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Entrez Neuron:
an OWL/RDFa–based Web Application for
Information Exploration and Integration in
Neuroscience
Matthias Samwald, Ernest Lim, Peter Masiar, Luis
Marenco, Huajun Chen, Thomas Morse, Gordon
Shepherd, Perry Miller and Kei Cheung
Yale Center for Medical informatics, Yale University
Medical University of Vienna, Vienna, Austria
School of Computer Science, Zhejiang University
Outline
• SenseLab Overview
• Entrez Neuron Project
– Semantic Data Conversion
– Semantic Data Browsing/Querying
• Future Development
• Online demo
Yale SenseLab Overview
SenseLab’s development was funded by the Human
Brain Project to disseminate information related to neuronal
membrane properties with special emphasis on the olfactory
system.
• A major information resource for international neuroscience research.
• Have garnered several million hits and unique visits over the years.
SenseLab Database
• SenseLab currently contains eight databases:
• These databases combine to provide neuronal,
genomics/genetics, proteomics and imaging information to the
neuroscience research community and the public.
• These resources have been used in neuroscience research,
teaching, thesis-writing and database design, and Semantic
Web exploration.
Snapshot of SenseLab Databases
http://senselab.med.yale.edu/
Entrez Neuron Project
A neuron-centric interface that
allows for keyword-based queries
against a coherent repository of OWL
ontologies about neuronal structure,
physiology, mathematical models and
microscopy.
Technical Approach
• Careful modeling of neuroscience domain
knowledge in consideration of reusing many
well-defined general purpose biomedical
ontologies.
• Convert legacy Senselab data to desired
RDF/OWL model.
• Map out to external biomedical resources.
• Provide integrated ontological browse, search
services over the knowledge base.
• Use RDFa to publish the knowledge as HTML.
Ontology modeling
• Basic ontology: an ontology containing basic class
hierarchies and relations was manually created,
based on the structure of existing SenseLab
databases.
• The ontologies were built upon established
foundational ontologies in order to maximize the
interoperability with other existing and forthcoming
biomedical Semantic Web resources. These
ontologies were:
– the Relation Ontology [RO] from the Open Biomedical
Ontologies repository [OBO], which defines basic relations such
as 'part of', 'participant of' or 'contained in'.
– the Basic Formal Ontology [BFO], which defines basic classes
such as 'process', 'object', 'quality' or 'function'.
Data conversion
• Based on this manually created basic
ontology, the data from the SenseLab
databases were then automatically
converted to OWL using programs written
in Java and Python.
• The automated export scripts extends the
manually created basic ontology through
the creation of subclasses, OWL property
restrictions and individuals.
Data Conversion: Mapping Out
• Mappings were made to the following
ontologies:
– the BAMS ontology which was derived from the
Brain Architecture Management System [BAMS]
– the Subcellular Anatomy Ontology (SAO) created by
the Cell Centered Database project. [SAO]
– the BirnLex ontology developed by members of the
Biomedical Informatics Research Network [BIRNLEX]
– the Common Anatomy Reference Ontology (CARO)
[CARO]
– the Gene Ontology [GO]
– the Ontology of Biomedical Investigation (OBI) [OBI]
Data Conversion: Mapping Out
Data Conversion: Mapping Out
Outcome of SenseLab
conversions
Ontology
Subject-predicateobject triples
('RDF triples')
Named classes
(including
imports)
Individuals
(including
imports)
Properties
(including
imports)
NeuronDB
21010
1400
1510
60
ModelDB
3720
1410
1800
60
BrainPharm
810
1710
1830
80
NeuronDB – BFO
mapping
380
1500
1510
70
NeuronDB – SAO
mapping
40
2160
1550
330
NeuronDB – Birnlex –
BAMS – OBI
mapping
130
3640
1650
190
Example Queries
Example query
Ontologies needed for query
Return all neuron types that are located in the Neocortex or some part of the
Neocortex, and show research notes and Pubmed references for each.
NeuronDB
Return all neurons that use GABA as a neurotransmitter and that have receptors for
Glutamate located on their dendrites.
NeuronDB, ModelDB
Return all neurons that might be affected in the early phase of Alzheimer's disease.
NeuronDB, BrainPharm
Return available mathematical models for all neurons that exhibit A-type potassium
ion currents on their membranes.
NeuronDB, ModelDB
W3C note on http://www.w3.org/TR/hcls-senselab/
But how can end-users profit?
Lack of user-friendly interfaces
Spectrum of Semantic Web user interfaces with two
extremes:
• Very flexible, but very generic and therefore not user
friendly
• Very specific and user-friendly, but only geared
towards a small set of ontological entities
Practical user interfaces probably need to be
positioned somewhere in the middle
Design the User Interface
Key Features
• Facet Search enabled by ontology
description.
• Use RDFa to encode the semantic
information to HTML
The Entrez Neuron Project
Future developments
•Adding more RDF/OWL data
– PDSP Ki database (ligand-receptor interactions)
– SWAN ontology (Alzheimer's disease hypotheses)
– Further OBO ontologies
•Querying and Reasoning
– Switch to using SPARQL (instead of Oracle RDF query language)
– Explore and expand reasoning capabilities
Future developments
• User interface
– Add more features to the existing user
interface
– 3D Visualization
• Community development
– Establish Entrez Neuron as an open
community platform
Acknowledgement
• Cell Centered Database: Maryann
Martone, Willy Wong
• Science Commons: Alan Ruttenberg
• Oracle: Melliyal Annamalai, Alan Wu
Thanks for your
Attention