AlzPharm: an RDF Use Case for Semantic Web in Neuroscience

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AlzPharm an RDF Use Case for Semantic Web in
Neuroscience
Yale Center for Medical Informatics (YCMI)
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SeS2006 Workshop, Beijing, China (Sept. 3, 2006)

• Authors
• Hugo Y.K. Lam (CBB Ph.D. Program)
• Kei Cheung (YCMI)
• Luis Marenco (YCMI)
• Perry Miller (YCMI)
• Nian Liu (YCMI)
• Chiquito Crasto (YCMI)
• Tim Clark (Mass. General Hospital, Harvard
  University)
• Yong Gao (Partners)
• June Kinoshita (AlzForum)
• Elizabeth Wu (AlzForum)
• Gwen Wong (AlzForum)
• Gordon Shepherd (Yale Neurobiology)
• Tom Morse (Yale Neurobiology)
• Susie Stephens (Oracle)

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Overview

• Most of the neuroscience databases are neither
  integrated nor interoperating
• A domain ontology is insufficient for integrating
  neuroscience data spanning multiple domains
• We present a Semantic Web approach to building an
  e-Neuroscience data integration framework, which
  involves using RDF as a standard data model to
  facilitate representation and integration of data

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e-Neuroscience

• Involves developing tools, technologies, and
  infrastructure to support multidisciplinary and
  collaborative science enabled by the Internet
• Aims to address data integration problem in
  neuroscience
• Fits the informatics-oriented goal of the Human
  Brain Project initiated by NIH
• Provides a better understanding of brain function
  by integrating different levels of brain data.

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Current Issues

• Registry
• Keyword-based search approach suffers from the
  problem of specificity and sensitivity
• Centralized approach to registering resources may
  not be scalable. E.g. NDG

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Current Issues (contd)

• No Links between related databases

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Semantic Web Approach

• Representing and Integrating Data

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Semantic Web

• Exposes the semantics of Web-accessible data in a
  standard machine-readable way so that the data
  can be more easily interpreted and integrated by
  computer programs (or Web agents)
• Components of the Semantic Web technologies
• Ontology
• Ontological Languages
• Semantic-Web-aware Tools (e.g., databases)

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RDF Data Modeling

• Uses the Oracle RDF Data Model (which is
  installed on a Linux server) to build a Semantic
  Web data warehouse for integrating datasets
  extracted from two independently-developed
  neuroscience databases
• BrainPharm (a subdatabase of SenseLab)
• SWAN (Semantic Web Applications in Neuromedicine)

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RDF Data Modeling

• BrainPharm
• A database under development to support research
  on drugs for the treatment of different
  neurological disorders (http//senselab.med.yale.e
  du/senselab/BrainPharm/alzData.asp)
• Contains pharmacological agents that act on
  neuronal receptors and signal transduction
  pathways in the normal brain and in nervous
  disorders such as Alzheimers Disease (AD)
• Enables searches for drug actions at the level of
  key molecular constituents, cell compartments and
  individual cells

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RDF Data Modeling

• SWAN (http//swan.mindinformatics.org/)
• A project to develop knowledge management tools
  and resources for Alzheimer Disease (AD)
  researchers, based on an ecosystem model of
  scientific discourse
• Uses an upper ontology, including the following
  components scientists, experiments,
  publications, bibliographic databases, research
  collaborations, scientific web communities, and
  etc
• Implemented using Semantic Web technology
• Represents data in RDF format,
• Currently stores a subset of data obtained from
  the Alzheimer Research Forum (http//www.alzforum.
  org)

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Data Conversion Loading

• The drug-related (chemical) information are
  extracted from BrainPharm
• The SWAN hypotheses and publications are
  extracted from Alzforum
• SWAN data are already available in RDF format
• BrainPharm exports data in its own XML format
  called EDSP (Electronic DataSet Protocol)
• Convert the EDSP/XML format into the
  corresponding RDF/XML format using XSL
  Transformation (XSLT)
• Load both the SWAN and BrainPharm RDF datasets
  into the Oracle RDF Data Model using its data
  loader program, which takes RDF data in N-triple
  format

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RDF Based Queries

• Oracle has extended SQL to provide support for an
  RDF query language, which allows users to perform
  queries against multiple RDF datasets
• The following two examples illustrate how such
  queries can be made to retrieve and integrate
  data from BrainPharm and SWAN

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RDF Based Queries

• Example One
• Target
• Query BrainPharm to group and count AD drugs
  based on their molecular targets
• Result
• There are 2 groups of drugs for AD.
• The first one contains 5 drugs that act as
  acetylcholinesterase inhibitors.
• The second one contains only 1 drug that is a
  N-methyl-D-aspartic acid (NMDA) receptor
  antagonist.

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RDF Based Queries

• Example One
• Query

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RDF Based Queries

• Example One
• Remarks
• Current implementations of RDF query languages
  (RQL) by specialized RDF stores do not support
  aggregate functions (e.g., COUNT, SUM and
  AVERAGE) via GROUP BY
• The Oracle RDF query language supports such
  functions, as it is a hybrid between RQL and SQL

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RDF Based Queries

• Example Two
• Target
• Retrieves the information (stored in BrainPharm)
  about the AD drug Donepezil and publications
  (stored in SWAN) whose titles or abstracts
  contain the term Donepezil (case-insensitive)
• Demonstrates the use of RDF inferencing based on
  the parent-child (is-a) relationship between the
  Publication class (e.g., original articles
  retrieved from PubMed) and ARFPublication class
  (e.g., PubMed articles that have been commented
  by researchers/curators associated with Alzforum)
  as defined in the SWAN RDF Schema

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RDF Based Queries

• Example Two
• Query (Partial)

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RDF Based Queries

• Example Two
• Result
• With the is-a inference rule incorporated into
  the query, it finds a total of 19 publications
  that are linked to claims and/or hypotheses that
  have to do with the effect of Donepezil on AD
  treatment
• Among these publications, one of them belongs to
  the ARFPublication class (i.e., one of the 19
  publications is ARF-commented)
• Given the ID (PubMed ID) of the commented
  publication, the user can retrieve the detailed
  comments through the Alzforum Web site

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RDF Based Queries

• Example Two
• Remarks
• In the SWAN dataset, publications (e.g., those
  retrieved from PubMed) are treated as instances
  of the Publication class
• We define publications that have been commented
  in the Alzforum as instances of the
  ARFPublication class
• The Oracle RDF Data Model allows us to create
  rules for hierarchical relationships from the
  RDFS for the data so that it enables us to find
  out all the publications and its subclasses (e.g.
  the ARF publications)

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AlzPharm
AlzForum
BrainPharm
Oracle/RDF
SWAN