1. Structuring Biomedical Papers as RDF Micropublications
Benjamin Weller, Jodi Schneider School of Information Science, University of Illinois at Urbana-Champaign
Problem
Searching Scientific Literature is Challenging:
It is time-consuming to sift through large amounts of scientific literature.
Certain types of search techniques are easiest: known item searching, searching for keywords in titles/abstracts.
But different kinds of information are important for different purposes: “facts” for interdisciplinary work vs. detailed evidence for domain experts.
Cannot effectively search for specific methods, materials, or outcomes.
Searchers may need domain knowledge.
Background
What is RDF?
RDF is a data modeling structure that uses standardized syntax and shared vocabularies.
What is a Micropublication?
A micropublication organizes the key information of a scientific publication into a flowchart-like format. It shows how scientific claims are supported by the data, methods, and materials found within a publication.
Envisioned Uses
Generate RDF micropublications using existing metadata present within scientific databases and/or additional metadata.
Provide incentives, and usable, machine-assisted interfaces, for authors and editors to annotate at time of publication.
Create new search tools that could use RDF micropublications to augment searching. For instance, qualifiedBy values could be used identify relevant controlled vocabulary for searching bibliographic databases.
Provide researchers with alternative ways to visualize and understand data, which may lead to new insights.
References
Clark, Tim Argument graphs: Literature-Data Integration for Robust and Reproducible Science. First International Workshop on Capturing Scientific Knowledge at K-Cap.
Clark, Tim, Paolo N. Ciccarese, and Carole A. Goble Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications. Journal of Biomedical Semantics. 5(1): 28. doi: /
De Calignon, Alix, Manuela Polydoro, Marc Suárez-Calvet, Christopher William, David H. Adamowicz, Kathy J. Kopeikina, Rose Pitstick, Naruhiko Sahara, Karen H. Ashe, George A. Carlson, Tara L. Spires-Jones, and Bradley T. Hyman Propagation of tau pathology in a model of early Alzheimer's disease. Neuron 73(4): doi: /j.neuron
Sandhu, Novejot and Jodi Schneider. (2018). Modeling Alzheimer’s Disease research claims, evidence, and arguments from a biology research paper. 9th Conference of the International Society for the Study of Argumentation.
Voigt, Christian April 3. so, what exactly is an argument map?
Objectives
Turn an existing visual micropublication for (De Calignon et al. 2012) into RDF.
Envision search tools that could be used to search for a study’s outcomes and methods.
:C1 a mp:Claim ;
rdfs:label "C1: Age Dependency";
mp:statement "Tau Pathology is Age Dependent in Mice (C1)";
mp:supportedBy :D1, :D2;
mp:supports :C0;
mp:qualifiedBy OntoAD:AD
Claim
:D1 a mp:Data ;
rdfs:label "D1: Epitope Immunostaining Analysis" ;
mp:statement "Immunostained antibodies used to recognize epitopes. Tested age dependency of Tau-1.";
mp:supportedBy :M1;
mp:supports :C1 .
Data
:M1 a mp:Method ;
rdfs:label "M1: Immunostaining";
mp:statement "Experimenters conducted immunohistochemisty using antibodies to recognize epitopes (M1). This was used to test the age dependency of tau expression.";
mp:supportedBy :U1, :U2, :U3;
mp:supports :D1 .
Methods
:U1 a mp:Material ;
rdfs:label "U1: rTgTauEC Mice";
mp:statement “Cells from these mice were used for the immunostaining done in (M1).";
mp:supports :M1, :M2;
mp:qualifiedBy mesh:D
Materials