Ontology

       　本体(ontology)的概念起源于哲学领域,是人类对自然界”存在论”的一种哲学观点,它意味着知识和知晓( knowing)。上世纪70-80年代信息科学特别是计算机科学开始了对自然世界认知的形式化的表示,既是可被计算机表示,解释和利用的知识的形式化的研究—即本体。所以领域本体是结构化的领域知识,并可以被计算机解释和利用。 领域本体对生物,医学信息变得越来越重要。在生物数据爆炸的时代,人们站在不同的角度对真实世界认知是不同的,并且描述概念的术语分类方法也是不同的,所用的术语也是层出不穷。如何实现对生命世界中这些概念理解上的共享,包括从不同的视角,不同的术语分类, 不同的主体( 人和机器)共享概念,这些都是为什么在当前生物医学信息研究中生物/医学知识的结构化表示成为热点的缘故。 从知识共享的上下文考虑,本体意味着”概念化的规范( specification of a conceptualization)”,即本体是对概念和关系的描述。例如开发专业词汇表时通常是概念性的,并不关注医生典型的使用情况。为了能够共享医生们典型使用的词汇,因此需要承认他们所使用的那些术语，正确解释它们，并把它们映射到受控词汇表。可以通过受控词汇表连接到数据库中的信息,然后利用这些知识查询数据库。例如当前典型的应用是关于基因产品知识的基因本体Gene Ontology（GO）和发育解剖学本体的合并，这样就便于实现基于组织的,利用原文和空间位置来查询基因表达数据库。 领域本体的研究和实现是可知识共享的公共信息平台基础的研究和实现。为此CMBI特准备了关于Ontology的特别报道，供实践参考,更多文献,请用相关关键词通过CMBI文献查询获取。

• Visualization and analysis of microarray and gene ontology data with treemaps
  
• uterine leiomyoma-proteomics and gene ontology analysis
  
• Towards a formalization of disease-specific ontologies for neuroinformatics
  
• THEA-ontology-driven analysis of microarray data
  
• The problem of pain management among persons with dementia, personhood, and the ontology of relationships
  
• The National Cancer Institute’s Thésaurus and Ontology
  
• The gene ontology categorizer
  
• The Gene Ontology Annotation (GOA) project
  
• The Gene Ontology Annotation (GOA) Database
  
• The Gene Ontology (GO) database and informatics resource
  
• Textpresso-an ontology-based information retrieval and extraction system for biological literature
  
• SEMEDA-ontology based semantic integration of biological databases
  
• Semantic search among heterogeneous biological databases based on gene ontology
  
• Retrieving definitional content for ontology development
  
• Prediction of human protein function according to Gene Ontology categories
  
• Predicting gene ontology biological process from temporal gene expression patterns
  
• Positional candidate gene selection from livestock EST databases using Gene Ontology
  
• PA-GOSUB-a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization
  
• Onto-Tools-an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments
  
• Ontology-based knowledge management of troglitazone-induced hepatotoxicity
  
• Ontology Recapitulates Physiology
  
• Ontology development for unified traditional Chinese medical language system
  
• Ontology concepts and tools for statistical genomics
  
• Ontologizing gene-expression microarray data
  
• Ontologies for proteomics
  
• OntoBlast function-From sequence similarities directly to potential functional annotations by ontology terms
  
• new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology
  
• NetAffx Gene Ontology Mining Tool
  
• Methodologies, tools and languages for building ontologies
  
• Mapping Gene Ontology to proteins based on protein-protein interaction data
  
• MAPPFinder-using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
  
• Learning ontologies from natural language texts
  
• Learnability-based further prediction of gene functions in Gene Ontology
  
• Knowledge acquisition, consistency checking and concurrency control for Gene Ontology
  
• Investigating semantic similarity measures across the Gene Ontology
  
• In silico gene function prediction using ontology-based pattern identification
  
• IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatic
  
• Handling multiple testing while interpreting microarrays with the Gene Ontology Database
  
• GOTree Machine (GOTM)-a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchies
  
• GOToolBox-functional analysis of gene datasets based on Gene Ontology
  
• GO-TermFinder--open source software for accessing Gene Ontology information and finding significantly
  
• GO-Mapper-functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms
  
• GoFish finds genes with combinations of Gene Ontology attributes
  
• GoFigure-automated Gene Ontology annotation
  
• GOblet-a platform for Gene Ontology annotation of anonymous sequence data
  
• GOAL-automated Gene Ontology analysis of expression profiles
  
• Gene-Ontology-based clustering of gene expression data
  
• Gene-Ontology analysis reveals association of tissue-specific 5' CpG-island genes with development and embryogenesis
  
• FatiGO-a web tool for finding significant associations of Gene Ontology terms with groups of genes
  
• Evaluation of ontology development tools for bioinformatics
  
• Data exploration tools for the Gene Ontology database
  
• Controlled vocabularies in bioinformatics-a case study in the gene ontology
  
• Context-based ontology building support in clinical domains using formal concept analysis
  
• Constructing ontology-driven protein family databases
  
• COMe-the ontology of bioinorganic proteins
  
• CLENCH-a program for calculating Cluster ENriCHment using the Gene Ontology
  
• ChipInfo-Software for extracting gene annotation and gene ontology information for microarray analysis
  
• Automatic annotation of protein motif function with Gene Ontology terms
  
• Automated Gene Ontology annotation for anonymous sequence data
  
• Applying Support Vector Machines for Gene Ontology based gene function prediction
  
• An ontology of randomized controlled trials for evidence-based practice
  
• An ontology of human developmental anatomy
  
• An ontology for collaborative construction and analysis of cellular pathways
  
• A short study on the success of the Gene Ontology
  
• A reference ontology for biomedical informatics
  
• A new hybrid approach to predict subcellular localization of proteins by incorporating gene ontology
  
• A framework for a distributed, hybrid, multiple-ontology clinical-guideline library
  
• Ontologies for proteomics
  
• COMe-the ontology of bioinorganic proteins
  
• Representing genetic sequence data for pharmacogenomics-an evolutionary approach using ontological
  
• Positional candidate gene selection from livestock EST databases using Gene Ontology
  
• Knowledge acquisition, consistency checking and concurrency control for Gene Ontology
  
• FatiGO-a web tool for finding significant associations of Gene Ontology terms with groups of genes
  
• Evaluation of ontology development tools for bioinformatics
  
• An ontology for collaborative construction and analysis of cellular pathways