- An Informed Consent Ontology (ICO) was developed to support informed consent data integration and reasoning. ICO is aligned with the Basic Formal Ontology (BFO), and logically represent the terms and their relations related to informed consent processes and contents. ICO contains 471 terms including 137 ICO-specific terms and the other terms imported from existing reliable ontologies. The ontology is available at http://icoontology.googlecode.com/.
I.
INTRODUCTION
The informed consent process is one of the fundamental
pillars of human research [
ICO was developed using a combination of top-down and
bottom-up approaches. The ‘backbone’ of ICO is formed by
adopting the Basic Formal Ontology (BFO) 2 as the upper
level ontology [
(IAO).
To further extend ICO, we started with manually
identifying and extracting a list of candidate terms by concept
extraction from the informed consent templates used at the
University of Michigan, which covers clinical research study,
behavioral research study and biobank areas. The candidate
terms were then mapped to several pre-identified resources,
especially the National Cancer Institute Thesaurus (NCIt) [
ICO was generated using the Web Ontology Language (OWL2). Protégé-OWL 4.2 was used for the ontology authoring and editing. New terms were generated using new ICO IDs with the prefix of “ICO_” followed by seven auto incremental digital numbers.
II.
has been deposited into the Ontobee program [
As of Aug. 14, 2014, ICO contains 471 terms (137 ICOspecific), including 385 classes (131 ICO-specific), 55 object properties (3 ICO-specific), 30 annotation properties (3 ICOspecific), and one datatype property.
terms are ultimately placed under ‘continuant’ and ‘occurent’ branches of BFO2. The top level ICO terms are placed under either OBI terms (e.g. informed consent process related terms) or IAO terms (e.g. informed consent document related terms). Various types of informed consent forms and their elements are represented in ICO. entity (BFO)
An example of a workflow starting form an ‘informed consent form design’ to the archiving of a ‘signed informed consent form’ is modeled using ICO (Fig. 2).
After an informed consent form is drafted, it must be approved by the ‘ informed consent regulatory body’. An approved informed consent form will then be subjected to the ‘informed consent form process’, which includes: 1) ‘explaining to participant candidate about informed consent study’ indicated in the informed consent form;; 2) ‘ assessment of participant candidate’s understanding ’ of the explanation; 3) ‘ participant candidate making voluntary decision of acceptance’ ;; and 4) ‘signing the informed consent form’. To ensure the participant make voluntary decision, it is necessary to explain to him/her adequate information. Those were captured in ICO as parts of ‘ explaining to participant candidate about informed consent study’, including: study purpose, study protocol, benefits and risks of participating, sampling procedure, sample usage, data derived from the study, data usage, and record confidentiality. Finally, the ‘signed informed consent form’ will be a rchived (‘ archiving signed informed consent form’) for future use (Fig. 2).
III.
Importing BFO and selected OBI and IAO terms provided a
basic syntactic and semantic framework for further ICO
development. ICO intends to capture both the depth and
breadth of informed consent in clinical study research domain,
and to be used in the following example applications: 1)
Automatic generation of electronic informed consent forms; 2)
Informed consent validation; 3) Biobank biospecimen storage,
processing, and data release. The development of ICO is in its
early stage. We look forward to future collaborations with
other related ontologies and research efforts [
for their valuable discussions and feedback. This research was supported by a University of Michigan interdisciplinary research award (MCubed) and by the National Center for Advancing Translational Sciences of the National Institutes of Health (NIH) under Award Number 2UL1TR000433-06. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding sources. Besides a full import of BFO 2 as our framework, we started from identifying reusable component from OBO foundry ontologies, especially OBI and IAO ontologies.
Based on this top-down procedure, we further expanded the ontology by extracting related terms from three informed consent templates used in University of Michigan. The terminology expertise then mapped the extracted terms to other existing resources: UMLS®, NCIt, BRIDG, OCRe, CHV, UCSD permission ontology, NCBO Bioportal repository and Ontobee repository.
The definitions and relations of ICO terms were finalized by manual review during ICO developers’ Fig.1 Portions of imported classes and meeting. ICO classes in current ICO. The current ICO (v.53) is written in RDF/OWL syntax. It contains 471 terms (137 ICO-specific), including 385 classes (131 ICO-specific), 55 object properties (3 ICO-specific), 30 annotation properties (3 ICO-specific), and one datatype property.