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Jodi Schneider, Carol Collins, Lisa E Hines,
John R Horn, and Richard Boyce
12th Argumentation, Dialogue, Persuasion
confe...
Are you taking any other medications?
Checks for known drug interactions
Prescribers consult drug interaction
references…
Medscape EpocratesMicromedex 2.0
…which are maintained by expert
pharmacists
Medscape EpocratesMicromedex 2.0
Goal: Support evidence-based updates
to drug-interaction reference DBs
• Make sense of the EVIDENCE
– New clinical trials
...
Drug Interaction Knowledge Base
(DIKB) - Boyce 2007-2009
– Hand-constructed knowledge base
– Safety issues when 2 drugs ar...
Drug Interaction Knowledge Base
(DIKB) - Boyce 2007-2009
– Hand-constructed knowledge base
– Safety issues when 2 drugs ar...
DIKB supports queries about
assertions & evidence:
• Get all assertions that are supported by a
U.S. FDA regulatory guidan...
Limitations of DIKB v1.2
• Minimal argumentation model
– swanco:citesAsSupportingEvidence
– swanco:citesAsRefutingEvidence...
Record deeper relationships between
assertions and evidence
• Assertions
– “there (is/is not) an interaction between A & B...
Micropublication: Claim + Support
(e.g. Attribution)
Micropublications: a Semantic Model for Claims, Evidence, Arguments a...
Constructs claim-argument network
across scientific papers
Micropublications: a Semantic Model for Claims, Evidence, Argum...
Model Data,
Methods,
Materials,
References
Micropublications: a Semantic Model for
Claims, Evidence, Arguments and
Annotat...
Micropublications Ontology
Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedic...
What does this do for the DIKB
• Network of claims with supports & challenges
• Can record materials, methods, data
• Quot...
"escitalopram does not
inhibit CYP2D6"
Support graph Challenge graph
Support graph
Methods
Methods section of challenge graph
Textual quotes
• Evidence
Direct Annotation with Domeo
http://swan.mindinformatics.org/ Paolo N Ciccarese
From individual documents to a
searchable claim-argument network
• "Pay as you go" annotation of source
documents with Dom...
Modeling arguments in scientific papers ArgDiaP 2014 05-23
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Modeling arguments in scientific papers ArgDiaP 2014 05-23

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Paper: http://jodischneider.com/pubs/argdiap2014.pdf

We present a motivating scenario for using argumentation within a scientific knowledge base. Our goal is to transform natural language papers, with the manual work of expert curators, into elaborated claim-argument networks.

In ongoing work, we are focusing on creating Micropublications (Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506 ) through manual annotation. Currently we are engaging with pharmaceutical curators to envision the most appropriate way to record evidence for the next generation of the the Drug Interaction Knowledge Base.

Presented at The 12th ArgDiaP Conference "From Real Data to Argument Mining"
https://sites.google.com/site/argdiapen/12th-argdiap

Published in: Technology, Health & Medicine
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  • https://sites.google.com/site/argdiapen/12th-argdiap

    Paper online:
    http://jodischneider.com/pubs/argdiap2014.pdf
  • Image from http://www.clipartbest.com/clipart-McLLpbGKi
  • Adverse drug events are a leading cause of death

    Image from https://www.njpharmacy.com/wp-content/uploads/2013/02/drug-interactions-checker.png
    Image from http://www.clipartbest.com/clipart-McLLpbGKi
  • Adverse drug events are a leading cause of death

    Images from

    http://www.knowabouthealth.com/android-version-of-medscape-app-ready-to-download/7568/
    Android Play store
    http://amazingsgs.blogspot.com/2011/10/top-5-free-android-medical-apps-for.html
  • Adverse drug events are a leading cause of death

    Images from

    http://www.knowabouthealth.com/android-version-of-medscape-app-ready-to-download/7568/
    Android Play store
    http://amazingsgs.blogspot.com/2011/10/top-5-free-android-medical-apps-for.html
  • Image from http://jama.jamanetwork.com/article.aspx?articleid=183454
  • http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/front-page.html
  • http://dbmi-icode-01.dbmi.pitt.edu/dikb-evidence/front-page.html
  • # How many pharmacokinetic studies in the DIKB could be used to support or refute
    # an increases AUC assertion?

    # How many AUC studies are in the DIKB that are based on data from the
    # product label?

    # Are the evidence use assumptions are concordant, unique, and non-ambiguous

    # Get all assertions that are supported by an FDA guidance statement

    # SHOW THE DISTRIBUTION OF THE LEVELS OF EVIDENCE FOR MECHANISTIC ASSERTIONS


    # WHAT ASSERTIONS ARE SUPPORTED/REFUTED BY JUST ONE TYPE OF EVIDENCE?

    ## which items in the DIKB have evidence for and against that is both
    ## from product labeling?

    # number of assertions in the system

    # number of evidence items for and against

    ## find assertions that are not supported by evidence

    # what single evidence items act as as support or rebuttal for multiple substrate_of assertions?

    #remove a older version of a redundant evidence item

    ## change evidence for to evidence against

    # has this evidence item been rejected

    # what other assertions are being supported/challeged by this evidnece item?
  • # How many pharmacokinetic studies in the DIKB could be used to support or refute
    # an increases AUC assertion?

    # How many AUC studies are in the DIKB that are based on data from the
    # product label?

    # Are the evidence use assumptions are concordant, unique, and non-ambiguous

    # Get all assertions that are supported by an FDA guidance statement

    # SHOW THE DISTRIBUTION OF THE LEVELS OF EVIDENCE FOR MECHANISTIC ASSERTIONS


    # WHAT ASSERTIONS ARE SUPPORTED/REFUTED BY JUST ONE TYPE OF EVIDENCE?

    ## which items in the DIKB have evidence for and against that is both
    ## from product labeling?

    # number of assertions in the system

    # number of evidence items for and against

    ## find assertions that are not supported by evidence

    # what single evidence items act as as support or rebuttal for multiple substrate_of assertions?

    #remove a older version of a redundant evidence item

    ## change evidence for to evidence against

    # has this evidence item been rejected

    # what other assertions are being supported/challeged by this evidnece item?
  • Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications
    Tim Clark, Paolo N. Ciccarese, Carole A. Goble
    http://arxiv.org/abs/1305.3506


  • What is wrong with this model?
    Limited automatic reasoning
    Limited integration with annotation
    What are the new opportunities?
    New model by the authors of SWAN/SIOC

  • Micropublications enable explicitly representing the warrant, i.e. the materials and methods that were used to collect the data. The data collected is considered meaningful due to a subfield’s approval of the materials and methods. This approval is the backing of claims made in every- day science (e.g. ‘paradigm’ science in the terms of [Kuhn2012]). With this model, truth-bearing Statements (possibly with Qualifiers) from biomedical communica- tions are explicitly connected to the Data, Material, and Methods. Attribution also has a place (for instance justifying use of a method by citing it in the literature). A subargument can be represented as a micropublication for a related claim, however far back we wish to extend the network.
  • SPARQL:unbound
  • https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxkZGlrcmFuZGlyfGd4OjE0ZGIwY2IwNzJhOWNjMjY
  • SPARQL:unbound
  • Transcript of "Modeling arguments in scientific papers ArgDiaP 2014 05-23"

    1. 1. Jodi Schneider, Carol Collins, Lisa E Hines, John R Horn, and Richard Boyce 12th Argumentation, Dialogue, Persuasion conference (ArgDiaP 2014) Warsaw, Poland 2014-05-25
    2. 2. Are you taking any other medications?
    3. 3. Checks for known drug interactions
    4. 4. Prescribers consult drug interaction references… Medscape EpocratesMicromedex 2.0
    5. 5. …which are maintained by expert pharmacists Medscape EpocratesMicromedex 2.0
    6. 6. Goal: Support evidence-based updates to drug-interaction reference DBs • Make sense of the EVIDENCE – New clinical trials – Adverse drug event reports – Drug product labels – Updates to regulatory information (U.S. FDA,…) – … • Significant discrepancies between different drug-interaction reference DBs http://jama.jamanetwork.com/article.aspx?articleid=183454
    7. 7. Drug Interaction Knowledge Base (DIKB) - Boyce 2007-2009 – Hand-constructed knowledge base – Safety issues when 2 drugs are taken together – Focus is on EVIDENCE
    8. 8. Drug Interaction Knowledge Base (DIKB) - Boyce 2007-2009 – Hand-constructed knowledge base – Safety issues when 2 drugs are taken together – Focus is on EVIDENCE All assumptions are linked to evidence Enables the system to identify when
    9. 9. DIKB supports queries about assertions & evidence: • Get all assertions that are supported by a U.S. FDA regulatory guidance statement • Are the evidence use assumptions are concordant, unique, and non-ambiguous? • Which assertions are supported/refuted by just one type of evidence?
    10. 10. Limitations of DIKB v1.2 • Minimal argumentation model – swanco:citesAsSupportingEvidence – swanco:citesAsRefutingEvidence • Cannot recover the source text – Document-level citation – Quote & section citation preferrable • Level of detail – Want more detail on data, methods, materials
    11. 11. Record deeper relationships between assertions and evidence • Assertions – “there (is/is not) an interaction between A & B” – “Enzyme E reduces clearance of drug D by 25%” • Evidence – Scientific literature – Drug product labeling – U.S. FDA guidance documents
    12. 12. Micropublication: Claim + Support (e.g. Attribution) Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506
    13. 13. Constructs claim-argument network across scientific papers Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506
    14. 14. Model Data, Methods, Materials, References Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506
    15. 15. Micropublications Ontology Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical Communications Tim Clark, Paolo N. Ciccarese, Carole A. Goble http://arxiv.org/abs/1305.3506
    16. 16. What does this do for the DIKB • Network of claims with supports & challenges • Can record materials, methods, data • Quotes can be naturally linked into the graph • We can query for every mp:Claim that has no support. – An assumption (mp:Claim) – Can have its own support graph, specified once – We can query the support graph
    17. 17. "escitalopram does not inhibit CYP2D6" Support graph Challenge graph
    18. 18. Support graph
    19. 19. Methods Methods section of challenge graph
    20. 20. Textual quotes
    21. 21. • Evidence
    22. 22. Direct Annotation with Domeo http://swan.mindinformatics.org/ Paolo N Ciccarese
    23. 23. From individual documents to a searchable claim-argument network • "Pay as you go" annotation of source documents with Domeo & Micropublications • Generates claim-argument network – Supports & challenges – Materials, methods, data – Quotes linked into the graph – … within & across documents • Query support
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