Modeling Arguments in Scientific Papers to Support Pharmacists

Jodi Schneider, Carol Collins, Lisa E Hines, John R Horn, and Richard Boyce

12th Argumentation, Dialogue, Persuasion conference (ArgDiaP 2014) Warsaw, Poland2014-05-25

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– 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

Drug Interaction Knowledge Base (DIKB) - Boyce 2007-2009

– Hand-constructed knowledge base– Safety issues when 2 drugs are taken together– Focus is on EVIDENCE

Drug Interaction Knowledge Base (DIKB) - Boyce 2007-2009

– Hand-constructed knowledge base– Safety issues when 2 drugs are taken together– Focus is on EVIDENCE

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?

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

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

Micropublication: Claim + Support (e.g. Attribution)

Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical CommunicationsTim Clark, Paolo N. Ciccarese, Carole A. Goblehttp://arxiv.org/abs/1305.3506

Constructs claim-argument network across scientific papers

Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical CommunicationsTim Clark, Paolo N. Ciccarese, Carole A. Goblehttp://arxiv.org/abs/1305.3506

Model Data, Methods, Materials, References

Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical CommunicationsTim Clark, Paolo N. Ciccarese, Carole A. Goblehttp://arxiv.org/abs/1305.3506

Micropublications Ontology

Micropublications: a Semantic Model for Claims, Evidence, Arguments and Annotations in Biomedical CommunicationsTim Clark, Paolo N. Ciccarese, Carole A. Goblehttp://arxiv.org/abs/1305.3506

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

"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 Domeo & Micropublications

• Generates claim-argument network– Supports & challenges– Materials, methods, data– Quotes linked into the graph– … within & across documents

• Query support