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On the Ontology Based Representation of Cell Lines 英文参考文献.doc

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On the Ontology Based Representation of Cell Lines 英文参考文献

OntheOntologyBasedRepresentationofCellLines MatthiasGanzinger1*,ShanHe1,2,KaiBreuhahn3,PetraKnaup1 1InstituteofMedicalBiometryandInformatics,HeidelbergUniversity,Heidelberg,Germany,2DepartmentofBiomedicalInformatics,UniversityofUtah,SaltLakeCity, Utah,UnitedStatesofAmerica,3InstituteofPathology,HeidelbergUniversity,Heidelberg,Germany Abstract Celllinesarefrequentlyusedashighlystandardizedandreproducibleinvitromodelsforbiomedicalanalysesandassays. Celllinesaredistributedbycellbanksthatoperatedatabasesdescribingtheirproducts.However,thedescriptionofthecell lines’propertiesarenotstandardizedacrossdifferentcellbanks.Existingcellline-relatedontologiesmostlyfocusonthe descriptionofthecelllines’names,butdonotcoveraspectsliketheoriginoroptimalgrowthconditions.Theobjectiveof thisworkistodevelopanontologythatallowsforamorecomprehensivedescriptionofcelllinesandtheirmetadata,which shouldcoverthedataelementsprovidedbycellbanks.Thiswillprovidethebasisforthestandardizedannotationofcell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks’ databases could be mapped to existing ontologies. As a result, we created a new ontology called cell culture ontology (CCONT)integratingexistingontologieswherepossible.CCONTprovidesclassesfromtheareasofcelllineidentification, origin,celllineproperties,propagationandtestsperformed. Citation: Ganzinger M, He S, Breuhahn K, Knaup P (2012) On the Ontology Based Representation of Cell Lines. PLoS ONE 7(11): e48584. doi:10.1371/ journal.pone.0048584 Editor:NatarajanKannan,UniversityofGeorgia,UnitedStatesofAmerica ReceivedMarch23,2012;Acce