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	Publisher	Comment
PLT-GCEM-0511a	Y	GCE	Plant Ecology: Biomass from Shoot Height and Flowering Status
PLT-GCEM-0511b	Y	GCE	Plant Ecology: Biomass from Shoot Height and Flowering Status (w/ Biomass)
PLT-GCED-0409	Y	GCE	Plant Ecology: Community Response to Fertilization
PLT-GCET-0608	Y	GCE	Plant Ecology: Plant Richness Survey
INS-GCEM-0511	Y	GCE	Terrestrial Insect Ecology: Grasshopper Abundance and Species Diversity
INV-GCEM-0511	Y	GCE	Aquatic Invertebrate Ecology: Crab Abundance based on Crab Hole Counts
INV-GCEM-0501a1	Y	GCE	Aquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Abundance
INV-GCEM-0501a2	Y	GCE	Aquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Size Distributions
FNG-GCEM-0401	H	GCE	Fungal Productivity: Ergosterol Content and Ascospore Release Rates
BCT-GCEM-0511a2	H	GCE	Bacterial Productivity: Surface Water Bacterial Productivity
PHP-GCEM-0511a	H	GCE	Phytoplankton Productivity: Surface Water Phytoplankton Productivity
ALG-GCED-0304a	Y	GCE	Algal Productivity: Benthic Chlorophyll Concentrations and Gross Oxygenic Photosynthesis Rates
ALG-GCED-0304c	H	GCE	Algal Productivity: Benthic Chlorophyll, Density, Porosity, Organic Content Concentrations, and Gross Oxygenic Photosynthesis Rates
MET-GCEM-0508a	Y	GCE	Meteorology: Annual Summaries of Daily Air Temperature and Precipitation
HYD-GCES-0508a	Y	GCE	Hydrography: Annual Summaries of Daily Averaged River Discharge
HYD-GCES-0508b	Y	GCE	Hydrography: Monthly Mean Water Levels
PHY-GCEM-0612a	Y	GCE	Continuous Salinity, Temperature and Depth
PHY-GCEM-0406a1	H	GCE	Physical Oceanography: Bin-Averaged CTD Profiles
PHY-GCEM-0406a2	H	GCE	Physical Oceanography: CTD, PAR, Oxygen, and Chlorophyll Profiles
GEL-GCEM-0508a	H	GCE	Geology: Soil Characteristics
GEL-GCEM-0508b	H	GCE	Geology: Soil Surface Elevation
GEL-GCEM-0508c	Y	GCE	Geology: Soil Accretion
ORG-GCEM-0511a	H	GCE	Organic Matter/Decomposition: Surface Water Dissolved Organic Carbon Concentrations
ORG-GCEM-0508a	Y	GCE	Organic Matter/Decomposition: Soil temperature and respiration
ORG-GCEM-0508b	H	GCE	Organic Matter/Decomposition: Rates of Decompisition and Root In-Growth
ORG-GCEM-0101	Y	GCE	Organic Matter/Decomposition: Ash-Free Dry Weight Analysis for Soil Samples
CHM-GCED-0303a	Y	GCE	Chemistry: Surface Water Samples for Total Dissolved Inorganic Carbon, Total Alkalinity, and pH
POR-GCED-0210	H	GCE	Pore-water Chemistry: Porewater Nutrients, Dissolved Organics, Redox Species, and Gasses in Estuarine Intertidal Sediments
NUT-GCEM-0210	Y	GCE	General Nutrient Chemistry: Water Quality Monitoring
NUT-GCEM-0206	H	GCE	General Nutrient Chemistry: Water Column Particulate Carbon and Nitrogen Concentrations
knb-lter-sbc.18.3	Y	SBC	Abundance and size of giant kelp
knb-lter-sbc.15.2	Y	SBC	Kelp Forest Community Dynamics monitoring algae and sessile invertebrate cover data
knb-lter-sbc.17.5	Y	SBC	Kelp Forest Community Dynamics monitoring, fish count data from 40 meter transects
knb-lter-sbc.17.5	Y	SBC	Kelp Forest Community Dynamics monitoring, fish count data from 40 meter transects
knb-lter-sbc.19.2	Y	SBC	Kelp Forest Community Dynamics, monitoring small or cryptic invertebrate and algae counts in 1 meter-square quadrats
knb-lter-sbc.14.5	Y	SBC	Time series of giant kelp biomass along the coasts of California and Baja, Mexico
pisco_subtidal.12.4	?	PISCO	Subtidal: Community Surveys: Fish Survey
pisco_recruitment.27.1	?	PISCO	Intertidal: 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

• 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

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