in TOS
and how to identify concepts that match user's query concept 'expectation', (e.g. query TOS, return concepts to Kepler, do a EcoGrid query). How to build a UI that is meaningful to users for such tasks.
- 12:00pm - 1:00pm Lunch
- SEEK-Taxon lunch, Franz, Stewart, Gales with CIPRES Miller, Jin, Lucie): Database common ground
- 1:00 pm - 5:30 pm
- Usability thread: which users assigned to which evaluations, next steps, roadmap (Laura w/ slides)
- TOS Data acquisition roadblocks, process, role of software tools, getting data into TOS with an import tool for usability testers
- Extracting concepts from online and monographic sources, just mammals?, (Susan, Aravind)
- May Tutorial Workshop Planning, Pennington for Romanello-Katz, Beach
- 8:00am Coffee
- 8:30 am - 12:00 pm
- Knowledge Representation / Annotation Breakout
- Overview of charge (Schildhauer, 15 minutes + 15 minutes discussion)
- GrOWL ontology editor (Krivov, 15 minute presentation + 15 minute discussion)
- Status of existing ontologies (Madin, 30 minutes presentation + 30 minutes discussion)
- 10:30-10:45 Break
- Ontologies in Kepler
- Storing and Managing Ontologies in Kepler
- Support for versioning, accessing, classifying, etc.
- Central versus Distributed storage
- Conventions for Kepler/SEEK ontologies
- LSIDs for identifying ontologies
- Labels (for concept and role names) and comments
- Storing ontologies in multiple versus one file (what should go in a single file?)
- Ontology curation and population in Kepler
- Allowing users to upload/provide new ontologies to Kepler
- Supporting multiple ontologies for actor quick search
- Ontology editing w/in Kepler
- Making Ontologies convenient for Kepler users
- Support for "views" and "templates", i.e., interfaces and methods for filtering, organizing, summarizing, and visualizing Ontologies
- Tools for SEEK ontology development
- Glossary support
- Documentation
- Browsing, familiarization
- Organization; "templates" and "views" (e.g., biodiversity templates, etc.)
- Improving the Annotation Tool
- Filling in Annotations via ontology constraints
- Defining what makes a "good" annotation, and how to guide users towards these
- Improvements to the UI, including selecting ontologies and "templated" annotations
- Working exercise: building annotations
- Target case studies: ENM and Biodiversity
- Start as whole group, discuss actor/data annotation needs and differences
- Possibly break into subgroups to work on annotations
- Update of EML to accomodate Taxon Concepts (Peet, Franz, Jones)
- Future Plans: events, objectives, deliverables
- 12:00pm - 1:00pm Lunch
- 1:00 pm - 5:30 pm
- Semantic Mediation / Data Integration Breakout
- Overview of charge (Ludaescher, 15 minutes + 15 minutes discussion)
- SCIA integration in Kepler (Wang, 15 minute presentation + 30 minute discussion)
- Working exercise: data integration approaches
- Case study requirements for integration
- Simple "smart" concatenation
- Extending to more complex (and realistic) examples
- Adequacy of annotations and ontologies for integration
- Data Management support for sms
- The EML actor as entry point for data integration
- How do we deal with multiple output formats from EML?
- How do we deal with null values?
- How do we carry out integration specifications given by sms?
- For example, using "R" to load instance data from multiple voluminous data sets (e.g., 3 100MB data files) and executing data integration "recipes"
- A database-style approach? (e.g., SQL)
- What approach do we use for representing data conversions?
- Examples: unit conversions, count/area = density, rescaling/projection
- Represent conversions within ontology?
- Represent conversions as actors (searched via annotations, e.g.)
- Define a new or leverage an existing representation for conversions (Prolog, SWRL, XML syntax a la STMML, MoML attributes)
- Use potpourri approach (i.e., try to accomodate multiple mechanisms)
- Taxon Breakout
- Bob Peet leaves; Less critical items
- 1:00 PM Taxon meets SMS and KR 1 Hr. Bertram, Mark, et al.
- NESCENT workshop proposal
- ESA Booth
- 8:00am Coffee
- Plenary
- BEAM Use cases: what needs to be accomplished
- 12:00pm - Adjourn
- Travel back to home institutions, only schedule flights that leave after 2:00 pm
All SEEK participants
Invited participants form other projects
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