Developing an Ontology-driven Data Collection Application

D. Bourges-Waldegga, PhD, T. Bashorb, H. R. Frost, MSa, L. Hadden, PhDa, M. Haendel, PhDc, C. Torniai, PhDc , D. MacFadden, MSa
aHarvard Medical School, Boston, MA, bWonder Lake Software, LLC, cOregon Health & Science University, Portland, OR

Abstract Challenges and approach

The eagle-i Consortium (www.eagle-i.org/home) is building a federated Modeling dichotomy

network of biomedical research resources aimed at facilitating resource  Eagle-i ontology is a domain model aimed at capturing biological
discovery and sharing. The cornerstone of the eagle-i system is an ontology knowledge.
that captures biomedical domain knowledge and drives the eagle-i software.  Application needs a model from which to derive behavior.
We discuss the technical approach and challenges of building a fully
ontology-driven data collection application. Complexity
 Eagle-i ontology is interoperable; it builds on an upper ontology and imports
numerous terms.
 Not all ontology constructs translate into user-level constructs.

eagle-i: ontology-centric architecture ⇒  Layered ontology architecture: application ontologies annotate domain
ontologies with application-specific information and restrictions

Type browser: Data Collection ETL Process Search etc…

allows
navigation of an Applications
EIOntModel API
NIF, PubMed, ontology
Entrez Gene, Search Application
branch
etc. eagle-i primary Jena/Pellet

Federated Network
types
(SPIN) eagle-i
ontology
Application- eagle-i-app-dataTools.owl
(OWL) specific
Ontologies

eagle-i-app.owl
Repository
(RDF)

Data Tools
ero.owl

Domain
Ontologies mesh-diseases.owl ro.owl iao.owl

Bfo.owl etc…

Required property
determined from Example
Benefits of an ontology-centric design class restrictions Human study is an application primary type – its upper hierarchy is excluded
Embedded class from application model
 Allows applications to seamlessly adapt to ontology evolution without relationship
code changes. determined from Thing
 Provides ontology developers with a mechanism to rapidly test and refine ontology
their models.
Entity

⇒ Produce high quality data. Processual entity

Object
⇒ Promote ontology development practices towards creating better
property:
biomedical ontologies. Planned process
ontology term

The eagle-i data collection tool Datatype

Occurrent
Property 1
property
Research Project
Property 2
Object
  Dynamically creates forms for a resource type by inspecting its property:
corresponding ontology class. instance list GWAS Human Study
  For each ontology property associated with a class, the tool generates
input fields. The kind of input field generated and its allowed values are
derived from OWL constructs.
Quantitative human
Epidemiological study Qualitative human study
study

Supported by NIH/NCRR ARRA award #U24RR029825