Semantic Systems Biology: Formal Knowledge Representation in Systems Biology for Model Construction, Retrieval, Validation and Discovery

  • Michel Dumontier
  • Leonid L. Chepelev
  • Robert Hoehndorf

Abstract

With the publication of the human genome, scientists worldwide opened champagne and let out a collective cheer for progress in biology. After all, the untold number of interactions of tens of thousands of genes, a greater number of their products and product derivatives, and tens of thousands of chemicals came much closer to complete characterization. Paradoxically however, while individual efforts produced important biological results, an integrated view of biology from systems perspective seemed ever more distant due to the complexity of data integration from multiple knowledge representation forms, formalisms, modeling paradigms, and conflicting scientific statements. To address this, semantic technologies have risen over the past decade with the promise of truly unifying biological knowledge and allowing cross-domain queries and model integration. In this chapter, we shall examine Semantic Web technologies and their applications to build, publish, query, discover, compare, validate, reason about, and evaluate models and knowledge in Systems Biology. We shall specifically address biological ontologies, open data repositories, modeling and annotation tools, and selected promising applications of Semantic Systems Biology. We firmly believe that it shall soon be possible to completely close the gap between facts, models, and results, and to fully apply the accrued models and facts to evaluate biological hypotheses on a system level, discovering meaning within the vast collection of biological knowledge and taking Systems Biology research to a new, unprecedented level.

Keywords

Systems biology Semantic web Bioinformatics Computational biology Ontology Semantic annotation Integration Query Validation Discovery Models Simulation Sustainability Protein Small molecule Pathway SBML RDF SPARQL OWL Type Relation Identifier Description Formal knowledge representation Automated reasoning Biology Biochemistry Artificial intelligence World Wide Web 

Acronyms

BFO

Basic formal ontology

ChEBI

Chemical entities of biological interest

DL

Description logic

EBI

European bioinformatics institute

FMA

Foundation model of anatomy

GO

Gene ontology

HCLS

Health care and life sciences

IAO

Information artifact ontology

IRI

International resource identifier

IUBMB

The international union of biochemistry and molecular biology

KiSAO

Kinetic simulation algorithm ontology

MIRIAM

Minimum information required in the annotation of models

MUO

Measurement unit ontology

NCBI

National center for biotechnology information

OBI

Ontology for biomedical investigations

OPB

Ontology for physics and biolog

OWL

Web ontology language

PATO

Phenotype and trait ontology

RDF

Resource description framework

RDFS

Resource description framework schema

RNAO

RNA ontology

SBML

Systems biology markup language

SBO

Systems biology ontology

SIO

Semanticscience integrated ontology

SPARQL

SPARQL query language

TEDDY

Terminology for the description of dynamics

XML

Extensible markup language

W3C

World Wide Web consortium

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Michel Dumontier
    • 1
  • Leonid L. Chepelev
    • 1
  • Robert Hoehndorf
    • 1
  1. 1.Carleton UniversityOttawaCanada

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