[obs] Joining DwC, OBOE, PO and PATO
Chris Mungall
CJMungall at lbl.gov
Tue Oct 26 08:56:01 PDT 2010
Hi Cam
I too haven't been part of previous discussions.
The example below will lead to an OWL-Full ontology, as you are
declaring PATO_0000320 to be an individual, when it's already declared
as a class.
You would be more interoperable with other OBO-compliant resources if
you model it this way, using the bfo bearer_of property to connect a
fruit individual with a color individual:
[] a oboe:Observation ;
oboe:ofEntity [
a oboe:Entity ;
a po:PO_0009001 ;
bfo:bearer_of [
a pato:PATO_0000320
] ;
] ;
I don't know much about the oboe ontology, an dhow these can
interoperate with OBO ontologies. Is oboe:Entity intended to be the
maximally general class? If so then it may be redundant to declare
this individual as being both type oboe:Entity and of type fruit
(since presumably fruits are entities).
Also, I don't know anything about the observation class, but to be
consistent with the ontology of biomedical investigations, you may
want to invert the above, such that the observation is a measurement
of the color instance
Cheers
Chris
On Oct 26, 2010, at 2:31 AM, Cam Webb wrote:
> Dear colleagues,
>
> I'd like to request some suggestions on semantic modeling of
> biological observations. I haven't be part of the previous
> discussions many of you have had in other forums, and face to face,
> so there may be a ready-made solution out there for what I am hoping
> to do, and which I would be very grateful to be pointed towards. If
> not, I hope this question falls within the domain of your interests.
>
> I'm interested in modeling morphological observations of plants in
> the field, as part of an expanding biodiversity inventory and
> informatics project in Indonesia. Please see: http://phylodiversity.net/xmalesia/
> for a demo site. We'll be collecting specimens, images, DNA, and
> making field observations (basic herbarium label data: tree
> diameter, flower color, etc). We'd then like to present these
> online as both a nice GUI-driven website and via a Linked Data model
> with a SPARQL endpoint. I haven't found a pre-existing RDF
> template, although Peter de Vries' work (e.g., http://lod.geospecies.org/ses/73F2V?format=html)
> and Steve Baskauf's work (e.g., http://bioimages.vanderbilt.edu/rdf/examples/lsu000/0428.rdf)
> come close. There is an active discussion on the tdwg-content
> mailing list right now about using Darwin Core in a semantic web
> context, including issues such as adding an Individual class and the
> best way to treat specimens and images. However, there is little
> discussion of observations on tdwg-content, so I thought I'd bring
> it up here (apologies to any of you who have see overlapping posts
> by me on tdwg-content).
>
> So, I'm wondering if OBOE terms can be used to link up from DwC
> concepts to OBO ontology terms with PATO qualities. Perhaps the
> best way to ask the questions is in the context of a specific
> example. Here is an attempt to model an observation of the fruit
> color of a particular individual (in Turtle):
>
>
> @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>
> a sernec:Individual ;
> sernec:derivativeOccurrence _:blank1 .
>
> _:blank1
> a dwc:Occurrence ;
> dcterms:created "2008-01-01" ;
> dcterms:spatial [
> geo:lon "109.95371" ;
> geo:lat "-1.25530" ;
> ] ;
> dcterms:creator "Cam Webb" ;
> dwc:basisOfRecord "HumanObservation" .
>
> # The details of the observation:
> [] a oboe:Observation ;
> oboe:ofEntity [
> a oboe:Entity ;
> ro:part_of _:blank1 ;
> a po:PO_0009001 ;
> ] ;
> oboe:hasMeasurement pato:PATO_0000320 .
>
> po:PO_0009001 rdfs:label "fruit" .
> pato:PATO_0000320
> rdfs:label "green" ;
> a oboe:Measurement .
>
> ( The network diagram is at: http://phylodiversity.net/cwebb/img/obs-eg.jpg
> )
>
>
> The model includes an Individual, its Occurrence at a particular
> place in space and time, and an Observation of a fruit that is
> part_of the Occurrence.
>
>
> My questions/issues are:
>
> 1. * Space-time information* Is this the best way to link the
> Observation to the Individual, i.e., via the Occurrence, or is it
> better to link the Observation directly to the Individual. In the
> former case, the time-space instance is specified in the Occurrence
> (as above), in the latter, the time-space instance would have to be
> added via an extra oboe:hasContext link from the Observation to
> another Observation of a Temporal Point entity. The latter way of
> linking the Individual is less satisfying in the context of Darwin
> Core, which already uses the Occurrence for "HumanObservations".
>
> 2. *part_of* If we want to record an observation of part of an
> organism, we could use the ro:part_of property to link the
> Observation of that part to the Individual which has that part. Two
> issues here, i) is it meristically valid to say that the Occurrence
> (the space-time instance of the continuant Individual) can have a
> part? As I read the definition of ro:part_of:
>
> ``For continuants: C part_of C' if and only if: given any c that
> instantiates C at a time t, there is some c' such that c'
> instantiates
> C' at time t, and c *part_of* c' at t.''
>
> I think a fruit_txyz0 is indeed part of plant_txyz0, but I am not
> well-verse in mereology. ii) Is there a way in the OBO/EQ
> ontologies to say `the observed Entity is the general class of
> fruits' rather than a specific instance of a fruit, which is what I
> imagine
>
> [] a po:Fruit ;
> ro:part_of :Individual123 .
>
> means. This is important, because our final observation of the
> nature of parts of an Individual is usually actually an average over
> many instances of those parts.
>
> 3. *Measurement* In the usage above, I have combined
> oboe:ofCharacteristic and oboe:hasValue into a single PATO quality
> term `green color'. Is this acceptable usage, within the intentions
> of OBOE? I.e. is it fair to assert that a pato:Quality is a
> oboe;Measurement? This solution is satisfying because the popular
> Entity-Quality model can then be mapped directly into OBOE, as
> above. Matt Jones mentioned that there was an effort underway by
> participants of SONet, DataONE, and the Data Conservancy, and
> possibly the Plant Trait observations ontology group to ``try to
> harmonize many of the existing observations models, including OBOE, O
> +M, and EQ, as well as more traditional models like Darwin Core.''
> I'm wondering if there are any documents available describing this
> ontology interoperability development process?
>
> An alternative to using the OBOE ontology at all is to use a
> phenotype-focussed ontology (i.e., an OBO one emerging from the
> phenoscape group), where a pato:quality ro:inheres_in a po:Fruit.
> However, I'm not sure there are terms yet published that can be used
> in RDF. Any updates on this would be vaulable.
>
> 4. *General* I would also appreciate any guidance on whether these
> questions are appropriate for a public forum, or whether modeling a
> particular set of data is a `private' enterprise and too full of
> context dependent decisions. The options for someone in my position
> are to design a model that represents the data as I see it, coining
> various new terms where needed, or to find/wait for a semantic
> template, with standardized terms, and fit my data into it. For
> data re-use (especially LOD applications) the latter is preferable,
> but I don't think we are at the stage yet of having an agreed upon
> template. No right or wrong here, but your opinions would be valued.
>
> Thanks for your time.
>
> Best wishes,
>
> Cam
>
>
> +-------------------------------------------------+
> | CAMPBELL O. WEBB |
> | Senior Research Scientist |
> | Arnold Arboretum of Harvard University |
> | [ Harvard University Herbaria, |
> | 22 Divinity Ave, Cambridge MA, 02138, USA ] |
> +-------------------------------------------------+
> | Mail: Kotak Pos 2, Sukadana, Kab. Kayong Utara |
> | Kalimantan Barat 78852, Indonesia |
> | Mobile/SMS: +62-813-9917-7663 (GMT+7) |
> | Skype: ctenolophon Twitter: @cmwbb |
> | Web/PGP: http://phylodiversity.net/cwebb/ |
> +-------------------------------------------------+
>
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