Ontologies in biology: design, applications and future challenges

Biological knowledge is inherently complex and so cannot readily be integrated into existing databases of molecular (for example, sequence) data. An ontology is a formal way of representing knowledge in which concepts are described both by their meaning and their relationship to each other. Unique identifiers that are associated with each concept in biological ontologies (bio-ontologies) can be used for linking to and querying molecular databases. This article reviews the principal bio-ontologies and the current issues in their design and development: these include the ability to query across databases and the problems of constructing ontologies that describe complex knowledge, such as phenotypes.

[1]  J. Affeldt,et al.  The feasibility study , 2019, The Information System Consultant’s Handbook.

[2]  P. Simons.  Parts: A Study in Ontology , 1991 .

[3]  Bob J. Wielinga,et al.  Using explicit ontologies in KBS development , 1997, Int. J. Hum. Comput. Stud..

[4]  José L. V. Mejino,et al.  Research Paper: Motivation and Organizational Principles for Anatomical Knowledge Representation: The Digital Anatomist Symbolic Knowledge Base , 1998, J. Am. Medical Informatics Assoc..

[5]  Elizabeth A. Kellogg,et al.  Plant Systematics: A Phylogenetic Approach , 2000 .

[6]  Robert H. Baud,et al.  Galen : a third generation terminology tool to support a multipurpose national coding system for surgical procedures , 1999, MIE.

[7]  M. Kanehisa,et al.  A heuristic graph comparison algorithm and its application to detect functionally related enzyme clusters. , 2000, Nucleic acids research.

[8]  S. Tapscott,et al.  A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems , 2001, Genome Biology.

[9]  The Virtue of Prosperity: Finding Values In An Age Of Techno-Affluence , 2000 .

[10]  Judith A Blake,et al.  Mouse Genome Database , 2000, Mammalian Genome.

[11]  Robert L. Scot Drysdale,et al.  Phenotypic Data in FlyBase , 2001, Briefings Bioinform..

[12]  Hsinchun Chen,et al.  Meeting medical terminology needs-the ontology-enhanced Medical Concept Mapper , 2001, IEEE Transactions on Information Technology in Biomedicine.

[13]  L. Stein,et al.  Gramene, a Tool for Grass Genomics , 2002, Plant Physiology.

[14]  Peter J. Tonellato,et al.  Rat Genome Database (RGD): mapping disease onto the genome , 2002, Nucleic Acids Res..

[15]  J. Blake,et al.  Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies. , 2002, Genome research.

[16]  S. Rhee,et al.  TAIR: a resource for integrated Arabidopsis data , 2002, Functional & Integrative Genomics.

[17]  Mariano Sigman,et al.  Global organization of the Wordnet lexicon , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  M Gerstein,et al.  GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. , 2002, Nucleic acids research.

[19]  Russ B. Altman,et al.  PharmGKB: the Pharmacogenetics Knowledge Base , 2002, Nucleic Acids Res..

[20]  W. Pearson,et al.  Current Protocols in Bioinformatics , 2002 .

[21]  Olivier Bodenreider,et al.  Evaluation of the UMLS as a terminology and knowledge resource for biomedical informatics , 2002, AMIA.

[22]  Frederick P. Roth,et al.  Predicting phenotype from patterns of annotation , 2003, ISMB.

[23]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[24]  Samson W. Tu,et al.  Protégé-2000: An Open-Source Ontology-Development and Knowledge-Acquisition Environment: AMIA 2003 Open Source Expo , 2003, AMIA.

[25]  Olivier Bodenreider,et al.  Evaluation of WordNet as a source of lay knowledge for molecular biology and genetic diseases: A feasibility study , 2003, MIE.

[26]  Purvesh Khatri,et al.  Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate , 2003, Nucleic Acids Res..

[27]  James J. Cimino,et al.  Linking Molecular Imaging Terminology to the Gene Ontology (GO) , 2002, Pacific Symposium on Biocomputing.

[28]  Judith A. Blake,et al.  MGD: the Mouse Genome Database , 2003, Nucleic Acids Res..

[29]  John W. Keele,et al.  Positional candidate gene selection from livestock EST databases using Gene Ontology , 2003, Bioinform..

[30]  Jonathan Bard,et al.  Ontologies: Formalising biological knowledge for bioinformatics. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[31]  Carlos Alberto Heuser,et al.  Integrating Biological Databases , 2003, SBBD.

[32]  Michael Gruenberger,et al.  Pathbase: a database of mutant mouse pathology , 2004, Nucleic Acids Res..

[33]  Peter D. Karp,et al.  MetaCyc: a multiorganism database of metabolic pathways and enzymes , 2005, Nucleic Acids Res..

[34]  Qunfeng Dong,et al.  MaizeGDB, the community database for maize genetics and genomics , 2004, Nucleic Acids Res..

[35]  Kara Dolinski,et al.  Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms , 2004, Nucleic Acids Res..

[36]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[37]  Judith A. Blake,et al.  The mouse Gene Expression Database (GXD): updates and enhancements , 2004, Nucleic Acids Res..

[38]  Peter D. Karp,et al.  MetaCyc: a multiorganism database of metabolic pathways and enzymes. , 2004, Nucleic acids research.