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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
1 2
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 [email protected]
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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