Representing addiction in Mental Functioning and Disease ontologies
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Transcript of Representing addiction in Mental Functioning and Disease ontologies
Wanting what we don’t want to wantRepresenting addiction
in interoperable bio-ontologies
Janna Hastings1,2
Nicolas le Novère1
Werner Ceusters3
Kevin Mulligan2
Barry Smith3
1 European Bioinformatics Institute, UK2 University of Geneva, Switzerland
3 University at Buffalo, USA
ICBO @ Graz, July 2012
2
Substance addiction
Wednesday, April 12, 2023 Image credit: Roberta F., Wikimedia Commons
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Substance addiction in DSM-IVWhen an individual persists in use
of alcohol or other drugs
despite problems related to use of the substance,
substance dependence may be diagnosed.
Compulsive and repetitive use may result in tolerance to the effect of the drug
and withdrawal symptoms when use is reduced or stopped.
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What do we know about addiction?
… actually, rather a lot
Behaviour of addicted
personsBrain
activation
Neural pathways
Biochemical pathways
Psychiatric treatment
Properties of the addictive substances
Metabolism and
excretion of substances
Toxicity
Genetic susceptibility
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How do we find data about addiction?
… many, many databases
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Behaviour of addicted
personsBrain
activation
Neural pathways
Biochemical pathways
Psychiatric treatment
Properties of the addictive substances
Metabolism and
excretion of substances
Toxicity
Genetic susceptibility
PSYCHOLOGY, OBSERVATION,
CLINICAL QUESTIONNAIRES MEDICAL RECORDSNEUROBIOLOGY
MODELS
FUNCTIONAL IMAGING
BIOACTIVITY
MODELSCHEMISTRY
GENES
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GO annotations ChEBI annotations
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The same applies to many types of data
PATHWAYS, biological processes
METABOLIC DATA (e.g. NMR)
GENE EXPRESSION
DATA
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Describing mechanism of actionWhen a portion of heroin is consumed, the molecule heroin (CHEBI:27808) participates in a binding process (GO:0031628) to mu-opioid receptors (PR:000001612). Similarly, when a portion of tobacco is smoked, the molecule nicotine (CHEBI:27808) participates in a binding process (GO:0033130) to nicotinic acetycholine receptors (GO:0005892). Those receptors are present on the dopaminergic neurons (NeuroLex – nlx:144018), of the nucleus accumbens, described in BIRNlex (birnlex:727).
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What is missing?
Biological knowledge & data: mechanisms, genetic variants etc.
Neuroscientific knowledge & data:
neurons, neurochemistry, brain structure & function
Psychological research into
canonical human functioning
Medical
DOMAIN-SPECIFIC ONTOLOGIES
GLUE
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Mental Functioning Ontology and Mental Disease Ontology
BFO
MFOGMS
MD
MFO-EM
Domain-neutral ontological upper level
Mental FunctioningOntology
Ontology for GeneralMedical Science
Emotion Ontology
Mental Disease Ontology(Current focus on affective disorders and addiction)
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Substance addictions can be characterised by the substances that they are addictions to
MF:0000071cocaine addiction MF:0010071
cocaine addictiondisease course
realized in
MF:0020071use of cocaine
has part
S:00100100portion of cocaine
has input
CHEBI:27958cocaine
has granular part
Chemical and metabolic data
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Addiction in the Mental Disease Ontology
MF:0000046addiction
MF:0000053process addiction
MF:0000053substance addiction
MF:0000054gambling addiction
MF:0000055sex addiction
MF:0000064internet addiction
MF:0000066benzodiazepine addiction
MF:0000065opiate addiction
MF:0000067diazepam addiction
MF:0000059heroin addiction
MF:0000068morphine addiction
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Canonical research can be related to non-canonical symptoms in the disease course
MF:0000053substance addiction
MF:0001053substance addiction
disease course
realized in
MF:0001001non-canonical (impaired)
planning process
MF:0001011failed attempts to
stop substance use
has part
MF:0001002non-canonical (impaired)
thinking process
MF:0001012preoccupation with
substance use
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Bridging to underlying mechanisms
Addictions hijack neurotransmitter receptors and pathways
dopamine(CHEBI:25375)
molecular entity (CHEBI:25375)
biological role (CHEBI:24432)
neurotransmitter(CHEBI:25512)
has role
neurotransmitter receptor activity
(GO:0030594)
Molecular function (GO:0003674)
realized in
subtype
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http://code.google.com/p/mental-functioning-ontology/
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AcknowledgementsColin Batchelor
Jane Lomax, David Osumi-Sutherland
Occasional and regular members of the Cambridge ontology discussion group
Christoph Steinbeck