Discovery of materials using“bottom-up”or“top-down”approach is of great interest in materials science.Layered materials consisting of two-dimensional(2D)building blocks provide a good platform to explore new mater...Discovery of materials using“bottom-up”or“top-down”approach is of great interest in materials science.Layered materials consisting of two-dimensional(2D)building blocks provide a good platform to explore new materials in this respect.In van der Waals(vdW)layered materials,these building blocks are charge neutral and can be isolated from their bulk phase(top-down),but usually grow on substrate.In ionic layered materials,they are charged and usually cannot exist independently but can serve as motifs to construct new materials(bottom-up).In this paper,we introduce our recently constructed databases for 2D material-substrate interface(2DMSI),and 2D charged building blocks.For 2DMSI database,we systematically build a workflow to predict appropriate substrates and their geometries at substrates,and construct the 2DMSI database.For the 2D charged building block database,1208 entries from bulk material database are identified.Information of crystal structure,valence state,source,dimension and so on is provided for each entry with a json format.We also show its application in designing and searching for new functional layered materials.The 2DMSI database,building block database,and designed layered materials are available in Science Data Bank at https://doi.org/10.57760/sciencedb.j00113.00188.展开更多
Lentil(Lens culinaris Medik.), a diploid(2n = 14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop specie...Lentil(Lens culinaris Medik.), a diploid(2n = 14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information(ESTs). In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information(NCBI) database to develop unigene-based simple sequence repeat(SSR) markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed.Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches(using E-value 1 × 10-5) against the public UniP rot(http://www.uniprot.org/) and NCBI(http://www.ncbi.nlh.nih.gov/) databases were performed. Further functional annotation was performed using PLAZA(version3.0) comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding.展开更多
1 Introduction Fresh or saline,lakes constantly exchange with other water bodies on the Earth.Together,they form a crucial part of the water cycle–one of the most important ecosystem functions supporting humans and o...1 Introduction Fresh or saline,lakes constantly exchange with other water bodies on the Earth.Together,they form a crucial part of the water cycle–one of the most important ecosystem functions supporting humans and other biological communities.Lakes have provided invaluable and irreplaceable ecosystem services(benefits)for the展开更多
The paper firstly analyses disadvantages in the traditional Web database systems. And then it puts forward a simplified framework called database-oriented Web framework (DOWF). In this framework, the pages and the dat...The paper firstly analyses disadvantages in the traditional Web database systems. And then it puts forward a simplified framework called database-oriented Web framework (DOWF). In this framework, the pages and the data are all managed by database system. In order to get keywords or search a special page, which the users accessed before, users access the static pages by common script procedure (CSP), and access the dynamic pages by functional script procedure (FSP) and CSP. The article expounds the method how to implement DOWF in details. The paper also analyses the mechanism of a DOWF site by implementing a prototype system. At last, the article gives the features of DOWS in search, in security, in reuse of pages and in offline waiting, etc. Key words database-oriented - Web framework - common script procedure (CSP) - functional script procedure (FSP) CLC number TP 391 Foundation item: Supported by Natural Science Foundation of Jiangsu Province (BK2003030).Biography: ZHU Qiao-ming (1963-), male, professor, research direction: Web information processing chinses information processing.展开更多
Homogeneous binary function products are frequently encountered in the sub-universes modeled by databases,spanning from genealogical trees and sports to education and healthcare,etc.Their properties must be discovered...Homogeneous binary function products are frequently encountered in the sub-universes modeled by databases,spanning from genealogical trees and sports to education and healthcare,etc.Their properties must be discovered and enforced by the software applications managing such data to guarantee plausibility.The(Elementary)Mathematical Data Model provides 17 types of dyadic-based homogeneous binary function product constraint categories.MatBase,an intelligent data and knowledge base management system prototype,allows database designers to simply declare them by only clicking corresponding checkboxes and automatically generates code for enforcing them.This paper describes the algorithms that MatBase uses for enforcing all 17 types of homogeneous binary function product constraint,which may also be employed by developers without access to MatBase.展开更多
目的建立一个综合了生物信息学和化学信息学的网络信息平台M&Function,致力于新药筛选和研究。方法通过数据挖掘,整合小分子药物的名称、结构、功能、分类等信息,建立一个小分子药物信息资源库。在此基础上,借助基于最大公共子结构(...目的建立一个综合了生物信息学和化学信息学的网络信息平台M&Function,致力于新药筛选和研究。方法通过数据挖掘,整合小分子药物的名称、结构、功能、分类等信息,建立一个小分子药物信息资源库。在此基础上,借助基于最大公共子结构(maximum common substructure,MCS)和Fingerprint的结构比对软件,通过统计分析,建立了功能预测系统,对活性小分子进行生物学功能预测。结果 M&Function平台拥有丰富的数据信息、内嵌的图形显示和数据统计插件人性化的网站设计,具有直观、高效、简便易用、测试数据结果可靠等优点。结论 M&Function平台不仅是一个小分子药物信息资源库,也是一个小分子功能预测平台,可以为高通量先导化合物的筛选提供信息准备和数据支持。网站可以通过http://lifecenter.sgst.cn/mcs/home.do进行访问。展开更多
Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased orga...Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs.In recent years,a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery.In addition to being used to annotate the proteome,these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease.Here,we present a comprehensive review of the major human protein bioinformatics databases.We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.展开更多
This paper defines a new kind of rule, probability functional dependency rule. The functional dependency degree can be depicted by this kind of rule. Five algorithms, from the simple to the complex, are presefited to ...This paper defines a new kind of rule, probability functional dependency rule. The functional dependency degree can be depicted by this kind of rule. Five algorithms, from the simple to the complex, are presefited to mine this kind of rule in different condition. The related theorems are proved to ensure the high efficiency and the correctness of the above algorithms.展开更多
Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools...Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states.The utilization of protein/gene interaction and genetic variation databases,coupled with pathway analysis can facilitate the identification of potential drug targets.By bridging the gap between molecular-level information and disease understanding,this review contributes insights into the impactful utilization of computational methods,paving the way for targeted interventions and therapeutic advancements in biomedical research.展开更多
基金Project supported by the National Natural Science Foundation of China(Grant Nos.61888102,52272172,and 52102193)the Major Program of the National Natural Science Foundation of China(Grant No.92163206)+2 种基金the National Key Research and Development Program of China(Grant Nos.2021YFA1201501 and 2022YFA1204100)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB30000000)the Fundamental Research Funds for the Central Universities.
文摘Discovery of materials using“bottom-up”or“top-down”approach is of great interest in materials science.Layered materials consisting of two-dimensional(2D)building blocks provide a good platform to explore new materials in this respect.In van der Waals(vdW)layered materials,these building blocks are charge neutral and can be isolated from their bulk phase(top-down),but usually grow on substrate.In ionic layered materials,they are charged and usually cannot exist independently but can serve as motifs to construct new materials(bottom-up).In this paper,we introduce our recently constructed databases for 2D material-substrate interface(2DMSI),and 2D charged building blocks.For 2DMSI database,we systematically build a workflow to predict appropriate substrates and their geometries at substrates,and construct the 2DMSI database.For the 2D charged building block database,1208 entries from bulk material database are identified.Information of crystal structure,valence state,source,dimension and so on is provided for each entry with a json format.We also show its application in designing and searching for new functional layered materials.The 2DMSI database,building block database,and designed layered materials are available in Science Data Bank at https://doi.org/10.57760/sciencedb.j00113.00188.
基金Financial assistance from ICARDA, Morocco, in the form of a brief projectgrant support from the Northern Pulse Growers Association and the USA Dry Pea and Lentil Council are gratefully acknowledged
文摘Lentil(Lens culinaris Medik.), a diploid(2n = 14) with a genome size greater than 4000 Mbp, is an important cool season food legume grown worldwide. The availability of genomic resources is limited in this crop species. The objective of this study was to develop polymorphic markers in lentil using publicly available curated expressed sequence tag information(ESTs). In this study, 9513 ESTs were downloaded from the National Center for Biotechnology Information(NCBI) database to develop unigene-based simple sequence repeat(SSR) markers. The ESTs were assembled into 4053 unigenes and then analyzed to identify 374 SSRs using the MISA microsatellite identification tool. Among the 374 SSRs, 26 compound SSRs were observed.Primer pairs for these SSRs were designed using Primer3 version 1.14. To classify the functional annotation of ESTs and EST–SSRs, BLASTx searches(using E-value 1 × 10-5) against the public UniP rot(http://www.uniprot.org/) and NCBI(http://www.ncbi.nlh.nih.gov/) databases were performed. Further functional annotation was performed using PLAZA(version3.0) comparative genomics and GO annotation was summarized using the Plant GO slim category. Among the synthesized 312 primers, 219 successfully amplified Lens DNA. A diverse panel of 24 Lens genotypes was used to identify polymorphic markers. A polymorphic set of 57 markers successfully discriminated the test genotypes. This set of polymorphic markers with functional annotation data could be used as molecular tools in lentil breeding.
文摘1 Introduction Fresh or saline,lakes constantly exchange with other water bodies on the Earth.Together,they form a crucial part of the water cycle–one of the most important ecosystem functions supporting humans and other biological communities.Lakes have provided invaluable and irreplaceable ecosystem services(benefits)for the
基金Funded by the National Natural Science Foundation of China(Grant No.50375071) ,the National Natural Science Foundation of Jiangsu Province Education Department ( Grant No. 2004JD028J) and the Science Foundation of Zhenjiang City( Grant No.2004JD020J)
文摘The paper firstly analyses disadvantages in the traditional Web database systems. And then it puts forward a simplified framework called database-oriented Web framework (DOWF). In this framework, the pages and the data are all managed by database system. In order to get keywords or search a special page, which the users accessed before, users access the static pages by common script procedure (CSP), and access the dynamic pages by functional script procedure (FSP) and CSP. The article expounds the method how to implement DOWF in details. The paper also analyses the mechanism of a DOWF site by implementing a prototype system. At last, the article gives the features of DOWS in search, in security, in reuse of pages and in offline waiting, etc. Key words database-oriented - Web framework - common script procedure (CSP) - functional script procedure (FSP) CLC number TP 391 Foundation item: Supported by Natural Science Foundation of Jiangsu Province (BK2003030).Biography: ZHU Qiao-ming (1963-), male, professor, research direction: Web information processing chinses information processing.
文摘Homogeneous binary function products are frequently encountered in the sub-universes modeled by databases,spanning from genealogical trees and sports to education and healthcare,etc.Their properties must be discovered and enforced by the software applications managing such data to guarantee plausibility.The(Elementary)Mathematical Data Model provides 17 types of dyadic-based homogeneous binary function product constraint categories.MatBase,an intelligent data and knowledge base management system prototype,allows database designers to simply declare them by only clicking corresponding checkboxes and automatically generates code for enforcing them.This paper describes the algorithms that MatBase uses for enforcing all 17 types of homogeneous binary function product constraint,which may also be employed by developers without access to MatBase.
文摘目的建立一个综合了生物信息学和化学信息学的网络信息平台M&Function,致力于新药筛选和研究。方法通过数据挖掘,整合小分子药物的名称、结构、功能、分类等信息,建立一个小分子药物信息资源库。在此基础上,借助基于最大公共子结构(maximum common substructure,MCS)和Fingerprint的结构比对软件,通过统计分析,建立了功能预测系统,对活性小分子进行生物学功能预测。结果 M&Function平台拥有丰富的数据信息、内嵌的图形显示和数据统计插件人性化的网站设计,具有直观、高效、简便易用、测试数据结果可靠等优点。结论 M&Function平台不仅是一个小分子药物信息资源库,也是一个小分子功能预测平台,可以为高通量先导化合物的筛选提供信息准备和数据支持。网站可以通过http://lifecenter.sgst.cn/mcs/home.do进行访问。
基金supported by the National Basic Research Program of China (Grant Nos. 2010CB912700 and 2011CB910601)
文摘Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs.In recent years,a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery.In addition to being used to annotate the proteome,these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease.Here,we present a comprehensive review of the major human protein bioinformatics databases.We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.
文摘This paper defines a new kind of rule, probability functional dependency rule. The functional dependency degree can be depicted by this kind of rule. Five algorithms, from the simple to the complex, are presefited to mine this kind of rule in different condition. The related theorems are proved to ensure the high efficiency and the correctness of the above algorithms.
基金This work was supported by EU funding within the NextGenerationEU-MUR PNRR Extended Partnership Initiative on Emerging Infectious Diseases(Project No.PE00000007,INF-ACT)。
文摘Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states.The utilization of protein/gene interaction and genetic variation databases,coupled with pathway analysis can facilitate the identification of potential drug targets.By bridging the gap between molecular-level information and disease understanding,this review contributes insights into the impactful utilization of computational methods,paving the way for targeted interventions and therapeutic advancements in biomedical research.
