ontology of sensors: some examples from biology barry smith national center for ontological research...

Ontology of Sensors: Some Examples from Biology

Barry SmithNational Center for Ontological Research (NCOR)

University at Buffalo

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An Introduction to "Beyond Semantic Sensor Network

Ontologies (SSNO)“Gary Berg-CrossOntology Summit 2015 Track B

Internet of Things: Toward Smart Networked Systems and Societies

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The Stimulus-Sensor-Observation Ontology

Design Pattern

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Ontology Summit 2015: Internet of Things: Toward Smart Networked Systems and Societies

Cory Henson

Sr. Research ScientistBosch Research and Technology Centercory.henson@us.bosch.com

Semantic Sensor Network Ontology:Past, Present, and Future

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Semantic Sensor Network Ontology

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Open Biological and Biomedical Ontologies (OBO) Foundry (http://obofoundry.org) 6

RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic

Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

Anatomy Ontology(FMA*, CARO)

Environment

Ontology(EnvO)

Infectious Disease

Ontology(IDO*)

Biological Process

Ontology (GO*)

Cell Ontology

(CL)

CellularComponentOntology

(FMA*, GO*) Phenotypic Quality

Ontology(PaTO)

Subcellular Anatomy Ontology (SAO)Sequence Ontology

(SO*) Molecular Function

(GO*)Protein Ontology(PRO*) Extension Strategy + Modular Organization

top level

mid-level

domain level

Information Artifact

Ontology(IAO)

Ontology for Biomedical

Investigations(OBI)

Ontology for General Medical Science (OGMS)

Basic Formal Ontology (BFO)

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IAO-Science IAO-IntelIAO-Computing

IAO-Biolo

gy

IAO-Physi

cs

IAO-Intel-Navy

IAO-Intel-Army

IAO-Intel-AirForce

IAO-Softwar

e

EMO-Email

Ontology

Each module built by downward population from its parent

top level

mid-level(generic hub)

domain level(spokes

populating downwards)

Information Artifact Ontology(IAO)

Basic Formal Ontology (BFO)

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Measuring the glucose concentration in blood

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Ontology for Biomedical Investigations

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http://www.jbiomedsem.com/content/1/S1/S711

Core terms

OBI: Overview

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OGMS

Ontology for General Medical Science,

http://code.google.com/p/ogms/

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Big Picture

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Nociceptive System

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Pain Ontology

http://philpapers.org/archive/SMITAO-12.pdf 17

Symptoms Signs Physical Basis Examples

Canonical PainPCT: Pain with concordant tissue damage

Pain Manifestation of tissue damageSignals 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 sunburnPain from strained musclePain from fracturePulpitis

Variant PainPNT: pain without concordant tissue damage

Pain Manifestation of some disorder in the patientSignals sent to nociceptive system Patient reports of pain are either exaggerated or muted relative to disorderActivation of emotion generating brain centers

Physical disorder of amplitude control mechanisms associated with the nociceptive systemIntact nociceptive system

Myofascial pain disorderTension-type headacheChronic back pain

NN: neuro-pathic nociception

Pain Neurological test confirming nerve damage

Disorder in the nociceptive system

Trigeminal neuralgiaPost-herpetic neuralgiaDiabetic neuropathyCentral pain

PRP: Pain-Related Phenomena Without PainPBWP: pain behavior without pain

Aaargh! Report of painSick role behaviors accompanied by normal clinical examinationGrossly 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 painMalingeringAnxiety-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 emergenciesPhysiological damping of the pain process caused by endorphins Placebo-induced opioid analgesiaGenetic insensitivity to pain

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The Pain Ontology as subtype of Sensing Ontology

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Four types of (pain) sensor failure

triggered by design inputs

triggered without inputs

triggered by self

generatesungrounded outputs

not triggered by design inputs 20

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