OBOE Ontology Extensions Meeting Agenda
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MINUTES
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|DATE | July 25-26, 2011 |
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|TYPE OF MEETING | Ontology Development, Annotations |
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|CALL IN | |
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|NOTES | Everyone |
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|ATTENDEES | Shawn Bowers, Ben Leinfelder, Chris Jones, |
| | Margaret O'Brien, Mark Schildhauer |
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**Initial Agenda**
- Review the Agenda for Day One and Day Two
- Drive the ontology development by annotating many datasets
- Annotating metadata fields
- Most common attributes in knb: Year, date, plot, species, site
- Develop design patterns for ontology class development
- Review and discuss syntactic changes to OBOE
- Modular files approach
- **oboe-core**
- **oboe-characteristics**
- **oboe-standards**
- oboe-spatial
- oboe-temporal
- oboe-taxa
- oboe-chemistry
- oboe-anatomy
- Spatial class additions (GML 3.2.1 entities)
- Use WCS ontology schema from iri.columbia.edu?
- Temporal class additions (GML 3.2.1 entities)
- Use WCS ontology schema from iri.columbia.edu?
- Taxanomic classes (Top level taxonomic rank classes)
- Ranks as classes vs. ranks as individual members of Rank?
- Other models?
- Anatomical class additions (portions of CARO & TAO)
- Authoritative definitions of terms
- Domain-agnostic URI? (purl.org?)
- Resolvable class definitions
- Discuss part/whole relationship approaches
- Has been an impediment to class development (need a solution)
ENVO (environment ontology) RO (relationship ontology)
Mark: RO is missing several notions of partonomy relationships
- Discuss OBOE Relationship class
- Discuss SBC implementation of hasPart/partOf wrt:
- Varzi, Winston et al. concepts recommended by Mark
- parts as individual units (cognitively salient parts, e.g. ships in a fleet)
- individualMemberOf
- hasIndividualMember
- parts as portion of a whole (dependent on the interaction as a whole, e.g. the left side, slice of pie)
- Self-connected 'parts'
- hasPortion ??
- portionOf ??
- material constitution (e.g. iron is part of steel)
- materialPortionOf
- hasMaterialPortion
- consituentOf
- hasConstituent
- mixture composition (same as parts as individual units?)
- conceptual inclusion (domain and range are parts of a model)
- functional components
- How to define protocols
- restrictions on entities/characteristics?
- Ask Ben
- Annotations (Day 2?)
- Morpho+semtools download: http://bespin.nceas.ucsb.edu/downloads/semtools/
NOTES:
- Morpho/tool enhancement
- individuals in the ontology should show up in the browser (GermanyCreek instance of Site)
- metadata (values) as observations ("floating context")
- primitive values vs. class/instance values in annotation syntax (value as static attribute of measurement or as a nested element of measurement)
- this also applies to attribute mapping syntax, where a value can be used here as well too
- in general need to deal with primitive value (entities) and non-primitive value entities (individuals/classes)
- add map conditions (e.g., if="species eq 'WCH'" value="jmx:Chinook") to annotation interface
- need to include in search and materialization
- need to add object-property range entity search in discovery tools
- e.g., CohoPopulation = Population and consistsOf only Coho
- other examples SmellingSalts made up of Amonium, or Hydrogen in Water
- searching for Coho would then match a dataset with observations of CohoPopulation
- need to support context in measurement types in morpho annotation editor
- e.g., ConcentrationOfAmmoniumInFreshWater, the InFreshWater is "lost" when an attribute tied to the measurement type
- the context observation can "float"
- an attribute could be tied to a measurement of the context observation
- multiple attributes could have the same context observation
- discussed oboe model w.r.t. entity, characteristic, value (entity)
- discussed using individuals, e.g.:
observation:
entity: "jmx:GermanyCreek"
versus
observation:
entity: "oboe:Location"
characteristic: "oboe:Name"
value: "Germany Creek"
- Note that above, we could also add an Id characteristic
observation:
entity: "oboe:Location"
characteristic: "oboe:Id"
value: "jmx:GermanyCreek"
- went through example JMX datasets to identify measurements (13 datasets):
- date (month, day, year)
- species (code, e.g., WCH)
- week #
- fork length
- weight
- k factor (condition index)
- location (creek)
- age
- card #
- pos #
- origin (wild, hatchery, etc.)
- trap type (screw trap, etc.)
- life stage
- trap set date (day, mo, yr, time)
- trap pulled date (day, mo, yr, time)
- counts (the main data collected)
- count of live smolt, dead smolt, lamperey w/eyes, w/out eyes, by fish species, etc.
- staff guage (height of creek)
- debris (in river)
- secchi (water clarity of river)
- discussed possible JMX use case:
- Excel to CSV to basic EML (automated)
- Requires some conventions on Excel like one table per sheet, one cell per attribute name, unique attribute names (Ok to have tables in "long" or "wide" form -- pivoted/unpivoted)
- Semantic annotation of attributes via pre-defined template / measurement types / value mappings
- Ability to select datasets, materialize to rdf triples, and execute data subsetting query (e.g., via SPARQL) ... e.g., for a specific year, location, species,
- Feed this subsetted data into model/data flow used by JMX (i.e., Mara [sp?])
- another more ambituous JMX use case:
- create a general routine to map from JMX observational data to the JMX/EPA uber schema
- this would help automate the conversion from ad-hoc spreadsheets to the uber schema (e.g., to make it easier for tribes)
July 26, 2011 Discussion
========================
Modeling Measurement Types
vs
- Organism
- PopulationSample
- CohoPopulationSample
- == PopulationSample AND consistsOf only Coho
- MetaPopulation
- (consists of population{1..n})
- Population
- (consists of Species{1..1})
- CohoPopulation
- Sample
- DiscreetSample
- OrganismTissueSample
- SensorSample
- PopulationSample
- takenFrom Population
- CohoPopulationSample
- Organism
- Animal
- ...
- Salmonid
- Salmon
- PacificSalmon
- CohoSalmon
- AliveSmoltCohoSalmon = AliveOrganism and SmoltStageOrganism
- AliveSmoltCohoSalmonPopulationSample
- AliveOrganism
- DeadOrganism
- FishStageOrganism
- SmoltStageOrganism
- YearlyStageOrganism
Mark: A characteristic can also be modeled as a measurement type
- e.g., temperate can be broken down to a measurement of kinetic energy in the molecules of the entity being measured (e.g., air, water, etc.)
- another example would be productivity, which has "surrogate" measures
OBOE organization, files
core model:
oboe-core.owl
All modules and/or extensions should import this file.
OBOE:
oboe.owl
imports of oboe-core and all domain modules only
does not have any extensions.
Domain modules:
oboe-[domain].owl
By building modules specific to scientific domains, (eg, oceanography, chemistry, hydrology), we can engage experts in those domains as needed.
OBOE Extensions:
oboe-sbclter.owl
extensions import oboe-core, and whatever domain modules they need. Extenstions are allowed to pull from any of the modules and make assertions between them.
TUCANNON LW
observation 'date'
entity oboe-temporal:TimeInstant
measurement m1
characteristic oboe-characteristics:Time
standard oboe-standards:Date (add)
context
oboe-characteristics:During 'week'
observation 'salmon'
entity jmx:PacificSalmon
measurement m2
characteristic oboe-taxa:TaxonType (add)
domain
entity jmx:WildChinookSalmon (add)
entity jmx:WildSteelHeadSalmon (add)
entity jmx:CohoSalmon (add)
measurement m5
characteristic oboe-characteristics:Length
standard oboe-standards:Millimeter
protocol jmx:ForkLengthProtocol (add)
precision 1
measurement m6
characteristic oboe-characteristics:Mass
standard oboe-standards:Gram
precision 0.1
measurement m7
characteristic jmx:FishCondition (add)
standard jmx:KFactor (add)
precision 0.01
context
oboe-characteristics:Within 'trap'
observation 'week'
entity jmx:FishingWeek (add under jmx:AdministrativeFeature)
measurement m3
characteristic oboe-core:Name
observation 'river'
entity jmx:TucannonCreek (individual of jmx:Creek)
observation 'trap'
entity jmx:RotaryScrewTrap (individual of jmx:Trap)
context
oboe-characteristics:Within 'river'
context
oboe-characteristics:At 'date'
context
oboe-characteristics:During 'week'
mapping
--------
map Date m1
map Species m2
if Species eq 'WCH'
value jmx:WildChinookSalmon
if Species eq 'WSH'
value jmx:WildSteelHeadSalmon
if Species eq 'FALL'
value jmx:????
if Species eq 'COHO'
value jmx:CohoSalmon
map Week m3
map Fork Length m5
map Weight m6
map K Factor m7
TUCANNON smolt catch
observation o1
entity jmx:LiveWildSpringOncorhynchustshawytschaSmoltPopulationSample
measurement m1
characteristic oboe-characteristics:Count
standard oboe-standards:Number
protocol jmx:TrapProtocol
context
Within 'trap'
observation o2
entity jmx:DeadWildSpringOncorhynchustshawytschaSmoltPopulationSample
measurement m2
characteristic oboe-characteristics:Count
standard oboe-standards:Number
protocol jmx:TrapProtocol
context
Within 'trap'
observation 'trap'
entity jmx:RotaryScrewTrap
context
Within 'creek'
also context of Secchi and Debris ???
observation 'creek'
entity jmx:UpperTucannonCreek
observation 'stream'
entity oboe-hydrology:Stream
measurement
characteristic oboe-characteristic:Length
standard oboe-standards:Meter
observation 'debris'
entity jmx:Debris
measurement
characteristic oboe-characteristics:Amount
context
Within 'stream'
observation 'secchi'
entity jmx:Water
measurement
characteristic oboe-characteristic:Depth (subclass Length)
standard oboe-standards:Meter
protocol jmx:SecchiProtocol
context
Within 'stream'
observation 'duration'
entity oboe-temporal:TimePeriod
measurement
characteristic oboe-characteristics:StartDate
standard oboe-standards:YearMonthDay
measurement
characteristic oboe-characteristics:StartTime
standard oboe-standards:HourMinute
measurement
characteristic oboe-characteristics:EndDate
standard oboe-standards:YearMonthDay
measurement
characteristic oboe-characteristics:EndTime
standard oboe-standards:HourMinute
Use case sample (Wednesday)
"tall table"
loc spp wt
--- --- ---
1 A 1
1 B 4
2 C 3
2 D 1
"wide table"
loc sppA sppB sppC sppD
--- ---- ---- ---- ----
1 1 4 - -
2 - - 3 1
"tall table" annotation
-----------------------
observation
entity jmx:Species
measurement m1
char Taxon
measurement m2
char Mass
map wt m2
if spp eq "A"
value jmx:SpeciesA
map wt m2
if spp eq "B"
value jmx:SpeciesB
map wt m2
if spp eq "C"
value jmx:SpeciesC
map wt m2
if spp eq "D"
value jmx:SpeciesD
"wide table" annotation
-----------------------
observation
entity jmx:SpeciesA
measurement mA
char Mass
observation
entity jmx:SpeciesB
measurement mB
char Mass
observation
entity jmx:SpeciesC
measurement mC
char Mass
observation
entity jmx:SpeciesD
measurement mD
char Mass