ICBO @ Graz, July 2012Wanting what we don’t want to want          Representing addiction     in interoperable bio-ontologi...
Substance addictionFriday, July 27, 2012     Image credit: Roberta F., Wikimedia Commons   2
Friday, July 27, 2012   3
Substance addiction in DSM-IVWhen an individual persists in use                         of alcohol or other drugsdespite p...
Friday, July 27, 2012   5
What do we know about addiction?      Behaviour                                          Neural                           ...
How do we find data about addiction?PSYCHOLOGY, OBSERVATION            ,                                                  ...
Friday, July 27, 2012   8
GO annotations   ChEBI annotationsFriday, July 27, 2012                                        9
The same applies to many types of data                                  METABOLIC                                DATA (e.g...
Describing mechanism of actionWhen a portion of heroin is consumed, themolecule heroin (CHEBI:27808) participates in abind...
What is missing?                                          GLUE                               DOMAIN-SPECIFIC ONTOLOGIES   ...
Mental Functioning Ontology and                 Mental Disease Ontology                                                 Do...
Substance addictions can be         characterised by the substances that                they are addictions to    MF:00000...
Addiction in the Mental Disease Ontology                                             MF:0000046                           ...
Canonical research can be related to            non-canonical symptoms in the                     disease course      MF:0...
Bridging to underlying mechanismsAddictions hijack neurotransmitter receptors andpathways                molecular entity ...
http://code.google.com/p/                        mental-functioning-ontology/Friday, July 27, 2012                        ...
Acknowledgements                               Colin BatchelorJane Lomax, David Osumi-SutherlandOccasional and regular mem...
Upcoming SlideShare
Loading in...5
×

Representing addiction in Mental Functioning and Disease ontologies

362

Published on

Enabling querying and browsing of biomedical and neuroscientific research on addiction using interoperable ontologies and cross-products. Presented at ICBO 2012.

Published in: Health & Medicine, Education
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
362
On Slideshare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
7
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide
  • Why am I interested in substance addiction? Co-morbidity with mood disorders. Serious condition in and of itself. Strikes vulnerable teenagers. Takes away something of the intrinsic self-directedness of humans. We will draw here on concrete examples from the domain of substance addiction. The choice of topic is arbitrary in the sense that another aspect of mental functioning would have worked just as well. Addiction is a primary mental health problem affecting an increasing percentage of the population in the developed world (NationalInstitute on Drug Abuse, 2007). The estimated death toll for 2000 due solely to use of tobacco was around 5 million worldwide (Ezzatiand Lopez, 2009). Furthermore, addiction is often co-morbid with other mental health conditions such as bipolar disorder and depression.
  • La Morfina, Santiago Rusinol y Prats
  • Pathway illustration sourced from KEGG: http://www.kegg.jp/kegg-bin/highlight_pathway?scale=1.0&map=map05030&keyword=addictionNMR spectrum illustration (of a derivative of cocaine) comes from http://www.justice.gov/dea/programs/forensicsci/microgram/journal_v4_num14/pg5.html
  • Computable representation of the symptoms of mental diseases, linked up to the questionnaires and other instruments that are used in diagnosisWhat sorts of things are the symptoms? What is known about normal functionings of the relevant sorts (so that we can compare data?)How do we use general search terms to also retrieve data at much lower levels of granularity, without doing massive annotation of irrelevant information (from the perspective of the lower-level researchers)?
  • Representing addiction in Mental Functioning and Disease ontologies

    1. 1. ICBO @ Graz, July 2012Wanting what we don’t want to want Representing addiction in interoperable bio-ontologies Janna Hastings1,2 Nicolas le Novère1 Werner Ceusters3 Kevin Mulligan2 Barry Smith3 1 European Bioinformatics Institute, UK 2 University of Geneva, Switzerland 3 University at Buffalo, USA
    2. 2. Substance addictionFriday, July 27, 2012 Image credit: Roberta F., Wikimedia Commons 2
    3. 3. Friday, July 27, 2012 3
    4. 4. Substance addiction in DSM-IVWhen an individual persists in use of alcohol or other drugsdespite problems related to use of the substance, substance dependence may be diagnosed.Compulsive and repetitive use may result in toleranceto the effect of the drug and withdrawal symptomswhen use is reduced or stopped.Friday, July 27, 2012 4
    5. 5. Friday, July 27, 2012 5
    6. 6. What do we know about addiction? Behaviour Neural Psychiatric of addicted pathways treatment persons Brain activation Metabolism and excretion of Biochemical pathways Properties of substances the addictive Toxicity substances Genetic susceptibility … actually, rather a lotFriday, July 27, 2012 6
    7. 7. How do we find data about addiction?PSYCHOLOGY, OBSERVATION , NEUROBIOLOGY MEDICAL RECORDSCLINICAL QUESTIONNAIRES MODELS Behaviour Neural Psychiatric of addicted pathways treatment persons Brain activation Metabolism FUNCTIONAL BIOACTIVITY IMAGING and excretion of Biochemical pathways Properties of substances the addictive Toxicity MODELS substances CHEMISTRY Genetic GENES susceptibility … many, many databases Friday, July 27, 2012 7
    8. 8. Friday, July 27, 2012 8
    9. 9. GO annotations ChEBI annotationsFriday, July 27, 2012 9
    10. 10. The same applies to many types of data METABOLIC DATA (e.g. NMR) GENE EXPRESSION PATHWAYS, biological DATAFriday, July 27, 2012 10 processes
    11. 11. Describing mechanism of actionWhen a portion of heroin is consumed, themolecule heroin (CHEBI:27808) participates in abinding process (GO:0031628) to mu-opioidreceptors (PR:000001612).Similarly, when a portion of tobacco is smoked, themolecule nicotine (CHEBI:27808) participates in abinding process (GO:0033130) to nicotinicacetycholine receptors (GO:0005892).Those receptors are present on the dopaminergicneurons (NeuroLex – nlx:144018), of the nucleusaccumbens, described in BIRNlex (birnlex:727).Friday, July 27, 2012 11
    12. 12. What is missing? GLUE DOMAIN-SPECIFIC ONTOLOGIES Neuroscientific Psychological Biological knowledge & data: research into knowledge & data:Medical neurons, neurochemistr canonical human mechanisms, genetic y, brain structure & functioning variants etc. functionFriday, July 27, 2012 12
    13. 13. Mental Functioning Ontology and Mental Disease Ontology Domain-neutral BFO ontological upper level Mental Functioning OGMS MF Ontology Ontology for General Medical Science MFO-EM Emotion Ontology MD Mental Disease Ontology (Current focus on affective disorders and addiction)Friday, July 27, 2012 13
    14. 14. Substance addictions can be characterised by the substances that they are addictions to MF:0000071 realized in MF:0010071 cocaine addiction cocaine addiction disease course has part S:00100100 has input MF:0020071 portion of cocaine use of cocaine has granular part CHEBI:27958 Chemical and cocaine metabolic dataFriday, July 27, 2012 14
    15. 15. Addiction in the Mental Disease Ontology MF:0000046 addiction MF:0000053 MF:0000053 process addiction substance addiction MF:0000054 MF:0000066 MF:0000065 gambling addiction benzodiazepine addiction opiate addiction MF:0000055 MF:0000067 MF:0000059 sex addiction diazepam addiction heroin addiction MF:0000064 MF:0000068 internet addiction morphine addiction Friday, July 27, 2012 15
    16. 16. Canonical research can be related to non-canonical symptoms in the disease course MF:0001002 MF:0001001non-canonical (impaired) non-canonical (impaired) thinking process planning process MF:0001012 MF:0001011 preoccupation with failed attempts to substance use stop substance use has part MF:0001053 MF:0000053 realized in substance addiction substance addiction disease courseFriday, July 27, 2012 16
    17. 17. Bridging to underlying mechanismsAddictions hijack neurotransmitter receptors andpathways molecular entity biological role Molecular function (CHEBI:25375) (CHEBI:24432) (GO:0003674) subtype neurotransmitter dopamine neurotransmitter receptor activity (CHEBI:25375) (CHEBI:25512) (GO:0030594) has role realized inFriday, July 27, 2012 17
    18. 18. http://code.google.com/p/ mental-functioning-ontology/Friday, July 27, 2012 18
    19. 19. Acknowledgements Colin BatchelorJane Lomax, David Osumi-SutherlandOccasional and regular members of theCambridge ontology discussion group Christoph SteinbeckFriday, July 27, 2012 19
    1. A particular slide catching your eye?

      Clipping is a handy way to collect important slides you want to go back to later.

    ×