Open exchange of scientific knowledge and European copyright: The case of biodiversity information

Background. The 7^th Framework Programme for Research and Technological Development is helping the European Union to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme “Horizon 2020” aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights.We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information.Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation.     

A web-based GIS tool for exploring the world's biodiversity: The Global Biodiversity Information Facility Mapping and Analysis Portal Application (GBIF-MAPA)

Legacy biodiversity data from natural history and survey collections are rapidly becoming available in a common format over the Internet. Over 110 million records are already being served from the Global Biodiversity Information Facility (GBIF). However, our ability to use this information effectively for ecological research, management and conservation lags behind. A solution is a web-based Geographic Information System for enabling visualization and analysis of this rapidly expanding data resource. In this paper we detail a case study system, GBIF Mapping and Analysis Portal Application (MAPA), developed for deployment at distributed database portals. Building such a system requires overcoming a series of technical and research challenges. These challenges include: assuring fast speed of access to the vast amounts of data available through these distributed biodiversity databases; developing open standards based access to suitable environmental data layers for analyzing biodiversity distribution; building suitably flexible and intuitive map interfaces for refining the scope and criteria of an analysis; and building appropriate web-services based analysis tools that are of primary importance to the ecological community and make manifest the value of online biodiversity GBIF data. After discussing how we overcome these challenges, we provide case studies showing two examples of the use of GBIF-MAPA analysis tools.     

Biodiversity Clearing-House Mechanism in China: present status and future needs

China is one of the 'megadiversity' countries of the world, and is therefore rich in biodiversity information. The decision making on biodiversity conservation and sustainable utilization demands sufficient, accurate, data and information which covers living things as well as natural background and human activities. It is estimated that 152 biodiversity databases have been developed in China, mainly distributed in the thematic information categories of forestry, nature reserve, forest ecosystem, animal, plant, crop germplasm resource, traditional Chinese medicine, water resource, geology/geography, and climate/meteorology, etc. The status quo of biodiversity information system was also reviewed and main information networks related to biodiversity were presented. There are problems in the CHM construction in China, such as insufficient funding, unreasonable organizational mechanism, and low-level information sharing. Future needs for the CHM construction were discussed.     

生物多样性数据集成模式初探

本文以生物多样性研究发展现状的分析为基础,为生物多样性保护政策的制定提供可靠的数据支持为目标,通过对国内外几个著名的生物多样性数据库建设情况的分析,从相关学者的需求出发,提出了设计一个多层次多角度并带有一定人工智能的生物多样性集成数据库的构想。该系统基于都柏林核心(Dublin Core)的数据规范,并符合基于开放文献预研的元数据互操作协议(The Open Archixles Initiative Protocol for Metadata Hatvesting,OAIPMH)的标准,是一个集文字、图件、图片、声音、影像为一体的,能够在网上和硬件载体(如光盘)上同时进行发布的分布式数据库平台。其网上数据库系统的子系统之间以及子系统和硬件载体之间可以通过元数据获取的开放档案倡议协议互相交换数据。     

DNA banking for plant breeding,biotechnology and biodiversity evaluation

The manipulation of DNA is routine practice in botanical research and has made a huge impact on plant breeding, biotechnology and biodiversity evaluation. DNA is easy to extract from most plant tissues and can be stored for long periods in DNA banks. Curation methods are well developed for other botanical resources such as herbaria, seed banks and botanic gardens, but procedures for the establishment and maintenance of DNA banks have not been well documented. This paper reviews the curation of DNA banks for the characterisation and utilisation of biodiversity and provides guidelines for DNA bank management. It surveys existing DNA banks and outlines their operation. It includes a review of plant DNA collection, preservation, isolation, storage, database management and exchange procedures. We stress that DNA banks require full integration with existing collections such as botanic gardens, herbaria and seed banks, and information retrieval systems that link such facilities, bioinformatic resources and other DNA banks. They also require efficient and well-regulated sample exchange procedures. Only with appropriate curation will maximum utilisation of DNA collections be achieved.     

上海市生物多样性信息管理系统的建立和应用

上海多样性信息管理系统是一个在因特网下发布的Ｗｅｂ数据库,用戾可以通过浏览器访问ｈｔｔｐ／／ｗｗｗ．ｉｂｓｆｕ．ｆｕｄａｎ．ｅｄｕ．ｃｎ来进行检索和查询。目前提供的主要数据库：鸟类资源 、两栖爬行动物及哺乳动物库：５个专类生物多样履数据库：绿化植物相关技术也在文中作了详细阐述。最后,就目前关于生物多样性信息系统建设中存在的问题发表了一些看法。     

Review: Milking robot utilization,a successful precision livestock farming evolution

Automatic milking systems (AMS), one of the earliest precision livestock farming developments, have revolutionized dairy farming around the world. While robots control the milking process, there have also been numerous changes to how the whole farm system is managed. Milking is no longer performed in defined sessions; rather, the cow can now choose when to be milked in AMS, allowing milking to be distributed throughout a 24 h period. Despite this ability, there has been little attention given to milking robot utilization across 24 h. In order to formulate relevant research questions and improve farm AMS management there is a need to determine the current knowledge gaps regarding the distribution of robot utilization. Feed, animal and management factors and their interplay on levels of milking robot utilization across 24 h for both indoor and pasture-based systems are here reviewed. The impact of the timing, type and quantity of feed offered and their interaction with the distance of feed from the parlour; herd social dynamics, climate and various other management factors on robot utilization through 24 h are provided. This novel review draws together both the opportunities and challenges that exist for farm management to use these factors to improved system efficiency and those that exist for further research.     

农田景观和管理方式对稻田系统植物多样性的复合影响

农田生物多样性对于维持农田生态系统服务功能和农业可持续发展具有重要意义.为揭示农田景观特征和管理方式对农田生态系统植物群落和物种多样性的影响,以有机稻田(ON)、常规化防稻田(天然林脚下,CN)、常规化防稻田(距天然林>10km,CF)系统为研究对象,调查了田内、田埂和沟渠生境的植物物种组成和多样性特征,并对三种类型稻...     

海洋保护区管理与保护成效评估的方法与进展

全球物种多样性的持续下降使得生物多样性保护面临巨大挑战, 海洋生物多样性的保护任务尤其艰巨。海洋保护区是保护生物多样性的有效方式之一, 如何对其成效进行评估是当前研究热点。然而, 目前针对海洋保护区的评估体系较少, 而且评估指标多侧重于管理成效。近年来随着全球生物多样性监测网络和数据库的建立, 以及多种新技术(如遥感、声呐系统、卫星追踪、基因组学等)在海洋生物多样性监测中的应用, 使得从生态系统到基因水平的多层次连续监测成为可能。基于此, 建议未来我国海洋保护区成效评估应在充分利用新技术方法的基础上, 加强长期科学监测, 建立并完善生物多样性监测数据库和信息共享机制, 发展跨学科的综合保护成效评估体系, 加强基于生物多样性监测的保护成效评估。     

Species richness in agroecosystems: the effect of landscape, habitat and farm management

It has been suggested that biodiversity in agroecosystems depends on both landscape heterogeneity and farm management, but at the same time, studies of biodiversity in relation to both landscape variables and farm management are rare. We investigated the species richness of plants, butterflies, carabids, rove beetles and the diversity of spiders in cereal fields, leys (grass and clover crop) and semi-natural pastures at 16 farms in Central East Sweden. The farms were divided into eight pairs of one conventional and one organic farm to enable us to separate the effects of landscape and farm management on biodiversity. The pairing was based on land use, location, and landscape features. Species richness of different taxonomic groups was generally not correlated. There were no differences in species richness between the farming systems, except for carabids that had higher numbers of species on conventional farms. The species richness generally increased with landscape heterogeneity on a farm scale. Habitat type had a major effect on the species richness for most groups, with most species found in pastures and leys. The correlations between species richness and landscape variables on a farm scale, and not on a scale of multiple farms, identify farmers as the important decision-maker in conservation issues for these taxonomic groups. We discuss the role of species richness of pests' natural enemies for biological control and conservation strategies of the more common species in the agricultural landscape.     

Performance management of manufacturing system networks

Performance management of communication networks is critical for speed, reliability, and flexibility of information exchange between different components, subsystems, and sectors (e.g., factory, engineering design, and administration) of production process organizations in the environment of computer integrated manufacturing (CIM). Essential to this distributed total manufacturing system is the integrated communications network over which the information leading to process interactions and plant management and control is exchanged. Such a network must be capable of handling heterogeneous traffic resulting from intermachine communications at the factory floor, CAD drawings, design specifications, and administrative information. The objective is to improve the efficiency in handling various types of messages, e.g., control signals, sensor data, and production orders, by on-line adjustment of the parameters of the network protocol. This paper presents a conceptual design, development, and implementation of a network performance management scheme for CIM applications including flexible manufacturing. The performance management algorithm is formulated using the concepts of: (1) Perturbation analysis of discrete event dynamic systems; (2) stochastic approximation; and (3) learning automata. The proposed concept for performance management can also serve as a general framework to assist design, operation, and management of flexible manufacturing systems. The performance management procedure has been tested via emulation on a network test bed that is based on the manufacturing automation protocol (MAP) which has been widely used for CIM networking. The conceptual design presented in this paper offers a step forward to bridging the gap between management standards and users' demands for efficient network operations since most standards such as ISO and IEEE address only the architecture, services, and interfaces for network management.     

Repurposing environmental DNA samples—detecting the western pearlshell (Margaritifera falcata) as a proof of concept

Information on the distribution of multiple species in a common landscape is fundamental to effective conservation and management. However, distribution data are expensive to obtain and often limited to high‐profile species in a system. A recently developed technique, environmental DNA (eDNA) sampling, has been shown to be more sensitive than traditional detection methods for many aquatic species. A second and perhaps underappreciated benefit of eDNA sampling is that a sample originally collected to determine the presence of one species can be re‐analyzed to detect additional taxa without additional field effort. We developed an eDNA assay for the western pearlshell mussel (Margaritifera falcata) and evaluated its effectiveness by analyzing previously collected eDNA samples that were annotated with information including sample location and deposited in a central repository. The eDNA samples were initially collected to determine habitat occupancy by nonbenthic fish species at sites that were in the vicinity of locations recently occupied by western pearlshell. These repurposed eDNA samples produced results congruent with historical western pearlshell surveys and permitted a more precise delineation of the extent of local populations. That a sampling protocol designed to detect fish was also successful for detecting a freshwater mussel suggests that rapidly accumulating collections of eDNA samples can be repurposed to enhance the efficiency and cost‐effectiveness of aquatic biodiversity monitoring.     

内蒙古典型草原优化放牧管理模拟研究——以内蒙古太仆寺旗为例

针对太仆寺旗公共草地全年连续放牧的传统放牧方式,通过控制性试验,并结合太仆寺旗多年的草地、家畜、经济和气象等数据,建立中国西部草地生态经济模型,对太仆寺旗典型草原公共放牧系统进行模拟分析。以草原生态恢复和牧民收入增加为目的,对典型草原的最适载畜率、家畜在冬春季节的合理补饲等问题进行探讨,提出了典型草原放牧管理优化模式。研究结果表明,从当年10月到翌年5月份,家畜能量需求与放牧、补饲能量供给严重不平衡,家畜体重下降;随着载畜率的增加,牧民年均净收入先增加后降低,在载畜率为2.275羊单位/hm2时,收入达到最高;太仆寺旗最适载畜率为每公顷1.55-2.275羊单位。降低载畜率、加强补饲、提高草地质量都有利于提高牧民收入。     

Biodiversity conservation in cocoa production landscapes: an overview

Cocoa agroforests that retain a floristically diverse and structurally complex shade canopy have the potential to harbour significant levels of biodiversity, yet few studies have documented the plant and animal species occurring within these systems or within landscapes dominated by cocoa production. In this special issue, we bring together nine studies from Latin America, Africa and Asia that document the contribution of cocoa agroforestry systems to biodiversity conservation, and explore how the design, management and location of these systems within the broader landscape influence their value as habitats, resources and biological corridors. Tree diversity within the cocoa production systems is variable, depending on management, cultural differences, location and farm history, among other factors. Animal diversity is typically highest in those cocoa agroforests that have high plant diversity, structurally complex canopies, and abundant surrounding forest cover. In general, both plant and animal diversity within cocoa agroforests is greater than those of other agricultural land uses, but lower than in the original forest habitat. There are several emerging threats to biodiversity conservation within cocoa production landscapes, including the loss of remaining forest cover, the simplification of cocoa shade canopies and the conversion of cocoa agroforestry systems to other agricultural land uses with lower biodiversity value. To counter these threats and conserve biodiversity over the long-term, land management should focus on conserving native forest habitat within cocoa production landscapes, maintaining or restoring floristically diverse and structurally complex shade canopies within cocoa agroforests, and retaining other types of on-farm tree cover to enhance landscape connectivity and habitat availability.     

Diffusion of precision livestock farming technologies in dairy cattle farms

The rising global demand for animal products and the growing public concerns about the environment and animal welfare require dairy farms to improve their efficiency and apply more sustainable farming systems. Precision Livestock Farming (PLF) could represent a valuable support in addressing these challenges. In recent years, dairy farms have been modernising and introducing new sensors and automatic systems for managing the herd. However, the diffusion of new technologies in Italian dairy farms is still limited and farmers are reluctant to invest in precision systems. The aim of the study was to investigate the presence of PLF tools in Italian dairy farms, the motivations, benefits and limits of technological investments from the farmers’ point of view and the factors affecting the diffusion of technology. From November 2020 to June 2021, an online questionnaire was distributed and 52 responses were obtained. About 79% of the farms were located in Lombardy. The more represented milking system was the conventional milking parlour (73%), followed by automatic milking (19%). The average age of respondents was quite low: 35% of them was less than 40 years old and more than 50% was between 40 and 60. Statistical analyses were performed to evaluate the effects of different factors on the presence of technology at farm. The age of the farmer, the milk production level and the presence of an automatic milking system influenced the technological level of the farm. Precision systems that provide information on animal activity for the management of reproduction and on milk yield and flow are the most popular and are considered among the most useful. Management of reproduction and milk production are the areas where farmers appear to show interest for future investments as well. Younger farmers appear to have implemented more PLF systems than older ones, and they show a propensity to invest in latest generation precision tools. Farmers seem to have a growing interest in PLF, but some limits have been identified: the investment costs, followed by the lack of time to check information from sensor systems and the difficulty in data interpretation. As PLF technologies can play an important role in the development of sustainable, animal-friendly and efficient livestock production, further improvements and efforts are necessary to increase the propensity to PLF of dairy farmers. Results can be useful in the Italian context but also in other countries where dairy farming is rapidly intensifying but PLF is encountering resistance.     

Improved management of farm dams increases vegetation cover,water quality,and macroinvertebrate biodiversity

In many farming landscapes, aquatic features, such as wetlands, creeks, and dams, provide water for stock and irrigation, while also acting as habitat for a range of plants and animals. Indeed, some species threatened by land‐use change may otherwise be considerably rarer—or even suffer extinction—in the absence of these habitats. Therefore, a critical issue for the maintenance of biodiversity in agricultural landscapes is the extent to which the management of aquatic systems can promote the integration of agricultural production and biodiversity conservation. We completed a cross‐sectional study in southern New South Wales (southeastern Australia) to quantify the efficacy of two concurrently implemented management practices—partial revegetation and control of livestock grazing—aimed at enhancing the vegetation structure, biodiversity value, and water quality of farm dams. We found that excluding livestock for even short periods resulted in increased vegetation cover. Relative to unenhanced dams (such as those that remained unfenced), those that had been enhanced for several years were characterized by reduced levels of turbidity, nutrients, and fecal contamination. Enhanced dams also supported increased richness and abundance of macroinvertebrates. In contrast, unenhanced control dams tended to have high abundance of a few macroinvertebrate taxa. Notably, differences remained between the macroinvertebrate assemblages of enhanced dams and nearby “natural” waterbodies that we monitored as reference sites. While the biodiversity value of semilotic, natural waterbodies in the region cannot be replicated by artificial lentic systems, we consider the extensive system of farm dams in the region to represent a novel ecosystem that may nonetheless support some native macroinvertebrates. Our results show that management interventions such as fencing and grazing control can improve water quality in farm dams, improve vegetation structure around farm dams, and support greater abundance and diversity of aquatic macroinvertebrates.     

A database for coconut crop improvement

Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA.

Availability     

生物多样性信息系统建设的现状及CBIS简介

为了实现生物多样性保护和持续利用,履行《生物多样性公约》,各国政府及组织建立了大量的生物多样性信息（数据库）系统,为保护和利用的决策提供科学的支持。信息技术特别是计算机网络的发展为生物多样性信息系统的建设提供了强有力的工具和基础,使全球化的信息共享成为可能。本文简要介绍了国际上几个著名的生物多样性信息系统的建设目的、内容、现状和特点,并对国内生物多样性信息系统建设的代表——中国生物多样性信息系统（CBIS）做了介绍。     

Biodiversity: bridging the gap between condition and conservation

The aim of this study is to create a two-tiered assessment combining restoration and conservation, both needed for biodiversity management. The first tier of this approach assesses the condition of a site using a standard bioassessment method, AUSRIVAS, to determine whether significant loss of biodiversity has occurred because of human activity. The second tier assesses the conservation value of sites that were determined to be unimpacted in the first step against a reference database. This ensures maximum complementarity without having to set a priori target areas. Using the reference database, we assign site-specific and comparable coefficients for both restoration (Observed/Expected taxa with >50% probability of occurrence) and conservation values (O/E taxa with <50%, rare taxa). In a trial on 75 sites on rivers around Sydney, NSW, Australia we were able to identify three regions: (1) an area that may need restoration; (2) an area that had a high conservation value and; (3) a region that was identified as having significant biodiversity loss but with high potential to respond to rehabilitation and become a biodiversity hotspot. These examples highlight the use of the new framework as a comprehensive system for biodiversity assessment.     

A flexible online metadata editing and management system

Our team developed a metadata editing and management system employing state of the art XML technologies initially aimed at the environmental sciences but with the potential to be useful across multiple domains. We chose a modular and distributed design for scalability, flexibility, options for customizations, and the possibility to add more functionality at a later stage. The system consists of a desktop design tool that generates code for the actual online editor, a native XML database, and an online user access management application. A Java Swing application that reads an XML schema, the design tool provides the designer with options to combine input fields into online forms with user-friendly tags and determine the flow of input forms. Based on design decisions, the tool generates XForm code for the online metadata editor which is based on the Orbeon XForms engine. The design tool fulfills two requirements: First data entry forms based on a schema are customized at design time and second the tool can generate data entry applications for any valid XML schema without relying on custom information in the schema. A configuration file in the design tool saves custom information generated at design time. Future developments will add functionality to the design tool to integrate help text, tool tips, project specific keyword lists, and thesaurus services.Cascading style sheets customize the look-and-feel of the finished editor. The editor produces XML files in compliance with the original schema, however, a user may save the input into a native XML database at any time independent of validity. The system uses the open source XML database eXist for storage and uses a MySQL relational database and a simple Java Server Faces user interface for file and access management. We chose three levels to distribute administrative responsibilities and handle the common situation of an information manager entering the bulk of the metadata but leave specifics to the actual data provider.