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KRSMS March 2007

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KR/SMS Annotation & Domain-Extension Ontology Meeting

Meeting Date and Location

  • Where: Room 201 on the second floor of NCEAS, Santa Barbara, California (805-892-2500)
  • Hotel: Holiday Inn, Santa Barbara
    • From the airport, you may book SuperRide Airport Shuttle (805-683-9636) or take a cab. A cab is $30-$35 one way (I think). If you have any problems, call Josh on 805-452-7017.
  • When: April Wednesday 4 to Friday 6, 2007 -- Arriving on Tuesday 3
  • Reimbursements: http://lternet-183.lternet.edu/doc_archive/forms/, forms will be given out on the first day.

The meeting will begin promptly at 8:00 am in the 2nd floor conference room at NCEAS in the Balboa Building, 735 State Street.

Meeting Goals

Define domain extensions ontologies based on select corpus of data sets

  • The first goal of the meeting will be to extract terms and concepts from a corpus of data sets ranging in their similarities and differences.
  • An OBOE extension ontology will be built from these terms and concepts

Annotate corpus of data sets based on OBOE

  • The second goal will be to annotate the corpus of data sets using the new extension ontology.
  • We will then hopefully demonstrate (or at least discuss) the process of discoverying and integrating these data sets based on their annotations with extension ontology terms.

Schedule

Wednesday
"Extension Ontologies"
Thursday
"Semantic Annotation"
Friday
"Directions and Publications"
8:00 Coffee Coffee Coffee
8:15 Presentations of recent KR work and discussion of meeting agenda Annotate data sets using extension ontology and temporary annotation tool Discussion about directions/responsibilities before end of SEEK project
10:15 Break Break Break
10:30 Divide data corpus among participants and start extracting terms and concepts Annotate data sets (Continued) Discussion about publishing KR work
12:30 Lunch Lunch Lunch
1:30 Contiue extracting terms and concepts Review of data set annotations and discussion about leveraging annotations for data discovery and integration Departures
3:15 Break Break
3:30 Build terms and concepts into an extension ontology in Protege for tomorrow's annotation tasks Discussion about leveraging annotations (Continued)
5:00 Finish Finish

Target Data sets

  • Comment (JSM): We will probably want to cut down on the number of data sets. Ideally we want to cover as many different types of data sets as possible, and also have several examples of similar/overlapping data sets which can be used for testing/discussion of semantic utilies (e.g., data merging).
Data/MetadataPublisherComment
PLT-GCEM-0511aGCEPlant Ecology: Biomass from Shoot Height and Flowering Status
PLT-GCEM-0511bGCEPlant Ecology: Biomass from Shoot Height and Flowering Status (w/ Biomass)
PLT-GCED-0409GCEPlant Ecology: Community Response to Fertilization
PLT-GCET-0608GCEPlant Ecology: Plant Richness Survey
INS-GCEM-0511GCETerrestrial Insect Ecology: Grasshopper Abundance and Species Diversity
INV-GCEM-0511GCEAquatic Invertebrate Ecology: Crab Abundance based on Crab Hole Counts
INV-GCEM-0501a1GCEAquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Abundance
INV-GCEM-0501a2GCEAquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Size Distributions
FNG-GCEM-0401GCEFungal Productivity: Ergosterol Content and Ascospore Release Rates
BCT-GCEM-0511a2GCEBacterial Productivity: Surface Water Bacterial Productivity
PHP-GCEM-0511aGCEPhytoplankton Productivity: Surface Water Phytoplankton Productivity
ALG-GCED-0304aGCEAlgal Productivity: Benthic Chlorophyll Concentrations and Gross Oxygenic Photosynthesis Rates
ALG-GCED-0304cGCEAlgal Productivity: Benthic Chlorophyll, Density, Porosity, Organic Content Concentrations, and Gross Oxygenic Photosynthesis Rates
MET-GCEM-0508aGCEMeteorology: Annual Summaries of Daily Air Temperature and Precipitation
HYD-GCES-0508aGCEHydrography: Annual Summaries of Daily Averaged River Discharge
HYD-GCES-0508bGCEHydrography: Monthly Mean Water Levels
PHY-GCEM-0612aGCEContinuous Salinity, Temperature and Depth
PHY-GCEM-0406a1GCEPhysical Oceanography: Bin-Averaged CTD Profiles
PHY-GCEM-0406a2GCEPhysical Oceanography: CTD, PAR, Oxygen, and Chlorophyll Profiles
GEL-GCEM-0508aGCEGeology: Soil Characteristics
GEL-GCEM-0508bGCEGeology: Soil Surface Elevation
GEL-GCEM-0508cGCEGeology: Soil Accretion
ORG-GCEM-0511aGCEOrganic Matter/Decomposition: Surface Water Dissolved Organic Carbon Concentrations
ORG-GCEM-0508aGCEOrganic Matter/Decomposition: Soil temperature and respiration
ORG-GCEM-0508bGCEOrganic Matter/Decomposition: Rates of Decompisition and Root In-Growth
ORG-GCEM-0101GCEOrganic Matter/Decomposition: Ash-Free Dry Weight Analysis for Soil Samples
CHM-GCED-0303aGCEChemistry: Surface Water Samples for Total Dissolved Inorganic Carbon, Total Alkalinity, and pH
POR-GCED-0210GCEPore-water Chemistry: Porewater Nutrients, Dissolved Organics, Redox Species, and Gasses in Estuarine Intertidal Sediments
NUT-GCEM-0210GCEGeneral Nutrient Chemistry: Water Quality Monitoring
NUT-GCEM-0206GCEGeneral Nutrient Chemistry: Water Column Particulate Carbon and Nitrogen Concentrations
2002lgcoverARCRelative percent cover was measured in moist acidic and moist non-acidic tundra
2002gsttbmARCAbove ground plant and below ground stem biomass in acidic tussock tundra
2001lgshttcnARCPercent carbon and percent nitrogen of above ground plant and belowground stem biomass samples in moist acidic and moist non-acidic tundra
2001gswsbm_nARCBiomass, nitrogen and carbon of plants in wet sedge tundra
2000gslaARCLeaf area for select species was measured in arctic tundra
1999SHretransARCFoliar and litter nutrients and retranslocation efficiencies for dominant species on moist acidic and non-acidic tundra
dataset269CAPHistoric Landuse
dataset276CAPHuman
dataset43CAPTransect Bird Survey with Data Synthesis]
dataset39CAPLichen Resurvey with Heavy Metal Analysis
pisco_subtidal.12.4PISCOSubtidal: Community Surveys: Fish Survey
pisco_recruitment.27.1PISCOIntertidal: Recruitment Monitoring: Recruitment collectors and Rock Clearings

Notes:

  • The majority of types of GCE Web-accessible datasets are represented above
  • Might consider using "derived" data from Worm et al study (Impacts of Biodiversity Loss on Ocean Ecosystem Services, Science, Nov 3, 2006); see here for supporting material containing data and references.

Annotation Tool

  • A simple tool has been built to record the annotation of data sets during the meeting. The tool can be found here, but will not be operating when the temporary server is sleeping.

Domain Ontology, Thesaurus, and Glossary Examples, Related Work

Ontologies

Thesauri

Glossaries

Participants

  • Shawn Bowers, UC Davis
  • Josh Madin, UC Santa Barbara
  • Deana Pennington, Univ. of New Mexico
  • Mark Schildhauer, UC Santa Barbara
  • ...


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This particular version was published on 28-Mar-2007 16:28:40 PDT by uid=madin,o=NCEAS.