复合注释：将多尺度数据和模型映射到生物医学本体的要求。
Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies.
作者信息
Cook Daniel L, Mejino Jose L V, Neal Maxwell L, Gennari John H
机构信息
Dept. of Physiology & Biophysics, University of Washington, Seattle, WA 98195, USA.
出版信息
Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:2791-4. doi: 10.1109/IEMBS.2009.5333830.
Abstract
Current methods for annotating biomedical data resources rely on simple mappings between data elements and the contents of a variety of biomedical ontologies and controlled vocabularies. Here we point out that such simple mappings are inadequate for large-scale multiscale, multidomain integrative "virtual human" projects. For such integrative challenges, we describe a "composite annotation" schema that is simple yet sufficiently extensible for mapping the biomedical content of a variety of data sources and biosimulation models to available biomedical ontologies.
摘要
当前用于注释生物医学数据资源的方法依赖于数据元素与各种生物医学本体及受控词汇表内容之间的简单映射。在此我们指出，这种简单映射对于大规模、多尺度、多领域的综合“虚拟人”项目而言是不够的。针对此类综合挑战，我们描述了一种“复合注释”模式，该模式简单但具有足够的可扩展性，可用于将各种数据源和生物模拟模型的生物医学内容映射到可用的生物医学本体。
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Pac Symp Biocomput. 2009:304-15.
2
Bridging biological ontologies and biosimulation: the ontology of physics for biology.连接生物本体与生物模拟：生物学的物理学本体
AMIA Annu Symp Proc. 2008 Nov 6;2008:136-40.
3
Integration of multi-scale biosimulation models via light-weight semantics.通过轻量级语义集成多尺度生物模拟模型。
Pac Symp Biocomput. 2008:414-25.
4
ChEBI: a database and ontology for chemical entities of biological interest.ChEBI：一个关于具有生物学意义的化学实体的数据库和本体。
Nucleic Acids Res. 2008 Jan;36(Database issue):D344-50. doi: 10.1093/nar/gkm791. Epub 2007 Oct 11.
5
Relations in biomedical ontologies.生物医学本体中的关系。
Genome Biol. 2005;6(5):R46. doi: 10.1186/gb-2005-6-5-r46. Epub 2005 Apr 28.
6
An ontology for cell types.一种细胞类型本体。
Genome Biol. 2005;6(2):R21. doi: 10.1186/gb-2005-6-2-r21. Epub 2005 Jan 14.
7
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Integration from proteins to organs: the Physiome Project.从蛋白质到器官的整合：生理组计划。
Nat Rev Mol Cell Biol. 2003 Mar;4(3):237-43. doi: 10.1038/nrm1054.
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