The Ontology of Sensors: A Critical Overview Barry Smith National Center for Ontological Research (NCOR) University at Buffalo 1

NCGIA 2

National Center for Geographic Information and Analysis (founded 1989) Buffalo / Maine / Santa Barbara 3

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5 Ling Bian Werner Kuhn

6 David Mark

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The Environment Ontology 10

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12 MIT Press, August 2015

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Ontology for Biomedical Investigations (OBI)

Figure 2. Core terms of the Biological Collections Ontology (BCO) and their relations to upper ontologies. Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, et al. (2014) Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. PLoS ONE 9(3): e doi: /journal.pone

Figure 2. Core terms of the Biological Collections Ontology (BCO) and their relations to upper ontologies. Walls RL, Deck J, Guralnick R, Baskauf S, Beaman R, et al. (2014) Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. PLoS ONE 9(3): e doi: /journal.pone Biological Collections Ontology (BCO) BFO OBI BFO OBI

18 NeuroPsychological) Testing) Ontology BFO OBI

Open Biomedical Ontologies Foundry 19

RELATION TO TIME GRANULARITY CONTINUANT OCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Human Disease Ontology (HDO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Ontology for General Medical Science (OGMS) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Original OBO Foundry ontologies (yellow = Gene Ontology) 20

Common Reference Ontologies for Plants (cROP)

Examples of BFO/OBO Foundry approach extended 22 UNEP Ontology Framework United Nations Environment Programme USGS National Map Ontologies United States Geological Survey TRIP OntologiesFederal Highway Administration (FHWA) Transportation Research Informatics Platform (TRIP) Common Core Ontologies / Joint Doctrine Ontology US Air Force Research Labs (AFRL) / Training and Doctrine Command (TRADOC) / Office of Naval Research …

Semantic Sensor Network Ontology 23

W3C Stimulus-Sensor-Observation Ontology Design Pattern 24 Stimuli =def. detectable changes in the environment Sensors =def. physical objects that perform observations

W3C Stimulus-Sensor-Observation Ontology Design Pattern 25 “Observations act as the nexus between incoming stimuli, the sensor, and the output of the sensor, i.e., a symbol representing a region in a dimensional space. Therefore, we regard observations as social, not physical, object.”

DOLCE Descriptive Ontology for Linguistic and Cognitive Engineering 26

SSN alignment to DOLCE 27

SSN alignment to DOLCE 28

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ssn:Observation subclass of: DUL:SituationDUL:Situation, things that have a ssn:observedProperty property who must be a ssn:Property, things that have exactly ssn:sensingMethodUsed property that is a ssn:Sensing, things that have exactly ssn:featureOfInterest property that is a ssn:FeatureOfInterest, things that have a ssn:sensingMethodUsed property who must be ssn:Sensing, things that have a DUL:includesEvent property who may be a ssn:Stimulus, things that have a ssn:observationResult property who must be a ssn:SensorOutput, things that have exactly ssn:observedBy property that is a ssn:Sensor, … ssn:observedPropertyssn:Propertyssn:sensingMethodUsedssn:Sensing ssn:featureOfInterestssn:FeatureOfInterest ssn:sensingMethodUsedssn:SensingDUL:includesEventssn:Stimulus ssn:observationResult ssn:SensorOutput ssn:observedByssn:Sensor 30

W3C paraphrase A Observation is something that is a Situation and has a observedProperty property who must be a Property and has exactly sensingMethodUsed property that is a Sensing and has exactly featureOfInterest property that is a FeatureOfInterest and has a sensingMethod- Used property who must be a Sensing and has a includesEvent property who may be a Stimulus and has a observationResult property who must be a SensorOutput and has exactly observedBy property that is a Sensor … Copyright W3C 31

Today Werner Kuhn: Modeling Events Alan Ruttenberg: From Image Ontologies to Sensor Ontologies Tomorrow Pier Buttigieg: Semantics for Sensing the Arctic Boyan Brodaric: Water Bodies and Sensor Ontologies Mark Jensen: The United Nations Environment Programme Sustainable Development Goals Ontology Initiative 32

Today Werner Kuhn: Modeling Events Alan Ruttenberg: From Image Ontologies to Sensor Ontologies Tomorrow Pier Buttigieg: Semantics for Sensing the Arctic Boyan Brodaric: Water Bodies and Sensor Ontologies Mark Jensen: The United Nations Environment Programme Sustainable Development Goals Ontology Initiative 33 DOLCE

Today Werner Kuhn: Modeling Events Alan Ruttenberg: From Image Ontologies to Sensor Ontologies Tomorrow Pier Buttigieg: Semantics for Sensing the Arctic Boyan Brodaric: Water Bodies and Sensor Ontologies Mark Jensen: The United Nations Environment Programme Sustainable Development Goals Ontology Initiative 34 BFO DOLCE

OBI: Measuring the glucose concentration in blood 35

OGMS Ontology for General Medical Science, 36

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Big Picture 38

Nociceptive System 39

Pain Ontology Pain Canonical Pain PCI: Pain with concordant tissue damage Variant Pain PNT: Pain without tissue damage Neuropathic nociception PRP: Pain-related phenomenon without pain PBWP: Pain behavior without pain TWP: Tissue damage without pain 40

SymptomsSignsPhysical BasisExamples Canonical Pain PCT: Pain with concordant tissue damage Pain Manifestation of tissue damage Signals sent to nociceptive system Activation of emotion- generating brain centers, which can produce increased heart rate, blood pressure, galvanic skin response. Peripheral tissue damage Intact nociceptive system Primary sunburn Pain from strained muscle Pain from fracture Pulpitis Variant Pain PNT: pain without concordant tissue damage Pain Manifestation of some disorder in the patient Signals sent to nociceptive system Patient reports of pain are either exaggerated or muted relative to disorder Activation of emotion generating brain centers Physical disorder of amplitude control mechanisms associated with the nociceptive system Intact nociceptive system Myofascial pain disorder Tension-type headache Chronic back pain NN: neuro- pathic nociception Pain Neurological test confirming nerve damage Disorder in the nociceptive system Trigeminal neuralgia Post-herpetic neuralgia Diabetic neuropathy Central pain PRP: Pain-Related Phenomena Without Pain PBWP: pain behavior without pain Aaargh! Report of pain Sick role behaviors accompanied by normal clinical examination Grossly exaggerated pain behaviors Identified external incentives Mental states such as anxiety, rather than peripheral tissue locus Disordered emotional or cognitive systems misinterpreting sensory signals Factitious pain Malingering Anxiety-induced pain report TWP: tissue- damage without pain No pain Manifestation of tissue damage normally of the sort to cause pain Suppression of pain system by one or other mechanism Stress associated with sudden emergencies Physiological damping of the pain process caused by endorphins Placebo-induced opioid analgesia Genetic insensitivity to pain 41

The Pain Ontology as subtype of Sensing Ontology SensingCanonical sensing Canonical sensing with concordant signal Variant sensing Sensing with non-concordant signal Hallucinating (sensing but no signal) Sensing-related phenomena with no sensing Sensing report but no sensing Signal but no sensing 42

Four types of (pain) sensor failure Pain Canonical Pain PCI: Pain with concordant tissue damage Variant Pain PNT: Pain without tissue damage Neuropathic nociception PRP: Pain-related phenomenon without pain PBWP: Pain behavior without pain TWP: Tissue damage without pain triggered by design inputs triggered without inputs triggered by self generates ungrounded outputs not triggered by design inputs 43

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