“Semantic Web” Applications in Bioinformatics

Amr AL-Hossary

M.B.B.Ch

Agenda

• Web & Semantic Web

• RDF & DRF Schema– Elements– Schema– Name space– Queries– Pain, Design Patters, And limits,

• Applications of SW in Bioinformatics

Web Today

• Documents for HUMANS

• Increasing dramatically

• Hard to process on semantic level– e.g. searching for “give her a ring” doesn’t

return “engage her”.

• Solution (semantic web)– annotating definitions– abstract representation of classes & relations

What is the Semantic Web?

Myths about Semantic Web…

• is Top-Down

• needs ontologies at the beginning

• requires all information to be converted to RDF

• must be centralized

• handles only binary relations

• requires the entire graph to exist on one memory store

Truths

• A means of describing (a Web of) Data

• A system defining and incorporating semantics

• A mechanism for making statements on things

• A format for associating metadata

• A strategy for federating data systems (with or without triplestore)

Needs

• shared definitions of knowledge domains, i.e. ontologies,

• association of concepts to existing data,

• metadata information describing information sources and contents,

• search tools able to make the best use of this additional information.

RDF

• (Directed) graph data model• Set of Binary relations (triples)

– Subject Predicate Object

• NOT like DBMS: Absence of a relation does NOT mean it is not present.

• XML and RDF/OWL are inherently different– XML = thesaurus document structure– RDF = thesaurus document content

Recombinant Data Space

• RDF is about Graphs rather than statements

• Separate Graphs can be merged easily into one aggregate graph

• Graphs can be filtered and pivoted, without losing meaning

Works in

Works in

Studied Sun of

Recombinant Data Space

AmrAmr

Medicine Zaynab Ali

Amr

N U

N U

Abolhouda

Recombinant Data Space

Amr

Medicine Zaynab Ali

Abolhouda

N U

Recombinant Data Space

Amr

Medicine

Abolhouda

N U

RDF Elements

• Resources R

• Properties P

• Literal Values L

• Assertions "R P L" or "R P R"

• Namespaces

RDF Schema

• RDF Schema (RDFS) is a vocabulary to create vocabularies...– Comparable to XML Schema or XML DTD– Used to standardize which “tags” the creator of a

graph is allowed to use for annotating resources

• Introduces notions such as "Class" and "Subclass„

• Helps define which relations a resource of a certain type may have

RDFS Namespace Elements

• X rdf:type rdfs:class– denotes that resource X is a class

• R rdf:type rdf:Property– denotes that resource R is a property

• R rdfs:domain X– denotes that the subject of R must be an X

• R rdfs:range Y– denotes that the object of R must be a Y

Cited from http://www.nettab.org/2007/slides/Tutorial_Stoermer.pdf

Query Languages

• RDQL

• SERQL

• SPARQL (upcoming W3C Standard)

SPARQL Example

PREFIX nettab<http://www.nettab.org/tutorial-ns#>

SELECT ?x ?y ?zWHERE { ?x nettab:givesTalk ?z }

Matching triple:Subject: http://www.nettab.org/tutorial-ns#hstPredicate: http://www.nettab.org/tutorial-ns#givesTalkObject: http://www.know-who.net/talks/nettab.ppt

Cited from http://www.nettab.org/2007/slides/Tutorial_Stoermer.pdf

RDF Limitation (& Design Patterns)

• N-ary Relations– It understands only Binary ralations– Amr Leads Pulse in 2009

• Exceptions– Human RBCs are Unnucleated

Example Applications of Semantic Web in Bioinformatics

Vocabularies (Thesauri)

• Example Thesauri in Medicine – UMLS– SNOMED– MESH– Galen

OKKAM (for ENS)

Addison’s disease in medical vocabularies

• Synonyms– Addisonian syndrome– Bronzed disease– Addison melanoderma– Asthenia pigmentosa– Primary adrenal deficiency– Primary adrenal insufficiency– Primary adrenocortical insufficiency– Chronic adrenocortical insufficiency

Eponym

Symptoms

Clinical Varieties

Disease of Endocrine System

Addison’s Disease

SNOMED International

Disease/Diagnosis

Disease of the Adrenal Gland

Endocrine Disease

Addison’s Disease

MeSH

Adrenal Gland Disease

Adrenal Gland Hypofunction

Disease

Endocrine Disorder

Adrenal Disorder

Corticoadrenal insufficiency

Addison’s Disease

AOD

Adrenal Cortical Disorder

Endocrine Diseases

Disorder of Adrenal Gland

Hypoadrenalism

Corticoadrenal insufficiency

Adrenal Hypofunction

Addison’s Disease

Read Codes

Organizing conceptEndocrine Diseases

Adrenal Gland Diseases

Hypoadrenalism

Adrenal cortical hypofunction

Adrenal Cortex Diseases

Adrenal Gland Hypofunction

Addison’s Disease

SNOMEDMeSHADORead Codes

UMLS

UMLS vocabularies available in RDF/OWL

• NCI Thesaurus (OWL)– http://ncicb.nci.nih.gov/core/EVS

• Gene Ontology– http://www.geneontology.org

• Repository of biomedical ontologies (OBO, OWL)– http://www.bioontology.org/ncbo/faces/index.xhtml

• User-defined Datatypes– Based on syntax used in Protégé– Semantics derived from XML Schema datatypes– For numbers: min, max, digits, fraction digits– For strings: length (min, max, equal), regular

• expression patterns– Class (Teenager complete restriction (age

someValuesFrom (datatype(xsd:int minInclusive(“13”^^xsd:int) maxInclusive(“19”^^xsd:int)))))

Biological Pathway eXchange (BioPAX)

• Represent:– Metabolic pathways– Signaling pathways– Protein-protein, molecular interactions– Gene regulatory pathways– Genetic interactions

• Community effort: pathway databases distribute pathway information in standard format

cPath

• cPath is a database and software suite for storing, visualizing, and analyzing biological pathways

cPath Key Features

• Identifier mapping system e.g. proteins

• Scalable pathway data aggregation

• Simple web interface for browse and query

• Standard web service API for application communication

• 100% open source– Java, Tomcat, MySQL, Lucene, Struts, YUI

• Local installation and customization

iHOP (information Hyperlink Over Protein)Adding value via text mining

Pathway Commons

A Genome – PhenomeIntegrated Approach for

Mining Disease-Causal Genesusing Semantic Web

Gudivada Ranga ChandraEmail : gudx6u@cchmc.org

Department of Biomedical Engineering/University of Cincinnati

Division of Biomedical Informatics/ Cincinnati Children’s Hospital Medical Center

Questions?

References• RDF standard and technologies (presentation)

Heiko Stoermer, University of Trento, Italy– http://www.nettab.org/2007/slides/Tutorial_Stoermer.pdf

• The Unified Medical Language System (UMLS) and the Semantic Web (presentation) Olivier Bodenreider, National Library of Medicine, USA

– http://www.nettab.org/2007/slides/Tutorial_Bodenreider.pdf• Semantic Web for Health Care and Life Science Interest Group: A Vision for Advancing

Research Communities (presentation)Eric Neumann, Teranode Co., USA.

– http://www.nettab.org/2007/slides/SemanticWeb_Neumann.pdf• OKKAM web site

– http://www.okkam.org/• Unified Medical Language System (UMLS)

– http://www.nlm.nih.gov/research/umls/• Biological Pathway eXchange (BioPAX)

– http://www.biopax.org/• cPath: Demo Site

– http://cbio.mskcc.org/cpath/• iHOP (information Hyperlink Over Protein)

– http://www.ihop-net.org/UniPub/iHOP/• Pathway Commons

– http://www.pathwaycommons.org/pc/