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

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	Status	Comment
GCE
PLT-GCEM-0511a	Y	Plant Ecology: Biomass from Shoot Height and Flowering Status
PLT-GCEM-0511b	Y	Plant Ecology: Biomass from Shoot Height and Flowering Status (w/ Biomass)
PLT-GCED-0409	Y	Plant Ecology: Community Response to Fertilization
PLT-GCET-0608	Y	Plant Ecology: Plant Richness Survey
INS-GCEM-0511	Y	Terrestrial Insect Ecology: Grasshopper Abundance and Species Diversity
INV-GCEM-0511	Y	Aquatic Invertebrate Ecology: Crab Abundance based on Crab Hole Counts
INV-GCEM-0501a1	Y	Aquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Abundance
INV-GCEM-0501a2	Y	Aquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Size Distributions
FNG-GCEM-0401	H	Fungal Productivity: Ergosterol Content and Ascospore Release Rates
BCT-GCEM-0511a2	H	Bacterial Productivity: Surface Water Bacterial Productivity
PHP-GCEM-0511a	H	Phytoplankton Productivity: Surface Water Phytoplankton Productivity
ALG-GCED-0304a	Y	Algal Productivity: Benthic Chlorophyll Concentrations and Gross Oxygenic Photosynthesis Rates
ALG-GCED-0304c	H	Algal Productivity: Benthic Chlorophyll, Density, Porosity, Organic Content Concentrations, and Gross Oxygenic Photosynthesis Rates
MET-GCEM-0508a	Y	Meteorology: Annual Summaries of Daily Air Temperature and Precipitation
HYD-GCES-0508a	Y	Hydrography: Annual Summaries of Daily Averaged River Discharge
HYD-GCES-0508b	Y	Hydrography: Monthly Mean Water Levels
PHY-GCEM-0612a	Y	Continuous Salinity, Temperature and Depth
PHY-GCEM-0406a1	H	Physical Oceanography: Bin-Averaged CTD Profiles
PHY-GCEM-0406a2	H	Physical Oceanography: CTD, PAR, Oxygen, and Chlorophyll Profiles
GEL-GCEM-0508a	H	Geology: Soil Characteristics
GEL-GCEM-0508b	H	Geology: Soil Surface Elevation
GEL-GCEM-0508c	Y	Geology: Soil Accretion
ORG-GCEM-0511a	H	Organic Matter/Decomposition: Surface Water Dissolved Organic Carbon Concentrations
ORG-GCEM-0508a	Y	Organic Matter/Decomposition: Soil temperature and respiration
ORG-GCEM-0508b	H	Organic Matter/Decomposition: Rates of Decompisition and Root In-Growth
ORG-GCEM-0101	Y	Organic Matter/Decomposition: Ash-Free Dry Weight Analysis for Soil Samples
CHM-GCED-0303a	Y	Chemistry: Surface Water Samples for Total Dissolved Inorganic Carbon, Total Alkalinity, and pH
POR-GCED-0210	H	Pore-water Chemistry: Porewater Nutrients, Dissolved Organics, Redox Species, and Gasses in Estuarine Intertidal Sediments
NUT-GCEM-0210	Y	General Nutrient Chemistry: Water Quality Monitoring
NUT-GCEM-0206	H	General Nutrient Chemistry: Water Column Particulate Carbon and Nitrogen Concentrations
SBC
knb-lter-sbc.18.3	Y	Abundance and size of giant kelp
knb-lter-sbc.15.2	Y	Kelp Forest Community Dynamics monitoring algae and sessile invertebrate cover data
knb-lter-sbc.17.5	Y	Kelp Forest Community Dynamics monitoring, fish count data from 40 meter transects
knb-lter-sbc.17.5	Y	Kelp Forest Community Dynamics monitoring, fish count data from 40 meter transects
knb-lter-sbc.19.2	Y	Kelp Forest Community Dynamics, monitoring small or cryptic invertebrate and algae counts in 1 meter-square quadrats
knb-lter-sbc.14.5	Y	Time series of giant kelp biomass along the coasts of California and Baja, Mexico
VCR
ALM7D8802A	Y	Temporal and spatial distribution of microbial biomass, growth and activity.
BPH8801A	Y	Hurricane record for the Virginia Coast Reserve
HHS8802A	Y	Plant distribution on Hog Island
RAB9001A	Y	Hog and Cobb Island nesting seabird study, part A.
RAB9001B	Y	Hog and Cobb Island nesting seabird study, part B.
RDD6B7501A	Y	Survey of island small mammals - trapping data
VCR03090	Y	Root biomass on Northern Hog Island
VCR03092	Y	Aboveground biomass of dune vegetation on the Hog Island chronosequence
VCR05113	H	Parramore Permanent Plot Resurvey: Tree data
VCR05115	Y	Parramore Permanent Plot Resurvey: Shrub data
VCR05117	Y	Parramore Permanent Plot Resurvey: Landcover Class Aggregation data
VCR05118	Y	Parramore Permanent Plot Resurvey: Subplot data
VCR05119	Y	Parramore Permanent Plot Resurvey: Clip plot data
VCR05120	Y	Parramore Permanent Plot Resurvey: Calibration Saltmarsh Plot data
VCR05122	Y	Parramore Permanent Plot Resurvey: Calibration Saltmarsh Stem data
VCR05123	Y	Parramore Permanent Plot Resurvey: LAI-Biomass data
VCR97015	Y	Inundation Experiment Permanent Plot Data : Biomass
VCR97016	Y	Inundation Experiment Permanent Plot Data : Bulk Density
VCR97017	Y	Inundation Experiment Permanent Plot Data : Macroorganic Material
VCR97022	Y	Plant distribution on Hog Island : T1 : Myrica allometry - dia.+wgt.
VCR97028	Y	Crab Burrows, Soil Nutrients, and Spartina alterniflora : nutrients
VCR97032	Y	Production data from Brownsville Marsh 1992
VCR97035	Y	Plant Cover Upper Phillips Creek
VCR97052	Y	Fertilization Above & Below Ground Biomass and Species Number on Hog Island Dunes
PISCO
pisco_subtidal.12.4	?	Subtidal: Community Surveys: Fish Survey
pisco_recruitment.27.1	?	Intertidal: Recruitment Monitoring: Recruitment collectors and Rock Clearings

Notes:

• Y = Yes, include in corpus; 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

Ontologies

• SWEET Ontologies
• SPIRE (and older SEEK) ontologies
• Plant Ontology
• Ordnance Survey Ontologies
• EcoLingua

Thesauri

• NBII Keyword Thesaurus
• GEMET Thesaurus
• The NASA Thesaurus
• E. V. Komarek Fire Ecology Thesaurus
• USGS Thesaurus

Glossaries

• EEA multilingual environmental glossary
• UCMP Glossary
• CHM Biodiversity Glossary

Participants

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

moose.txt

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