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NIF Webinar, 24 April 2012Mental Functioning Ontology     for interdisciplinary researchinto mental disease, emotions and ...
Why mental             functioning?                                       I want…Oxytocin is believed to play a role in va...
Many chemicals                     can affect mental functioning                                             The Chemical ...
How does mental functioning                             actually work?                                                    ...
Theories of mental functioning have                                                       Abducted!    testable implicatio...
Existing vocabularies        don’t include          computable           definitions
Mental Functioning Ontology (MF)Tuesday, April 24, 2012              7
Modules under development:                   Mental diseases and emotions                                                 ...
Motivation and GoalsTuesday, April 24, 2012                          9
Bio-ontologies facilitate            interdisciplinary scientific research1. Standardised vocabulary with definitions and ...
Modern scientific research relies on                 computational support     Patient histories,                   EHR   ...
Ontology for standardisation                                        Semantics-free unique identifiers that are            ...
Ontology annotations are generic                across multiple databasesID           Patient             Finding type    ...
Population-wide science depends on                aggregation of dataAre there genes significantly enriched in all peoplew...
Ontology for hierarchical organisation                                              MD:0000046                            ...
Research involves comparison of results       to existing data arising from other      projects, stored in public database...
Tuesday, April 24, 2012   17
Tuesday, April 24, 2012   18
To amass the correct search criteria to find the data for    each comparison requires careful manual examination    … and ...
A shared community ontology for          annotation allows unified searching              across databases (e.g. GOA)     ...
Computers can’t “see” implicit                   relationships between entities Substance addiction is characterised by sy...
Ontologies capture explicit computable               relationships between entities      MD:0001002                       ...
Related entities are themselves used        in annotations                                MD:0001002                      ...
Different domains operate at different          levels of granularity and focus                                      METAB...
Urine samples of addicted patients reveal metabolites                                        NMR data for                 ...
Ontology relationships can explicitly          bridge across different ontologies at                    different levels  ...
Current status and ongoing work             in the Emotion OntologyTuesday, April 24, 2012                    27
The Emotion Ontology (MFO-EM)                                                       BFO:Entity                            ...
Types of emotionTuesday, April 24, 2012                      29
To define the characteristics of different     emotions start with canonical emotionsEmotion types (such as fear) show eno...
Canonical fear                                fear                                  subtype                             ca...
Canonical and non-canonical fearCanonical fear gives rise to action tendenciesthat are conformant to the perceived dangerP...
Types of appraisalTuesday, April 24, 2012                        33
Types of subjective feelingsTuesday, April 24, 2012                            34
Types of physiological responsesTuesday, April 24, 2012                  35
Types of emotional behaviourTuesday, April 24, 2012                       36
Annotation of data from Cognitive             Neuroscience of Emotion Study Task                                   Annotat...
(Part of) the biochemical basis of                      emotion is in ChEBI Emotions are effected in part by neurotransmit...
Biological processes in affective                             disordersSome mental diseases involve altered emotionalfunct...
Availability, ContactsMental Functioning Ontology available at:http://mental-functioning-ontology.googlecode.com/svn/trunk...
Acknowledgements                                          Thanks!Buffalo Ontologists    Barry Smith, Werner Ceusters, Mark...
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Mental functioning ontology for interdisciplinary research into mental disease, emotions and drugs

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Presented at the Neuroscience Information Framework (NIF) webinar series on 24/04/2012. An overview of the Mental Functioning Ontology aims and objectives.

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Mental functioning ontology for interdisciplinary research into mental disease, emotions and drugs

  1. 1. NIF Webinar, 24 April 2012Mental Functioning Ontology for interdisciplinary researchinto mental disease, emotions and drugs Janna Hastings1,2 (ChEBI, MF and the Emotion Ontology) 1 Cheminformatics and Metabolism, European Bioinformatics Institute, UK 2 Swiss Center for Affective Sciences, University of Geneva, Switzerland
  2. 2. Why mental functioning? I want…Oxytocin is believed to play a role in various behaviors,including orgasm, social recognition, pair bonding, anxiety …it is sometimes referred to as the "love hormone".The inability to secrete oxytocin and feel empathy is I think…linked to sociopathy, psychopathy, narcissism andgeneral manipulativeness. Tuesday, April 24, 2012 2
  3. 3. Many chemicals can affect mental functioning The Chemical OntologyTuesday, April 24, 2012 3
  4. 4. How does mental functioning actually work? EEGBiology Mouse Psychology Human Cognitive Science fMRI Genetic PET profiling GeneNeuroscience expression analysis Psychiatry Metabolic Chemistry Self-reports analysis Questionnaires
  5. 5. Theories of mental functioning have Abducted! testable implications for research Replaced! into mental diseaseCapgras delusion:a disorder in which a personholds a delusion that a friend,spouse, parent, or other closefamily member has been replacedby an identical-looking impostor. Faulty perception? Normal perception, faulty reasoning? Faulty emotional reaction to perception? Overactive imagination? TESTABLE IMPLICATIONS
  6. 6. Existing vocabularies don’t include computable definitions
  7. 7. Mental Functioning Ontology (MF)Tuesday, April 24, 2012 7
  8. 8. Modules under development: Mental diseases and emotions 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)Tuesday, April 24, 2012 8
  9. 9. Motivation and GoalsTuesday, April 24, 2012 9
  10. 10. Bio-ontologies facilitate interdisciplinary scientific research1. Standardised vocabulary with definitions and synonyms for unified database annotations2. Hierarchical organisation for aggregation and multi- level comparison of results3. Community adoption for comparison of results to other project results worldwide4. Explicit relationships and underlying logic for automated reasoning to related entities5. Explicit bridging relationships between different ontologies for exploring underlying mechanismsTuesday, April 24, 2012 10
  11. 11. Modern scientific research relies on computational support Patient histories, EHR Synthesis Caregiver, Datapscyhiatric reports Analysis Genomic and Data metabolomic profiles Reporting Questionnaires Data Publication and self-reports Brain scans Tuesday, April 24, 2012 11
  12. 12. Ontology for standardisation Semantics-free unique identifiers that are stable and maintained MD:0000901 CODE (MD) indicates WHICH ONTOLOGY substance abuse A numeric identifier is unique per term is a Unambiguous preferred label together MD:0000902 with a textual definition guide the annotation marijuana abuse of this ontology term to associated data is abuse of substance S:09090909 Synonyms and other metadata are collected marijuana to facilitate searching, disambiguation and --------------------------- text processing Synonym: cannabis Synonym: THC Synonyms may be in several languages Synonym: dronabinol or reflect differing naming practices in different disciplinesTuesday, April 24, 2012 12
  13. 13. Ontology annotations are generic across multiple databasesID Patient Finding type Detail1111 Smith, John MF:0000902 Occasional (marijuana abuse)1111 Smith, John MF:0000903 Occasional (alcohol abuse)1111 Smith, John MF:0000904 Frequent (nicotine abuse) Same IDsSample ID Sample type Conditions Genotype1111 Illumina Golden Gate MF:0000903; MF:0000902 …Tuesday, April 24, 2012 13
  14. 14. Population-wide science depends on aggregation of dataAre there genes significantly enriched in all peoplewho suffer from some addiction?Are there differences between those people whosuffer from substance addiction compared to thosewho suffer from process addictions?Are there differences between those people whosuffer from opiate substance addictions and thosewho suffer from addictions to benzodiazepines?Tuesday, April 24, 2012 14
  15. 15. Ontology for hierarchical organisation MD:0000046 addiction MD:0000053 MD:0000053 process addiction substance addiction MD:0000054 MD:0000066 MD:0000065 gambling addiction benzodiazepine addiction opiate addiction MD:0000055 MD:0000067 MD:0000059 sex addiction diazepam addiction heroin addiction MD:0000064 MD:0000068 internet addiction morphine addictionEvery ‘sex addiction’ is a ‘process addiction’, every ‘process addiction’ is an ‘addiction’Every ‘heroin addiction’ is an ‘opiate addiction’, every ‘opiate addiction’ is a ‘substanceaddiction’, every ‘substance addiction’ is an ‘addiction’. And so on.Tuesday, April 24, 2012 15
  16. 16. Research involves comparison of results to existing data arising from other projects, stored in public databasesA researcher obtains brain scans for several addicted patients. In orderto determine how they compare to existing scans of other addictedpatients and to non-addicted patients, (s)he looks in public databases.Relating to addiction, manual examination of the BrainMap databasesearchcriteria suggests two patient diagnosis categories that maybe relevant: alcoholism and pathologicalgambling… as well as many unstructured keywordsTuesday, April 24, 2012 16
  17. 17. Tuesday, April 24, 2012 17
  18. 18. Tuesday, April 24, 2012 18
  19. 19. To amass the correct search criteria to find the data for each comparison requires careful manual examination … and that’s only one database out of hundredsTuesday, April 24, 2012 19
  20. 20. A shared community ontology for annotation allows unified searching across databases (e.g. GOA) RIKEN BrainMap Neuroimaging PlatformBrede NiftifMRI Data OpenfMRI NeuroSynth CenterTuesday, April 24, 2012 20
  21. 21. Computers can’t “see” implicit relationships between entities Substance addiction is characterised by symptoms such as preoccupation with substance and repeated failed attempts to control the use of the substance. These are non- canonical thinking and planning activities. But, there is no easy way to automatically compare with data from other conditions that have similar symptoms. Patient data – Patient data – Patient data – impaired rational preoccupation or addicted patients control of actions other compulsive or planning thinkingTuesday, April 24, 2012 21
  22. 22. Ontologies capture explicit computable relationships between entities MD:0001002 MD:0001001non-canonical (impaired) non-canonical (impaired) thinking process planning process MD:0001012 MD:0001011 Relationships preoccupation with failed attempts to are named substance use stop substance use and have definitions has part MD:0001053 They are used MD:0000053 realized in substance addiction substance addiction for automated disease course reasoning and questionTuesday, April 24, 2012 answering22
  23. 23. Related entities are themselves used in annotations MD:0001002 non-canonical (impaired) thinking process Patient data on Patient data on symptom symptom assessment assessment MD:0001001 (Dysexecutive (Addiction) non-canonical (impaired) syndrome) planning process … which allows patient data from disparate diseases (and research into normal functioning) to be comparedTuesday, April 24, 2012 23
  24. 24. Different domains operate at different levels of granularity and focus METABOLIC DATA (e.g. NMR) GENE EXPRESSION PATHWAYS, biological DATATuesday, April 24, 2012 24 processes
  25. 25. Urine samples of addicted patients reveal metabolites NMR data for metabolites of cocaine is found in metabolomics databases -- indexed by small moleculesTuesday, April 24, 2012 25
  26. 26. Ontology relationships can explicitly bridge across different ontologies at different levels MD:0000071 realized in MD:0010071 cocaine addiction cocaine addiction disease course has part S:00100100 has input MD:0020071 portion of cocaine use of cocaine has granular part CHEBI:27958 Chemical and cocaine metabolic dataTuesday, April 24, 2012 26
  27. 27. Current status and ongoing work in the Emotion OntologyTuesday, April 24, 2012 27
  28. 28. The Emotion Ontology (MFO-EM) BFO:Entity BFO MFO BFO:Continuant BFO:Occurrent MFO-EM BFO:Independent BFO:Dependent Continuant Continuant BFO:Process Organism BFO:Disposition Bodily Process Physiological Response to Emotion Process Mental Process Cognitiveinheres_in Representation Appraisal Process Emotional Action Tendencies Affective is_output_of Representation Appraisal Emotional Behavioural Process Subjective Emotional Feeling has_part agent_of Emotion Occurrent
  29. 29. Types of emotionTuesday, April 24, 2012 29
  30. 30. To define the characteristics of different emotions start with canonical emotionsEmotion types (such as fear) show enormous variance across instancesJust as do anatomical types, e.g. human bodiesOntology expresses what is always true… But also aims to saysomething useful for representation of domain knowledge.Solution: encode such knowledge in ‘canonical’ types canonical Has part appraisal Has output Appraisal of fear process dangerousness Canonical fear results from an appraisal of dangerousness Tuesday, April 24, 2012 30
  31. 31. Canonical fear fear subtype canonical fear EMOTION COMPONENT CHARACTERISTIC FOR FEAR Action tendency Fight-or-flight Subjective emotional feeling Negative, tense, powerless Behavioural response Characteristic fearful facial expression Characteristic appraisal Something is dangerous to meTuesday, April 24, 2012 31
  32. 32. Canonical and non-canonical fearCanonical fear gives rise to action tendenciesthat are conformant to the perceived dangerPhobia =disposition giving rise to non-canonical fearlaridaphobia : intense fear of seagullsTuesday, April 24, 2012 32
  33. 33. Types of appraisalTuesday, April 24, 2012 33
  34. 34. Types of subjective feelingsTuesday, April 24, 2012 34
  35. 35. Types of physiological responsesTuesday, April 24, 2012 35
  36. 36. Types of emotional behaviourTuesday, April 24, 2012 36
  37. 37. Annotation of data from Cognitive Neuroscience of Emotion Study Task Annotation class in MFO/MFOEM Recognition of gender in emotional facial Visual perception of emotional facial expressions expressions (subClassOf perception) Recall of personal emotional memories Memory of emotional episodes with instructions to try re-create feeling (subClassOf memory) Listening to emotional sounds (e.g. grunts Auditory perception of emotional stimuli of disgust) (subClassOf perception) Viewing emotional film extracts Visual and auditory perception of emotional stimuli (subClassOf perception) The link from perception of emotional fear in facial expressions to canonical fear is subject to empirical researchTuesday, April 24, 2012 37
  38. 38. (Part of) the biochemical basis of emotion is in ChEBI Emotions are effected in part by neurotransmitters such as dopamine, tryptophanmolecular entity biological role Molecular function emotion (CHEBI:25375) (CHEBI:24432) (GO:0003674) (MFOEM:1) subtype neurotransmitter happiness dopamine neurotransmitter receptor activity (MFOEM:42) (CHEBI:25375) (CHEBI:25512) (GO:0030594) has role realized in part of Tuesday, April 24, 2012 38
  39. 39. Biological processes in affective disordersSome mental diseases involve altered emotionalfunctioning. (E.g. depression, bipolar disorder) Disposition Process mental emotion biological process disease Mechanism of action: complex down-regulation disturbances in non-canonical of dopaminergic depression underlying sadness system systems (GO:0032227) realized in has partTuesday, April 24, 2012 39
  40. 40. Availability, ContactsMental Functioning Ontology available at:http://mental-functioning-ontology.googlecode.com/svn/trunk/ontology/MF.owlEmotion Ontology available at:http://emotion-ontology.googlecode.com/svn/trunk/ontology/MFOEM.owlDiscussion mailing lists:mfo-discuss@googlegroups.comemotion-ontology@googlegroups.comTuesday, April 24, 2012 40
  41. 41. Acknowledgements Thanks!Buffalo Ontologists Barry Smith, Werner Ceusters, Mark JensenEmotion Researchers in Geneva Kevin Mulligan, David Sander, Julien DeonnaChemistry, Biology, Neuroscience Christoph Steinbeck, Nicolas le Novère, Colin Batchelor, David Osumi-Sutherland, Jane Lomax, Jessica Turner, Angela LairdTuesday, April 24, 2012 41

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