Your SlideShare is downloading. ×
0
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Modeling arguments in scientific papers ArgDiaP 2014 05-23
Upcoming SlideShare
Loading in...5
×

Thanks for flagging this SlideShare!

Oops! An error has occurred.

×
Saving this for later? Get the SlideShare app to save on your phone or tablet. Read anywhere, anytime – even offline.
Text the download link to your phone
Standard text messaging rates apply

Modeling arguments in scientific papers ArgDiaP 2014 05-23

391

Published on

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

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
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
391
On Slideshare
0
From Embeds
0
Number of Embeds
3
Actions
Shares
0
Downloads
3
Comments
0
Likes
0
Embeds 0
No embeds

Report content
Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
No notes for slide
  • 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

    • 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. Are you taking any other medications?
    • 3. Checks for known drug interactions
    • 4. Prescribers consult drug interaction references… Medscape EpocratesMicromedex 2.0
    • 5. …which are maintained by expert pharmacists Medscape EpocratesMicromedex 2.0
    • 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. "escitalopram does not inhibit CYP2D6" Support graph Challenge graph
    • 18. Support graph
    • 19. Methods Methods section of challenge graph
    • 20. Textual quotes
    • 21. • Evidence
    • 22. Direct Annotation with Domeo http://swan.mindinformatics.org/ Paolo N Ciccarese
    • 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

    ×