Ontologies in Quantitative Biology A Basis for Comparison, Integration, and Discovery 英文参考文献.docVIP

Essay OntologiesinQuantitativeBiology:ABasisfor Comparison,Integration,andDiscovery LarsJ.Jensen1*,PeerBork2,3* 1Novo NordiskFoundationCenter for Protein Research, FacultyofHealth Sciences, UniversityofCopenhagen, Copenhagen, Denmark, 2EuropeanMolecularBiology Laboratory,Heidelberg,Germany,3MaxDelbru¨ckCenterforMolecularMedicine,Berlin-Buch,Germany Biology is rapidly changing from a descriptive to a data-driven discipline in which the discovery of novel findings depends on the comparison and integra- tion of massive data sets. As a conse- form the conceptual basis of molecular biology. For example, they focus on classificationofandrelationshipsbetween biological entities or concepts such as amino acids [2] and protein structures [3,4], protein and domain families [5–7], as well as associated molecular functions [7,8]andbiochemicalpathways[9]. words ontology or ontologies. By 2007 that number had increased by more than an order of magnitude, and more than two thirds ontologies of the abstracts that mention mention specifically GO quence, ontologies—systematic descrip- (Figure 2), which is also reflected in the steady rise in the number of the citations toGOandassociatedresources.Thiscan, in part, be attributed to the use of GO withinrapidlygrowingresearchareassuch ascomparativegenomics,transcriptomics, and proteomics. Another important con- tribution is that the GO consortium worked closely together with the commu- nities behind key model organism data- basestoensurethatvastamountsofGO- based annotations would be provided for eachoftherespectivegenomes. tions of specific biological attributes—are becoming more and more important for describing the existing biological knowl- edge. Despite an increasing awareness about ontologies among biologists, much work remains to be done before many researchfieldsinbiologycanbenefitfrom capturing the knowledge in such a way. We explore, here, the use of biological ontologies,illustratehowontologiescanbe usedtomakedisc