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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 Thursday Friday
8:00 Coffee Coffee Coffee
8:15 Meeting agenda and goals
Select dataset corpus
continued Discussion about directions/responsibilities before end of SEEK project
10:15 Break Break Break
10:30 Current OBOE status
Current extension ontologies (units, entities, characteristics)
Top-level organization for extensions
continued Discussion about publishing KR work
12:30 Lunch Lunch Lunch
1:30 Select datasets to annotate
Identify terms and concepts
Refine extensions
Define annotation
continued Departures
3:15 Break Break
3:30 continued Review of data set annotations and discussion about leveraging annotations for data discovery and integration
5:00 Finish Finish

Target Data sets

  • Comment (JSM): We probably want to cut down on the number of data sets in the corpus. I think that ideally we should attempt to cover as many different data set types as possible, but also have several examples of similar/overlapping data sets which can be used for testing/discussion of semantic utilies (e.g., data merging).
Data/Metadata StatusComment
GCE
PLT-GCEM-0511aYGCEPlant Ecology: Biomass from Shoot Height and Flowering Status
PLT-GCEM-0511bYGCEPlant Ecology: Biomass from Shoot Height and Flowering Status (w/ Biomass)
PLT-GCED-0409YGCEPlant Ecology: Community Response to Fertilization
PLT-GCET-0608YGCEPlant Ecology: Plant Richness Survey
INS-GCEM-0511YGCETerrestrial Insect Ecology: Grasshopper Abundance and Species Diversity
INV-GCEM-0511YGCEAquatic Invertebrate Ecology: Crab Abundance based on Crab Hole Counts
INV-GCEM-0501a1YGCEAquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Abundance
INV-GCEM-0501a2YGCEAquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Size Distributions
FNG-GCEM-0401HGCEFungal Productivity: Ergosterol Content and Ascospore Release Rates
BCT-GCEM-0511a2HGCEBacterial Productivity: Surface Water Bacterial Productivity
PHP-GCEM-0511aHGCEPhytoplankton Productivity: Surface Water Phytoplankton Productivity
ALG-GCED-0304aYGCEAlgal Productivity: Benthic Chlorophyll Concentrations and Gross Oxygenic Photosynthesis Rates
ALG-GCED-0304cHGCEAlgal Productivity: Benthic Chlorophyll, Density, Porosity, Organic Content Concentrations, and Gross Oxygenic Photosynthesis Rates
MET-GCEM-0508aYGCEMeteorology: Annual Summaries of Daily Air Temperature and Precipitation
HYD-GCES-0508aYGCEHydrography: Annual Summaries of Daily Averaged River Discharge
HYD-GCES-0508bYGCEHydrography: Monthly Mean Water Levels
PHY-GCEM-0612aYGCEContinuous Salinity, Temperature and Depth
PHY-GCEM-0406a1HGCEPhysical Oceanography: Bin-Averaged CTD Profiles
PHY-GCEM-0406a2HGCEPhysical Oceanography: CTD, PAR, Oxygen, and Chlorophyll Profiles
GEL-GCEM-0508aHGCEGeology: Soil Characteristics
GEL-GCEM-0508bHGCEGeology: Soil Surface Elevation
GEL-GCEM-0508cYGCEGeology: Soil Accretion
ORG-GCEM-0511aHGCEOrganic Matter/Decomposition: Surface Water Dissolved Organic Carbon Concentrations
ORG-GCEM-0508aYGCEOrganic Matter/Decomposition: Soil temperature and respiration
ORG-GCEM-0508bHGCEOrganic Matter/Decomposition: Rates of Decompisition and Root In-Growth
ORG-GCEM-0101YGCEOrganic Matter/Decomposition: Ash-Free Dry Weight Analysis for Soil Samples
CHM-GCED-0303aYGCEChemistry: Surface Water Samples for Total Dissolved Inorganic Carbon, Total Alkalinity, and pH
POR-GCED-0210HGCEPore-water Chemistry: Porewater Nutrients, Dissolved Organics, Redox Species, and Gasses in Estuarine Intertidal Sediments
NUT-GCEM-0210YGCEGeneral Nutrient Chemistry: Water Quality Monitoring
NUT-GCEM-0206HGCEGeneral Nutrient Chemistry: Water Column Particulate Carbon and Nitrogen Concentrations
knb-lter-sbc.18.3YSBCAbundance and size of giant kelp
knb-lter-sbc.15.2YSBCKelp Forest Community Dynamics monitoring algae and sessile invertebrate cover data
knb-lter-sbc.17.5YSBCKelp Forest Community Dynamics monitoring, fish count data from 40 meter transects
knb-lter-sbc.17.5YSBCKelp Forest Community Dynamics monitoring, fish count data from 40 meter transects
knb-lter-sbc.19.2YSBCKelp Forest Community Dynamics, monitoring small or cryptic invertebrate and algae counts in 1 meter-square quadrats
knb-lter-sbc.14.5YSBCTime series of giant kelp biomass along the coasts of California and Baja, Mexico
ALM7D8802AYVCRTemporal and spatial distribution of microbial biomass, growth and activity.
BPH8801AYVCRHurricane record for the Virginia Coast Reserve
HHS8802AYVCRPlant distribution on Hog Island
RAB9001AYVCRHog and Cobb Island nesting seabird study, part A.
RAB9001BYVCRHog and Cobb Island nesting seabird study, part B.
RDD6B7501AYVCRSurvey of island small mammals - trapping data
VCR03090YVCRRoot biomass on Northern Hog Island
VCR03092YVCRAboveground biomass of dune vegetation on the Hog Island chronosequence
VCR05113HVCRParramore Permanent Plot Resurvey: Tree data
VCR05115YVCRParramore Permanent Plot Resurvey: Shrub data
VCR05117YVCRParramore Permanent Plot Resurvey: Landcover Class Aggregation data
VCR05118YVCRParramore Permanent Plot Resurvey: Subplot data
VCR05119YVCRParramore Permanent Plot Resurvey: Clip plot data
VCR05120YVCRParramore Permanent Plot Resurvey: Calibration Saltmarsh Plot data
VCR05122YVCRParramore Permanent Plot Resurvey: Calibration Saltmarsh Stem data
VCR05123YVCRParramore Permanent Plot Resurvey: LAI-Biomass data
VCR97015YVCRInundation Experiment Permanent Plot Data : Biomass
VCR97016YVCR Inundation Experiment Permanent Plot Data : Bulk Density
VCR97017YVCRInundation Experiment Permanent Plot Data : Macroorganic Material
VCR97022YVCRPlant distribution on Hog Island : T1 : Myrica allometry - dia.+wgt.
VCR97028YVCRCrab Burrows, Soil Nutrients, and Spartina alterniflora : nutrients
VCR97032YVCRProduction data from Brownsville Marsh 1992
VCR97035YVCRPlant Cover Upper Phillips Creek
VCR97052YVCRFertilization
pisco_subtidal.12.4?PISCOSubtidal: Community Surveys: Fish Survey
pisco_recruitment.27.1?PISCOIntertidal: Recruitment Monitoring: Recruitment collectors and Rock Clearings

Notes:

  • The majority of types of GCE Above & Below Ground Biomass and Species Number on Hog Island Dunes
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
  • Serguei Krivov, UV
  • 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 06-Apr-2007 15:50:48 PDT by uid=bowers,o=SDSC.