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	Extracting terms and concepts (Continued)	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 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	Publisher	Comment
PLT-GCEM-0511a	GCE	Plant Ecology: Biomass from Shoot Height and Flowering Status
PLT-GCEM-0511b	GCE	Plant Ecology: Biomass from Shoot Height and Flowering Status (w/ Biomass)
PLT-GCED-0409	GCE	Plant Ecology: Community Response to Fertilization
PLT-GCET-0608	GCE	Plant Ecology: Plant Richness Survey
INS-GCEM-0511	GCE	Terrestrial Insect Ecology: Grasshopper Abundance and Species Diversity
INV-GCEM-0511	GCE	Aquatic Invertebrate Ecology: Crab Abundance based on Crab Hole Counts
INV-GCEM-0501a1	GCE	Aquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Abundance
INV-GCEM-0501a2	GCE	Aquatic Invertebrate Ecology: Infaunal and Epifaunal Mollusc Size Distributions
FNG-GCEM-0401	GCE	Fungal Productivity: Ergosterol Content and Ascospore Release Rates
BCT-GCEM-0511a2	GCE	Bacterial Productivity: Surface Water Bacterial Productivity
PHP-GCEM-0511a	GCE	Phytoplankton Productivity: Surface Water Phytoplankton Productivity
ALG-GCED-0304a	GCE	Algal Productivity: Benthic Chlorophyll Concentrations and Gross Oxygenic Photosynthesis Rates
ALG-GCED-0304c	GCE	Algal Productivity: Benthic Chlorophyll, Density, Porosity, Organic Content Concentrations, and Gross Oxygenic Photosynthesis Rates
MET-GCEM-0508a	GCE	Meteorology: Annual Summaries of Daily Air Temperature and Precipitation
HYD-GCES-0508a	GCE	Hydrography: Annual Summaries of Daily Averaged River Discharge
HYD-GCES-0508b	GCE	Hydrography: Monthly Mean Water Levels
PHY-GCEM-0612a	GCE	Continuous Salinity, Temperature and Depth
PHY-GCEM-0406a1	GCE	Physical Oceanography: Bin-Averaged CTD Profiles
PHY-GCEM-0406a2	GCE	Physical Oceanography: CTD, PAR, Oxygen, and Chlorophyll Profiles
GEL-GCEM-0508a	GCE	Geology: Soil Characteristics
GEL-GCEM-0508b	GCE	Geology: Soil Surface Elevation
GEL-GCEM-0508c	GCE	Geology: Soil Accretion
ORG-GCEM-0511a	GCE	Organic Matter/Decomposition: Surface Water Dissolved Organic Carbon Concentrations
ORG-GCEM-0508a	GCE	Organic Matter/Decomposition: Soil temperature and respiration
ORG-GCEM-0508b	GCE	Organic Matter/Decomposition: Rates of Decompisition and Root In-Growth
ORG-GCEM-0101	GCE	Organic Matter/Decomposition: Ash-Free Dry Weight Analysis for Soil Samples
CHM-GCED-0303a	GCE	Chemistry: Surface Water Samples for Total Dissolved Inorganic Carbon, Total Alkalinity, and pH
POR-GCED-0210	GCE	Pore-water Chemistry: Porewater Nutrients, Dissolved Organics, Redox Species, and Gasses in Estuarine Intertidal Sediments
NUT-GCEM-0210	GCE	General Nutrient Chemistry: Water Quality Monitoring
NUT-GCEM-0206	GCE	General Nutrient Chemistry: Water Column Particulate Carbon and Nitrogen Concentrations

2002lgcover	ARC	Relative percent cover was measured in moist acidic and moist non-acidic tundra
2002gsttbm	ARC	Above ground plant and below ground stem biomass in acidic tussock tundra
2001lgshttcn	ARC	Percent carbon and percent nitrogen of above ground plant and belowground stem biomass samples in moist acidic and moist non-acidic tundra
2001gswsbm_n	ARC	Biomass, nitrogen and carbon of plants in wet sedge tundra
2000gsla	ARC	Leaf area for select species was measured in arctic tundra
1999SHretrans	ARC	Foliar and litter nutrients and retranslocation efficiencies for dominant species on moist acidic and non-acidic tundra

dataset269	CAP	Historic Landuse
dataset276	CAP	Human
dataset43	CAP	Transect Bird Survey with Data Synthesis]
dataset39	CAP	Lichen Resurvey with Heavy Metal Analysis

pisco_subtidal.12.4	PISCO	Subtidal: Community Surveys: Fish Survey
pisco_recruitment.27.1	PISCO	Intertidal: Recruitment Monitoring: Recruitment collectors and Rock Clearings
SA002	Andrews	Vascular plant list
SA003	Andrews	Bird species list
CF004	Andrews	Stream and groundwater chemistry
FS111	Andrews	Conversion factors for forest products
SP004	Andrews	Seasonal relationships between soil and carbon
SP018	Andrews	Microclimate gradients
DF001	Andrews	Fire history
DF014	Andrews	Dendrochronology
DH001	SEV	Lightning strike data
SEV006	SEV	Pinyon branch demongraphy
SEV016	SEV	Southern Oscillation Index
SEV022	SEV	Litter fall collection data
SEV050	SEV	Spectral reflectance of biomass
SEV079	SEV	Evapotranspiration

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 02-Apr-2007 10:54:19 PDT by uid=dpennington,o=LTER.