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

http://commons.wikimedia.org/wiki/User:Roberta_F.

Wednesday, April 12, 2023 3


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.


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


How do we find data about addiction?

… many, many databases


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


GO annotations ChEBI annotations


The same applies to many types of data

PATHWAYS, biological processes

METABOLIC DATA (e.g. NMR)

GENE EXPRESSION

DATA


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).


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


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)


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


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


Canonical research can be related to non-canonical symptoms in the disease course



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


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


http://code.google.com/p/mental-functioning-ontology/


AcknowledgementsColin Batchelor

Jane Lomax, David Osumi-Sutherland

Occasional and regular members of the Cambridge ontology discussion group

Christoph Steinbeck

Representing addiction in Mental Functioning and Disease ontologies

Health & Medicine

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