Gene over-expression or under-expression is closely associated with human diseases, which contributes to phenotypic variations and diversity. To our best knowledge, there is no single open specific resource available ...Gene over-expression or under-expression is closely associated with human diseases, which contributes to phenotypic variations and diversity. To our best knowledge, there is no single open specific resource available to provide the association information between gene over- or under-expression and various diseases. In this study, we presented a comprehensive disease-associated over- and under-expressed gene database （OUGene） based on our proposed text mining pipeline and several open curated databases. It contains total 41,269 unique associa- tions between 7,238 over- or under-expressed genes and 1,480 diseases, which are supported by 81,974 evidence sentences from 56,442 articles. The OUGene is compre- hensive and covers most important therapeutic areas. Meanwhile a new scoring system is designed to rank the associations based on benchmarking against hand-curated data. OUGene provides an easy-of-use web interface for researchers to analyze these data and visualize the associ- ated networks, which can give insights to the complex relationships between over- and under-expressed genes and diseases at a system level. It is available at www.csbio.sjtu. edu.cn/bioinf/OUGene/.展开更多
Complementing our previous publications, this paper presents the information schema constructs （ISCs） that underpin the programming of specific system manifestation feature （SMF） orientated information management ...Complementing our previous publications, this paper presents the information schema constructs （ISCs） that underpin the programming of specific system manifestation feature （SMF） orientated information management and composing system models. First, we briefly present （1） the general process of pre-embodiment design with SMFs, （2） the procedures of creating genotypes and phenotypes of SMFs, （3） the specific procedure of instantiation of phenotypes of SMFs, and （4） the procedure of system model management and processing. Then, the chunks of information needed for instantiation of phenotypes of SMFs are discussed, and the ISCs designed for instantiation presented. Afterwards, the information management aspects of system modeling are addressed. Methodologically, system modeling involves （1） placement of phenotypes of SMF in the modeling space, （2） combining them towards the desired architecture and operation, （3） assigning values to the parameters and checking the satisfac- tion of constraints, and （4） storing the system model in the SMFs-based warehouse database. The final objective of the reported research is to develop an SMFs-based toolbox to support modeling of cyber-physical systems （CPSs）.展开更多
文摘Gene over-expression or under-expression is closely associated with human diseases, which contributes to phenotypic variations and diversity. To our best knowledge, there is no single open specific resource available to provide the association information between gene over- or under-expression and various diseases. In this study, we presented a comprehensive disease-associated over- and under-expressed gene database （OUGene） based on our proposed text mining pipeline and several open curated databases. It contains total 41,269 unique associa- tions between 7,238 over- or under-expressed genes and 1,480 diseases, which are supported by 81,974 evidence sentences from 56,442 articles. The OUGene is compre- hensive and covers most important therapeutic areas. Meanwhile a new scoring system is designed to rank the associations based on benchmarking against hand-curated data. OUGene provides an easy-of-use web interface for researchers to analyze these data and visualize the associ- ated networks, which can give insights to the complex relationships between over- and under-expressed genes and diseases at a system level. It is available at www.csbio.sjtu. edu.cn/bioinf/OUGene/.
文摘Complementing our previous publications, this paper presents the information schema constructs （ISCs） that underpin the programming of specific system manifestation feature （SMF） orientated information management and composing system models. First, we briefly present （1） the general process of pre-embodiment design with SMFs, （2） the procedures of creating genotypes and phenotypes of SMFs, （3） the specific procedure of instantiation of phenotypes of SMFs, and （4） the procedure of system model management and processing. Then, the chunks of information needed for instantiation of phenotypes of SMFs are discussed, and the ISCs designed for instantiation presented. Afterwards, the information management aspects of system modeling are addressed. Methodologically, system modeling involves （1） placement of phenotypes of SMF in the modeling space, （2） combining them towards the desired architecture and operation, （3） assigning values to the parameters and checking the satisfac- tion of constraints, and （4） storing the system model in the SMFs-based warehouse database. The final objective of the reported research is to develop an SMFs-based toolbox to support modeling of cyber-physical systems （CPSs）.
