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Science Environment for Ecological Knowledge




KRSMS March 2007

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:, 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.


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
PLT-GCEM-0511aY+Plant Ecology: Biomass from Shoot Height and Flowering Status
PLT-GCEM-0511bY+Plant Ecology: Biomass from Shoot Height and Flowering Status (w/ Biomass)
PLT-GCEM-0211bY+Plant allometry at GCE sampling sites 1-10 in October, 2002
PLT-GCED-0409Y+Plant Ecology: Community Response to Fertilization
PLT-GCET-0608YPlant Ecology: Plant Richness Survey
INS-GCEM-0511Y+Terrestrial Insect Ecology: Grasshopper Abundance and Species Diversity
INV-GCEM-0511Y+Aquatic Invertebrate Ecology: Crab Abundance based on Crab Hole Counts
INV-GCEM-0501a1Y+Aquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Abundance
INV-GCEM-0501a2Y+Aquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Size Distributions
FNG-GCEM-0401HFungal Productivity: Ergosterol Content and Ascospore Release Rates
BCT-GCEM-0511a2HBacterial Productivity: Surface Water Bacterial Productivity
PHP-GCEM-0511aHPhytoplankton Productivity: Surface Water Phytoplankton Productivity
ALG-GCED-0304aYAlgal Productivity: Benthic Chlorophyll Concentrations and Gross Oxygenic Photosynthesis Rates
ALG-GCED-0304cHAlgal Productivity: Benthic Chlorophyll, Density, Porosity, Organic Content Concentrations, and Gross Oxygenic Photosynthesis Rates
MET-GCEM-0508aYMeteorology: Annual Summaries of Daily Air Temperature and Precipitation
HYD-GCES-0508aY+Hydrography: Annual Summaries of Daily Averaged River Discharge
HYD-GCES-0508bYHydrography: Monthly Mean Water Levels
PHY-GCEM-0612aYContinuous Salinity, Temperature and Depth
PHY-GCEM-0406a1HPhysical Oceanography: Bin-Averaged CTD Profiles
PHY-GCEM-0406a2HPhysical Oceanography: CTD, PAR, Oxygen, and Chlorophyll Profiles
GEL-GCEM-0508aHGeology: Soil Characteristics
GEL-GCEM-0508bHGeology: Soil Surface Elevation
GEL-GCEM-0508cYGeology: Soil Accretion
ORG-GCEM-0511aHOrganic Matter/Decomposition: Surface Water Dissolved Organic Carbon Concentrations
ORG-GCEM-0508aYOrganic Matter/Decomposition: Soil temperature and respiration
ORG-GCEM-0508bHOrganic Matter/Decomposition: Rates of Decompisition and Root In-Growth
ORG-GCEM-0101YOrganic Matter/Decomposition: Ash-Free Dry Weight Analysis for Soil Samples
CHM-GCED-0303aYChemistry: Surface Water Samples for Total Dissolved Inorganic Carbon, Total Alkalinity, and pH
POR-GCED-0210HPore-water Chemistry: Porewater Nutrients, Dissolved Organics, Redox Species, and Gasses in Estuarine Intertidal Sediments
NUT-GCEM-0210YGeneral Nutrient Chemistry: Water Quality Monitoring
NUT-GCEM-0206HGeneral Nutrient Chemistry: Water Column Particulate Carbon and Nitrogen Concentrations
knb-lter-sbc.18.3YAbundance and size of giant kelp
knb-lter-sbc.15.2YKelp Forest Community Dynamics monitoring algae and sessile invertebrate cover data
knb-lter-sbc.17.5YKelp Forest Community Dynamics monitoring, fish count data from 40 meter transects
knb-lter-sbc.17.5YKelp Forest Community Dynamics monitoring, fish count data from 40 meter transects
knb-lter-sbc.19.2YKelp Forest Community Dynamics, monitoring small or cryptic invertebrate and algae counts in 1 meter-square quadrats
knb-lter-sbc.14.5YTime series of giant kelp biomass along the coasts of California and Baja, Mexico
ALM7D8802AYTemporal and spatial distribution of microbial biomass, growth and activity.
BPH8801AYHurricane record for the Virginia Coast Reserve
HHS8802AYPlant distribution on Hog Island
RAB9001AYHog and Cobb Island nesting seabird study, part A.
RAB9001BYHog and Cobb Island nesting seabird study, part B.
RDD6B7501AYSurvey of island small mammals - trapping data
VCR03090YRoot biomass on Northern Hog Island
VCR03092YAboveground biomass of dune vegetation on the Hog Island chronosequence
VCR05113HParramore Permanent Plot Resurvey: Tree data
VCR05115YParramore Permanent Plot Resurvey: Shrub data
VCR05117YParramore Permanent Plot Resurvey: Landcover Class Aggregation data
VCR05118YParramore Permanent Plot Resurvey: Subplot data
VCR05119YParramore Permanent Plot Resurvey: Clip plot data
VCR05120YParramore Permanent Plot Resurvey: Calibration Saltmarsh Plot data
VCR05122YParramore Permanent Plot Resurvey: Calibration Saltmarsh Stem data
VCR05123YParramore Permanent Plot Resurvey: LAI-Biomass data
VCR97015YInundation Experiment Permanent Plot Data : Biomass
VCR97016YInundation Experiment Permanent Plot Data : Bulk Density
VCR97017YInundation Experiment Permanent Plot Data : Macroorganic Material
VCR97022YPlant distribution on Hog Island : T1 : Myrica allometry - dia.+wgt.
VCR97028YCrab Burrows, Soil Nutrients, and Spartina alterniflora : nutrients
VCR97032YProduction data from Brownsville Marsh 1992
VCR97035YPlant Cover Upper Phillips Creek
VCR97052YFertilization Above & Below Ground Biomass and Species Number on Hog Island Dunes
WO8802AY+Spartina alterniflora leaf measurements, part A
pisco_cbs.56.17YIntertidal: Coastal Biodiversity Surveys: Quadrat Surveys
pisco_cbs.55.22YIntertidal: Coastal Biodiversity Surveys: Swath Surveys
pisco_snbs.1.7Yntertidal: Biodiversity Surveys: OSU: Spatially-nested Biodiversity Surveys
pisco_recruitment.27.1YIntertidal: Recruitment Monitoring: OSU: Recruitment collectors and Rock Clearings
pisco_recruitment.62.3YIntertidal: Recruitment Monitoring: UCSC: Recruitment collectors and Rock Clearings


  • Y = Yes, include in corpus (+ = complete); H = possibly include, need more information about methods/data
  • The majority of types of 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





  • 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 page last changed on 24-May-2007 19:21:08 PDT by uid=bowers,o=SDSC.