I am convenor of a group charged with recommending positions about Knowledge Organization Systems (KOS) to GBIF. Among the things that will be in our report will be a survey important vocabularies and ontologies for biodiversity Knowledge Organization. Not only will OBOE be among those discussed, but one of its architects, Mark Schildauer, is a member of the work group. Similarly re: the OBO ontologies. When our report is drafted, it will be opened for public comment both as to what we recommend and what we may have missed. Meanwhile, there is a survey at http://surveymonkey.com/GBIFKOSurvey to which all are invited to participate if you haven't already. If you have favorite KOS resources, there is good opportunity to list them there.
Also, the TDWG 2010 Thursday sessions on Observations will, I believe, soon have their notes on the TDWG website (if not there already).
Bob Morris
On Fri, Oct 22, 2010 at 1:03 AM, Cam Webb cwebb@oeb.harvard.edu wrote:
Hi Kevin,
I can't help but feel we are getting into a much more complicated area of biodiversity ( or any observation oriented field for that matter ) and that there must be other ontologies or models that we could follow or reuse.
If you are referring specifically to adding depth to the observations of Individuals, I think one might look first at OBOE (OBOE: Extensible Observation Ontology) from the SEEK group at NCEAS:
http://ecoinformatics.org/oboe/oboe.1.0/oboe.owl
In summary, this describes an Observation of an Entity, with the Observation comprising a Measurement of the Value for a Characteristic of the Entity:
@prefix oboe: http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# .
[] a oboe:Observation ; oboe:ofEntity [ a oboe:Entity ; ] ; oboe:hasMeasurement [ a oboe:Measurement ; oboe:ofCharacteristic [ a oboe:Characteristic ; ] ; oboe:hasValue [ a oboe:Entity ; ] ; ] .
If we assert that a dwc:Occurrence is an instance of oboe:Entity, with dwc:basisOfRecord of "HumanObservation", with a dc:creator and dc:created (i.e., the space-time intersection of an Individual and a human observer), we can marry these two ontologies quite nicely. Please see Example 1, below, for a description of the fruit color of an individual plant.
What's nice about the OBOE model is that it contains all three possible parts of an observation: the entity, the characteristic and the value. This allows direct mapping to the Prometheus Description Model (structure
- property + state = entity + characteristic + value; Pullan et al. 2005,
Taxon 54:751-765), and indirect mapping to the popular EQ model (entity + quality, where quality = characteristic + value; Mabee et al. 2007, doi:10.1016/j.tree.2007.03.013). However, it doesn't map easily to the DELTA or SDD data models (character + character-state, where character = entity + characteristic and character-state = value).
Because of the well-developed OBO ontologies, we can directly employ terms from, say, the Plant Ontology (po), for an oboe:Entity, and terms from PATO, the quality ontology, for a oboe:Measurement, combining characteristic and value into a quality. We need to assert that a pato:quality is equivalent to a oboe:Measurement and possibly that a po:PO_0000001 (top level `plant structure') is an oboe:Entity. We can also employ the OBO relational ontology (ro) to indicate that a fruit is ro:part_of the particular space-time Occurrence of an Individual (this might require a bit more discussion!).
So, it seems that using only well-established vocabularies, we can make semantic statements about the characteristics of individuals originally defined primarily using DwC terms. Please see example 2, below for a fairly slim, usable model of a description of the fruit color of an individual plant. The image of the model is at:
http://phylodiversity.net/cwebb/img/tdwg-obs.jpg
Again, any comments on this model will be much appreciated. Are you aware of other attempts to join DwC Occurrence models with OBOE models?
Best,
Cam
====================== Example 1 =======================================
@prefix oboe: http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# . @prefix dwc: http://rs.tdwg.org/dwc/terms/ . @prefix dcterms: http://purl.org/dc/terms/ . @prefix sernec: http://bioimages.vanderbilt.edu/rdf/terms# . @prefix geo: http://www.w3.org/2003/01/geo/wgs84_pos# . @prefix : <#> .
http://phylodiversity.net/xmalesia/indiv/9 a sernec:Individual ; sernec:derivativeOccurrence _:blank1 .
_:blank1 # The Occurrence of the Individual... a dwc:Occurrence ; # ... at a position in space-time... dcterms:created "2008-01-01" ; dcterms:spatial [ a dcterms:Location ; geo:lon "109.95371" ; geo:lat "-1.25530" ; dwc:coordinateUncertaintyInMeters "100" ; ] ; # is a recordable OBOE Entity a oboe:Entity ; # as recorded by a human dcterms:creator "Cam Webb" ; dwc:basisOfRecord "HumanObservation" .
# The details of the observation: [] a oboe:Observation ; oboe:ofEntity [ # The observed entity is actually *part of* the occurrence # of the Individual at a particular Space and Time a :Fruit ; :partOf _:blank1 ; ] ; oboe:hasMeasurement [ oboe:ofCharacteristic :Color ; oboe:hasValue :Green ; ] .
:Fruit a oboe:Entity . :Color a oboe:Characteristic . :Green a oboe:Entity .
========================================================================
====================== Example 2 =======================================
@prefix oboe: http://ecoinformatics.org/oboe/oboe.1.0/oboe-core.owl# . @prefix dwc: http://rs.tdwg.org/dwc/terms/ . @prefix dcterms: http://purl.org/dc/terms/ . @prefix sernec: http://bioimages.vanderbilt.edu/rdf/terms# . @prefix geo: http://www.w3.org/2003/01/geo/wgs84_pos# . @prefix ro: http://www.obofoundry.org/ro/ro.owl# . @prefix pato: http://purl.org/obo/owl/PATO# . @prefix po: http://purl.org/obo/owl/PO# . @prefix rdfs: http://www.w3.org/2000/01/rdf-schema# .
http://phylodiversity.net/xmalesia/indiv/9 sernec:derivativeOccurrence _:blank1 .
_:blank1 a dwc:Occurrence ; dcterms:created "2008-01-01" ; dcterms:spatial [ geo:lon "109.95371" ; geo:lat "-1.25530" ; dwc:coordinateUncertaintyInMeters "100" ; ] ; dcterms:creator "Cam Webb" ; dwc:basisOfRecord "HumanObservation" .
# The details of the observation: [] a oboe:Observation ; oboe:ofEntity [ ro:part_of _:blank1 ; a po:PO_0009001 ; # Fruit ] ; oboe:hasMeasurement pato:PATO_0000320 . # Green color
po:PO_0009001 rdfs:label "fruit" . pato:PATO_0000320 rdfs:label "green" .
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