Ontologies in biology: Design, applications and future challenges

被引：221

作者：

Bard, JBL ^{[1
]}

Rhee, SY

机构：

[1] Univ Edinburgh, Edinburgh EH8 9XD, Midlothian, Scotland

[2] Carnegie Inst Sci, Stanford, CA 94305 USA

来源：

NATURE REVIEWS GENETICS | 2004年 / 5卷 / 03期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1038/nrg1295

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：213 / 222

页数：10

共 34 条

[11] TAIR: A resource for integrated Arabidopsis data [J].

Garcia-Hernandez M. ;

Berardini T.Z. ;

Chen G. ;

Crist D. ;

Doyle A. ;

Huala E. ;

Knee E. ;

Lambrecht M. ;

Miller N. ;

Mueller L.A. ;

Mundodi S. ;

Reiser L. ;

Rhee S.Y. ;

Scholl R. ;

Tacklind J. ;

Weems D.C. ;

Wu Y. ;

Xu I. ;

Yoo D. ;

Yoon J. ;

Zhang P. .

Functional & Integrative Genomics, 2002, 2 (6) :239-253

[12] Positional candidate gene selection from livestock EST databases using Gene Ontology [J].

Harhay, GP ;

Keele, JW .

BIOINFORMATICS, 2003, 19 (02) :249-255

[13] The Gene Ontology (GO) database and informatics resource [J].

Harris, MA ;

Clark, J ;

Ireland, A ;

Lomax, J ;

Ashburner, M ;

Foulger, R ;

Eilbeck, K ;

Lewis, S ;

Marshall, B ;

Mungall, C ;

Richter, J ;

Rubin, GM ;

Blake, JA ;

Bult, C ;

Dolan, M ;

Drabkin, H ;

Eppig, JT ;

Hill, DP ;

Ni, L ;

Ringwald, M ;

Balakrishnan, R ;

Cherry, JM ;

Christie, KR ;

Costanzo, MC ;

Dwight, SS ;

Engel, S ;

Fisk, DG ;

Hirschman, JE ;

Hong, EL ;

Nash, RS ;

Sethuraman, A ;

Theesfeld, CL ;

Botstein, D ;

Dolinski, K ;

Feierbach, B ;

Berardini, T ;

Mundodi, S ;

Rhee, SY ;

Apweiler, R ;

Barrell, D ;

Camon, E ;

Dimmer, E ;

Lee, V ;

Chisholm, R ;

Gaudet, P ;

Kibbe, W ;

Kishore, R ;

Schwarz, EM ;

Sternberg, P ;

Gwinn, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D258-D261

[14] PharmGKB: The Pharmacogenetics Knowledge Base [J].

Hewett, M ;

Oliver, DE ;

Rubin, DL ;

Easton, KL ;

Stuart, JM ;

Altman, RB ;

Klein, TE .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :163-165

[15] Extension and integration of the gene ontology (GO): Combining GO vocabularies with external vocabularies [J].

Hill, DP ;

Blake, JA ;

Richardson, JE ;

Ringwald, M .

GENOME RESEARCH, 2002, 12 (12) :1982-1991

[16] The mouse Gene Expression Database (GXD): updates and enhancements [J].

Hill, DP ;

Begley, DA ;

Finger, JH ;

Hayamizu, TF ;

McCright, IJ ;

Smith, CM ;

Beal, JS ;

Corbani, LE ;

Blake, JA ;

Eppig, JT ;

Kadin, JA ;

Richardson, JE ;

Ringwald, M .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D568-D571

[17]

Judd W.S., 2015, PLANT SYSTEMATICS PH

[18] Predicting phenotype from patterns of annotation [J].

King, Oliver D. ;

Lee, Jeffrey C. ;

Dudley, Aimee M. ;

Janse, Daniel M. ;

Church, George M. ;

Roth, Frederick P. .

BIOINFORMATICS, 2003, 19 :i183-i189

[19] MetaCyc: a multiorganism database of metabolic pathways and enzymes [J].

Krieger, CJ ;

Zhang, PF ;

Mueller, LA ;

Wang, A ;

Paley, S ;

Arnaud, M ;

Pick, J ;

Rhee, SY ;

Karp, PD .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D438-D442

[20] MaizeGDB, the community database for maize genetics and genomics [J].

Lawrence, CJ ;

Dong, OF ;

Polacco, ML ;

Seigfried, TE ;

Brendel, V .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D393-D397

← 1 2 3 4 →