Ontology of Sensors Some Examples from Biology Barry

Ontology of Sensors: Some Examples from Biology Barry Smith National Center for Ontological Research (NCOR) University at Buffalo 1

An Introduction to "Beyond Semantic Sensor Network Ontologies (SSNO)“ Gary Berg-Cross Ontology Summit 2015 Track B Internet of Things: Toward Smart Networked Systems and Societies 1 2

The Stimulus-Sensor. Observation Ontology Design Pattern 3

Ontology Summit 2015: Internet of Things: Toward Smart Networked Systems and Societies Semantic Sensor Network Ontology: Past, Present, and Future Cory Henson Sr. Research Scientist Bosch Research and Technology Center cory. henson@us. bosch. com 4

Semantic Sensor Network Ontology 5

RELATION TO TIME GRANULARITY CONTINUANT INDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) CELL AND CELLULAR COMPONENT Cell (CL) MOLECULE OCCURRENT DEPENDENT Anatomical Organ Entity Function (FMA, (FMP, CPRO) Phenotypic CARO) Biological Process Quality (GO) (Pa. TO) Cellular Component Function (FMA, GO) (GO) Molecule (Ch. EBI, SO, Rna. O, Pr. O) Molecular Function (GO) Molecular Process (GO) Open Biological and Biomedical Ontologies (OBO) Foundry (http: //obofoundry. org) 6

top level mid-level Basic Formal Ontology (BFO) Information Artifact Ontology (IAO) Anatomy Ontology (FMA*, CARO) Cell Ontology (CL) domain level Cellular Component Ontology (FMA*, GO*) Ontology for Biomedical Investigations (OBI) Environment Ontology (Env. O) Subcellular Anatomy Ontology (SAO) Sequence Ontology (SO*) Protein Ontology (PRO*) Ontology for General Medical Science (OGMS) Infectious Disease Ontology (IDO*) Phenotypic Quality Ontology (Pa. TO) Biological Process Ontology (GO*) Molecular Function (GO*) Extension Strategy + Modular Organization 7

top level mid-level (generic hub) Basic Formal Ontology (BFO) Information Artifact Ontology(IAO) IAO-Science domain level (spokes populating IAO- IAOdownwards) Biology Physics IAO-Intel IAO-Computing IAOIAO-Intel. IAO-Army Air. Force Navy Software EMOEmail Ontology Each module built by downward population from its parent 8

Measuring the glucose concentration in blood 9

Ontology for Biomedical Investigations 10

http: //www. jbiomedsem. com/content/1/S 7 11

OBI: Overview Core terms 12

OGMS Ontology for General Medical Science, http: //code. google. com/p/ogms/ 13

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Big Picture 15

Nociceptive System 16

Pain Ontology Pain Canonical Pain PCI: Pain with concordant tissue damage PRP: Pain-related phenomenon without pain Variant Pain PNT: Pain without tissue damage Neuropathic nociception PBWP: Pain behavior without pain http: //philpapers. org/archive/SMITAO-12. pdf TWP: Tissue damage without pain 17

Symptoms Signs Physical Basis Examples Canonical Pain PCT: Pain with Pain concordant tissue damage 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 Primary sunburn Intact nociceptive Pain from strained muscle system Pain from fracture Pulpitis PNT: pain Pain without concordant tissue damage 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 Myofascial pain disorder amplitude control Tension-type headache mechanisms associated with Chronic back pain the nociceptive system Intact nociceptive system NN: neuropathic nociception Neurological test confirming nerve damage Disorder in the nociceptive system Variant Pain 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 TWP: tissuedamage without pain No pain Manifestation of tissue damage normally of the Suppression of pain system by Stress associated with sudden sort to cause pain one or other mechanism emergencies Physiological damping of the pain process caused by endorphins 18 Placebo-induced opioid analgesia Genetic insensitivity to pain Mental states such as anxiety, Factitious pain rather than peripheral tissue Malingering locus Anxiety-induced pain report Disordered emotional or cognitive systems misinterpreting sensory signals

The Pain Ontology as subtype of Sensing Ontology Sensing Canonical sensing with concordant signal Variant sensing Sensing with nonconcordant signal Hallucinating (sensing but no signal) Sensing-related phenomena with no sensing Sensing report but no sensing Signal but no sensing 19

Four types of (pain) sensor failure Pain Canonical Pain PCI: Pain with concordant tissue damage triggered by design inputs Variant Pain PNT: Pain without tissue damage triggered without inputs Neuropathic nociception triggered by self PRP: Pain-related phenomenon without pain PBWP: Pain behavior without pain generates ungrounded outputs TWP: Tissue damage without pain not triggered by design inputs 20

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