苜蓿属（Medicago L.）种质资源描述规范和数据标准的制定及应用

依据苜蓿种质资源的特点及研究状况,论述了苜蓿种质资源描述规范、数据标准和数据质量控制规范的制定原则、适用范围、应用措施.对于促进整合全国苜蓿种质资源,规范苜蓿种质资源的搜集、整理、保存、鉴定、评价、信息与实物共享机制的建立具有重要的意义.     

湖南省农作物种质资源收集保护和创新利用进展

根据湖南省第一次(1956-1957年)和第二次(1979-1983年)全国农作物种质资源调查、收集及研究利用的工作开展情况,总结了湖南省种质资源保护和利用的现状及取得的成果,特别是水稻、油菜、辣椒、茶叶等在资源创新利用上取得了优异成绩;分析了湖南省农作物种质资源保护仍存在地方品种资源日益减少、资源收集困难、农作物种质资源保存体系不够完善、资源专业团队缺乏、资源利用率低等限制本地区农作物种质资源创新利用的问题。提出了以"第三次全国农作物种质资源普查与收集行动"为契机,建立完善的种质资源保护体系、精准评价体系及共享共用机制等促进农作物种质资源保存与利用工作良性循环的建议。     

《芒属种质资源描述规范和数据标准》的制定

目前芒属植物被视为最有前景的木质纤维素能源作物,在中国、美国、日本和欧洲国家得到了广泛研究和利用。但截至目前依然没有统一的芒属植物种质资源描述规范,一定程度上阻碍了其信息的共享与交流。鉴于此,本研究通过开展芒属植物种质资源描述和数据制定技术标准研究,旨在为芒属能源作物品种的选育、审定与推广提供科学规范的依据。本文论述了芒属种质资源描述规范、数据标准与数据质量控制规范的制定原则、方法与内容,对于促进整合全国芒属种质资源,规范芒属种质资源的收集、保存、评价具有指导作用。     

国家农作物种质资源平台的建立和应用

农作物种质资源是生物多样性的重要组成部分, 是作物育种和农业生产的物质基础。长期以来, 我国农作物种质资源标准不统一、资源保存相对分散、信息网络设施薄弱, 制约了农作物种质资源的共享利用。本文提出了国家农作物种质资源平台的概念和架构, 它是一个虚拟式的农作物种质资源机构, 由国家长期种质库、国家复份种质库、国家中期种质库、国家种质圃和国家种质信息中心组成。阐述了农作物种质资源技术规范体系构建的原则和方法, 建立了由110种作物的描述规范、数据规范和数据质量控制规范组成的技术规范体系。提出了以信息共享带动实物共享的思路、方法和途径, 建成了拥有39万份种质信息的国家农作物种质资源数据库和中国作物种质资源信息网(http://www.cgris.net/)。创建了日常性服务、展示性服务、针对性服务、需求性服务和引导性服务等5种农作物种质资源服务模式, 有效解决了农作物种质资源共享利用的难题。     

基于SOA的农作物种质资源调查信息系统研究

在研究面向服务体系结构(SOA)基础上,采用价值链分析方法识别了农作物种质资源调查服务域,提出基于SOA的农作物种质资源调查信息系统体系结构参考模型,详述了参考模型的层次结构,定义了各个服务模块功能。该参考模型为系统进一步编码和实现奠定了基础。     

甘肃省干旱地区抗逆农作物种质资源调查与分析

调查、收集甘肃省干旱地区抗逆农作物种质资源,为甘肃抗逆农作物种质资源保护、研究、利用提供基础材料。2011～2013年采用查阅文献、访问和实地调查相结合的方法,对分布在甘肃干旱地区18个县(市、区)、48个乡(镇)、81个行政村的抗逆农作物种质资源的保存及利用现状进行了调查,并对种质进行了收集。共收集到粮食作物、经济作物、蔬菜及野生资源材料845份,分属16科46属62种,其中抗旱种质27份,耐盐碱种质4份,高抗锈病种质14份。 本文对调查地区抗逆农作物种质资源现状、消长情况及原因和调查、收集到的资源种类及其利用价值进行了分析,并对甘肃省干旱地区抗逆农作物种质资源的保护、开发和利用进行了讨论。     

农作物种质资源登记区块链模型研究

农作物种质资源工作发展至今取得了巨大的成就,但也存在着农作物种质资源家底不清、共享利用效率不高及种质权属不清等问题,开展农作物种质资源登记工作能够有效解决以上问题。本研究从资源登记信息的流向角度出发,梳理了登记的整体工作流程,并结合区块链技术的优势,提出了农作物种质资源登记区块链网络模型。首先根据农作物种质资源登记的业务特点,确定登记主体和登记流程,从数据的填报、审核与共享3个阶段阐明了资源登记的整体流程。在此基础上设计了农作物种质资源登记区块链网络模型、工作流模型和数据模型,并根据农作物种质资源实际工作需求改善了DPOS共识机制,给出了激励机制的构建方式。农作物种质资源登记区块链模型通过去中心化实现登记数据的分布式存储,通过共识机制增加数据的可靠性,通过区块链的特殊数据结构确保链中数据难篡改、易追溯,提高数据安全性,为今后资源登记系统的设计提供了新思路。     

江苏农业种质资源平台运行管理信息系统建设

为促进农业种质资源开放共享,江苏省于2005年启动农业种质资源保护与利用平台建设,经过十多年的努力,初步建成了"四位一体""库圃结合"的农业种质资源保护与利用体系,涵盖农作物、林木、水产和家养动物4大类共计30个省级种质库(圃),有力地支撑了江苏现代农业品种创新与产业发展。由于平台跨学科、跨行业建设,种质库(圃)遍布全省不同地区,涉及不同性质的责任主体,给平台运行管理带来了一定的难度,且存在平台运行服务数据采集时间滞后、统计程序繁杂、管理工作效率较低等不足。为进一步提高平台的运行管理效率,促进种质资源的有效利用,本文设计构建了一套B/S模式的农业种质资源平台运行管理信息系统,用于平台线上工作流管理,实现运行服务数据的统一管理和运行服务成效的可视化展示。该系统的建立为平台的管理和决策提供了可视化数据支撑。     

浙江地方瓠瓜种质资源的表型鉴定与遗传多样性分析

"第三次全国农作物种质资源普查与收集行动"浙江项目组共新收集到瓠瓜地方种质资源51份。本研究对该51份瓠瓜种质进行田间种植鉴定,共调查了15个主要农艺性状,发现这批种质在多个性状上变异丰富;基于农艺性状的聚类分析将这批种质分为3个类群,其中第I类群的综合农艺性状表现优异,可直接或间接开发利用。利用22个瓠瓜核心SNP分子标记对这批种质进行基因型鉴定,基于基因型的聚类分析和群体结构分析均将这批种质划分为2大类群,发现类群分布主要与种质资源的地理位置相关。综合比较2种种质资源聚类分析方法,认为在二者并非完全吻合的情况下,采用分子标记的方法区分种质资源更加准确和客观。本研究结果为瓠瓜地方种质资源的开发利用提供了理论依据。     

广西十万大山农作物种质资源调查收集及多样性分析

广西十万大山是重要的生物多样性富集地,研究广西十万大山农作物种质资源多样性,对保护当地重要农作物种质资源和挖掘优良基因具有十分重要的意义。本研究以"第三次全国农作物种质资源普查与收集行动"收集的各类种质资源为对象,整理和分析十万大山农作物种质资源的种类、分布及其多样性。结果表明:在十万大山收集的181份农作物种质资源中,包括粮食作物78份、经济作物53份、蔬菜39份、果树11份,隶属于22科39属44种;按种质类型包括地方品种资源146份、野生资源35份。针对广西十万大山受产业发展不平衡和现代农作物种植结构调整的影响,导致农作物种质资源急剧减少、许多优异种质资源濒临消失的现状,建议实施异位保存和原生境保护相结合的策略,并通过加快资源鉴定评价与开发利用,促进当地优异种质资源在乡村振兴和经济建设中的可持续利用。     

Assessment of Data Quality: Errors of Measurement and Errors of Process

As projects progress from pilot studies with few simple variables and small samples, the research process as a whole becomes qualitatively more complex and subject to an array of contamination by errors and mistakes. Data usually undergo a series of manipulations (e.g., recording, computer entry, transmission) prior to final statistical analysis. The process, then, consists of numerous operations only ending with eventual statistical analysis and write-up. We present a means of estimating the impact of process error in the same terms as psychometric reliability and discuss the implications for reducing the impact of errors on overall data quality.     

MEXPRESS: visualizing expression,DNA methylation and clinical TCGA data

Background

In recent years, increasing amounts of genomic and clinical cancer data have become publically available through large-scale collaborative projects such as The Cancer Genome Atlas (TCGA). However, as long as these datasets are difficult to access and interpret, they are essentially useless for a major part of the research community and their scientific potential will not be fully realized. To address these issues we developed MEXPRESS, a straightforward and easy-to-use web tool for the integration and visualization of the expression, DNA methylation and clinical TCGA data on a single-gene level (http://mexpress.be).

Results

In comparison to existing tools, MEXPRESS allows researchers to quickly visualize and interpret the different TCGA datasets and their relationships for a single gene, as demonstrated for GSTP1 in prostate adenocarcinoma. We also used MEXPRESS to reveal the differences in the DNA methylation status of the PAM50 marker gene MLPH between the breast cancer subtypes and how these differences were linked to the expression of MPLH.

Conclusions

We have created a user-friendly tool for the visualization and interpretation of TCGA data, offering clinical researchers a simple way to evaluate the TCGA data for their genes or candidate biomarkers of interest.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1847-z) contains supplementary material, which is available to authorized users.     

Four spatial points that define enzyme families

The catalytic properties of enzymes, containing the Asp-His-Ser triads are deeply investigated for a long time. Serine endopeptidases, cutinases, acetylcholinesterases, cellulases, among other enzymes, contain these triads. We found that solely the geometric properties of just four points in the spatial structure of these enzymes are characteristic to their family (Fig. 3).     

The European Pollen Database: past efforts and current activities

Pollen stratigraphies are the most spatially extensive data available for the reconstruction of past land-cover change. Detailed knowledge of past land-cover is becoming increasingly important to evaluate the present trends in, and drivers of, vegetation composition. The European Pollen Database (EPD) was established in the late 1980s and developed in the early 1990s to provide a structure for archiving, exchanging, and analysing Quaternary pollen data from Europe. It provides a forum for scientists to meet and engage in collaborative investigations or data analysis. In May 2007 several EPD support groups were developed to assist in the task of maintaining and updating the database. The mapping and data accuracy work group (MADCAP) aims to produce an atlas of past plant distributions as detected by pollen analyses in Europe, in order to meet the growing need for this data from palaeoecologists and the wider scientific community. Due to data handling problems in the past, a significant number of EPD datasets have errors. The initial task of the work group, therefore, was a systematic review of pollen sequences, in order to identify and correct errors. The EPD currently (January 2009) archives 1,032 pollen sequences, of which 668 have age-depth models that allow chronological comparison. Many errors have been identified and corrected, or flagged for users, most notably errors in the pollen count data. The application of spatial analyses to pollen data is related to the number of data points that are available for analysis. We therefore take this opportunity to encourage the submission of pollen analytical results to the EPD or other relevant pollen databases. Only in this way will the scientific community be able to gain a better understanding of past vegetation dynamics.     

imzML--a common data format for the flexible exchange and processing of mass spectrometry imaging data

The application of mass spectrometry imaging (MS imaging) is rapidly growing with a constantly increasing number of different instrumental systems and software tools. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software. imzML data is divided in two files which are linked by a universally unique identifier (UUID). Experimental details are stored in an XML file which is based on the HUPO-PSI format mzML. Information is provided in the form of a 'controlled vocabulary' (CV) in order to unequivocally describe the parameters and to avoid redundancy in nomenclature. Mass spectral data are stored in a binary file in order to allow efficient storage. imzML is supported by a growing number of software tools. Users will be no longer limited to proprietary software, but are able to use the processing software best suited for a specific question or application. MS imaging data from different instruments can be converted to imzML and displayed with identical parameters in one software package for easier comparison. All technical details necessary to implement imzML and additional background information is available at www.imzml.org.     

Providing information on environmental change: Data management,discovery and access in the UK Environmental Change Network Data Centre

Development of a clearer understanding of the causes and consequences of environmental change is an important issue globally. The consequent demand for objective, reliable and up-to-date environmental information has led to the establishment of long-term integrated environmental monitoring programmes, including the UK's Environmental Change Network (ECN). Databases form the core information resource for such programmes. The UK Environmental Change Network Data Centre manages data on behalf of ECN (as well as other related UK integrated environmental monitoring networks) and provides a robust and integrated system of information management. This paper describes how data are captured – through standardised protocols and data entry systems – as well more recent approaches such as wireless sensors. Data are managed centrally through a database and GIS. Quality control is built in at all levels of the system. Data are then made accessible through a variety of data access methods – through bespoke web interfaces, as well as third-party data portals. This paper describes the informatics approach of the ECN Data Centre which aims to develop a seamless system of data capture, management and data access interfaces to support research.