The establishment of China's core biodiversity metadata standard

Biodiversity metadata provide service to query, management and use of actual data sets. The progress of the development of metadata standards in China was analyzed, and metadata required and/or produced based on the Convention on Biological Diversity were reviewed. A biodiversity metadata standard was developed based on the characteristics of biodiversity data and in line with the framework of international metadata standards. The content of biodiversity metadata is divided into two levels. The first level consists of metadata entities and elements that are necessary to exclusively identify a biodiversity data set, and is named as Core Metadata. The second level comprises metadata entities and elements that are necessary to describe all aspects of a biodiversity data set. The standard for core biodiversity metadata is presented in this paper, which is composed of 51 elements belonging to 6 categories (entities), i.e. inventory information, collection information, information on the content of the data set, management information, access information, and metadata management information. The name, definition, condition, data type, and field length of metadata elements in these six categories (entities) are also described.     

中国的野生动物红外相机监测需要统一的标准

采用及时、可靠的方法对物种开展有效监测是生物多样性保护的基础。红外相机技术可以获得兽类物种的影像、元数据和分布信息, 是监测生物多样性的有效途径。这项技术在野外便于部署, 规程易于标准化, 可提供野生动物凭证标本(影像)以及物种拍摄位置、拍摄日期与时间、拍摄细节(相机型号等)等附属信息。这些特性使得我们可以积累数以百万计的影像资料和野生动物监测数据。在中国, 红外相机技术已得到广泛应用, 众多机构正在使用红外相机采集并存储野生动物影像以及相关联的元数据。目前, 亟需对红外相机元数据结构进行标准化, 以促进不同机构之间以及与外部保护团体之间的数据共享。迄今全球已建立有数个国际数据共享平台, 例如Wildlife Insights, 但他们离不开与中国的合作, 以有效追踪全球可持续发展的进程。达成这样的合作需要3个基础: 共同的数据标准、数据共享协议和数据禁用政策。我们倡议, 中国保护领域的政府主管部门、机构团体一起合作, 共同制定在国内单位之间以及与国际机构之间共享监测数据的政策、机制与途径。     

Tabular strategies for metadata in ecology,evolution, and the environmental sciences

Data support knowledge development and theory advances in ecology and evolution. We are increasingly reusing data within our teams and projects and through the global, openly archived datasets of others. Metadata can be challenging to write and interpret, but it is always crucial for reuse. The value metadata cannot be overstated—even as a relatively independent research object because it describes the work that has been done in a structured format. We advance a new perspective and classify methods for metadata curation and development with tables. Tables with templates can be effectively used to capture all components of an experiment or project in a single, easy‐to‐read file familiar to most scientists. If coupled with the R programming language, metadata from tables can then be rapidly and reproducibly converted to publication formats including extensible markup language files suitable for data repositories. Tables can also be used to summarize existing metadata and store metadata across many datasets. A case study is provided and the added benefits of tables for metadata, a priori, are developed to ensure a more streamlined publishing process for many data repositories used in ecology, evolution, and the environmental sciences. In ecology and evolution, researchers are often highly tabular thinkers from experimental data collection in the lab and/or field, and representations of metadata as a table will provide novel research and reuse insights.     

TRiDaBASE: A stand-alone database for storage,analysis and exchange of dendrochronological metadata

Dendrochronological data formats in general offer limited space for recording associated metadata. Such information is often recorded separately from the actual time series, and often only on paper. TRiDaBASE has been developed to improve metadata administration. It is a relational Microsoft Access database that allows users to register digital metadata according to TRiDaS, to generate TRiDaS XML for uploading to TRiDaS-based analytical systems and repositories, and to ingest TRiDaS XML created elsewhere for local querying and analyses.     

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。     

Organization of marine phenology data in support of planning and conservation in ocean and coastal ecosystems

Among the many effects of climate change is its influence on the phenology of biota. In marine and coastal ecosystems, phenological shifts have been documented for multiple life forms; however, biological data related to marine species' phenology remain difficult to access and is under-used. We conducted an assessment of potential sources of biological data for marine species and their availability for use in phenological analyses and assessments. Our evaluations showed that data potentially related to understanding marine species' phenology are available through online resources of governmental, academic, and non-governmental organizations, but appropriate datasets are often difficult to discover and access, presenting opportunities for scientific infrastructure improvement. The developing Federal Marine Data Architecture when fully implemented will improve data flow and standardization for marine data within major federal repositories and provide an archival repository for collaborating academic and public data contributors. Another opportunity, largely untapped, is the engagement of citizen scientists in standardized collection of marine phenology data and contribution of these data to established data flows. Use of metadata with marine phenology related keywords could improve discovery and access to appropriate datasets. When data originators choose to self-publish, publication of research datasets with a digital object identifier, linked to metadata, will also improve subsequent discovery and access. Phenological changes in the marine environment will affect human economics, food systems, and recreation. No one source of data will be sufficient to understand these changes. The collective attention of marine data collectors is needed—whether with an agency, an educational institution, or a citizen scientist group—toward adopting the data management processes and standards needed to ensure availability of sufficient and useable marine data to understand marine phenology.     

中国农田土壤动物长期监测样地科学调查监测的实施方法

我国农田土壤动物面临严峻的多样性丧失问题, 建设监测样地并开展长期监测是解决该问题的重要途径, 但至今国内外仍缺乏农田土壤动物长期监测样地科学调查监测的实施方法。依据BCI 50 ha大型固定样地建设规范, 参照我国已建成的森林和农田土壤动物大型固定样地监测经验, 本文提出了农田土壤动物长期监测样地科学调查监测的实施方法。首先, 需要明确科学问题, 确定科学调查监测应遵守的基本原则。其次, 需要规范长期调查监测涉及的专业术语, 依据研究目的和实际情况选择地点和样地, 参照建设规范和农田特征建立农田土壤动物大型固定样地。第三, 以研究农田土壤动物多样性为核心, 揭示土壤动物在农田生态系统健康和功能中的作用, 有选择性地开展4类27项科学指标的长期监测工作, 要求按照统一的、规范化的工作流程开展野外调查和室内实验。最后, 要科学规范地完成标本的鉴定描述和保存保管, 研发体现农田土壤动物特征的数据库和管理信息系统。希望本文的研究结果能推动我国乃至世界范围的规范化样地建设和标准化网络监测, 为我国农田土壤动物评估与保护提供长期可靠的数据支撑。     

From Reductionism to Reintegration: Solving society’s most pressing problems requires building bridges between data types across the life sciences

Decades of reductionist approaches in biology have achieved spectacular progress, but the proliferation of subdisciplines, each with its own technical and social practices regarding data, impedes the growth of the multidisciplinary and interdisciplinary approaches now needed to address pressing societal challenges. Data integration is key to a reintegrated biology able to address global issues such as climate change, biodiversity loss, and sustainable ecosystem management. We identify major challenges to data integration and present a vision for a “Data as a Service”-oriented architecture to promote reuse of data for discovery. The proposed architecture includes standards development, new tools and services, and strategies for career-development and sustainability.

Data integration is key to the reintegration of biology and the pursuit of global issues such as climate change, biodiversity loss, and sustainable ecosystem management. This Essay defines the primary challenges in data integration and presents a vision for a "Data as a Service" (DaaS) oriented architecture that enables frictionless data reuse, hypothesis testing, and discovery.     

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a ‘Big Data’ approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence‐only or presence–absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi‐source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter‐ or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi‐source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA‐based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals.     

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。     

Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012)

The Global Biodiversity Information Facility and the Genomic Standards Consortium convened a joint workshop at the University of Oxford, 27-29 February 2012, with a small group of experts from Europe, USA, China and Japan, to continue the alignment of the Darwin Core with the MIxS and related genomics standards. Several reference mappings were produced as well as test expressions of MIxS in RDF. The use and management of controlled vocabulary terms was considered in relation to both GBIF and the GSC, and tools for working with terms were reviewed. Extensions for publishing genomic biodiversity data to the GBIF network via a Darwin Core Archive were prototyped and work begun on preparing translations of the Darwin Core to Japanese and Chinese. Five genomic repositories were identified for engagement to begin the process of testing the publishing of genomic data to the GBIF network commencing with the SILVA rRNA database.     

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。     

Linking of digital images to phylogenetic data matrices using a morphological ontology

Images are paramount in documentation of morphological data. Production and reproduction costs have traditionally limited how many illustrations taxonomy could afford to publish, and much comparative knowledge continues to be lost as generations turn over. Now digital images are cheaply produced and easily disseminated electronically but pose problems in maintenance, curation, sharing, and use, particularly in long-term data sets involving multiple collaborators and institutions. We propose an efficient linkage of images to phylogenetic data sets via an ontology of morphological terms; an underlying, fine-grained database of specimens, images, and associated metadata; fixation of the meaning of morphological terms (homolog names) by ostensive references to particular taxa; and formalization of images as standard views. The ontology provides the intellectual structure and fundamental design of the relationships and enables intelligent queries to populate phylogenetic data sets with images. The database itself documents primary morphological observations, their vouchers, and associated metadata, rather than the conventional data set cell, and thereby facilitates data maintenance despite character redefinition or specimen reidentification. It minimizes reexamination of specimens, loss of information or data quality, and echoes the data models of web-based repositories for images, specimens, and taxonomic names. Confusion and ambiguity in the meanings of technical morphological terms are reduced by ostensive definitions pointing to features in particular taxa, which may serve as reference for globally unique identifiers of characters. Finally, the concept of standard views (an image illustrating one or more homologs in a specific sex and life stage, in a specific orientation, using a specific device and preparation technique) enables efficient, dynamic linkage of images to the data set and automatic population of matrix cells with images independently of scoring decisions.     

Beyond the “Code”: A Guide to the Description and Documentation of Biodiversity in Ciliated Protists (Alveolata,Ciliophora)

Recent advances in molecular technology have revolutionized research on all aspects of the biology of organisms, including ciliates, and created unprecedented opportunities for pursuing a more integrative approach to investigations of biodiversity. However, this goal is complicated by large gaps and inconsistencies that still exist in the foundation of basic information about biodiversity of ciliates. The present paper reviews issues relating to the taxonomy of ciliates and presents specific recommendations for best practice in the observation and documentation of their biodiversity. This effort stems from a workshop that explored ways to implement six Grand Challenges proposed by the International Research Coordination Network for Biodiversity of Ciliates (IRCN‐BC). As part of its commitment to strengthening the knowledge base that supports research on biodiversity of ciliates, the IRCN‐BC proposes to populate The Ciliate Guide, an online database, with biodiversity‐related data and metadata to create a resource that will facilitate accurate taxonomic identifications and promote sharing of data.     

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.     

Caries-preventive effect of glass ionomer and resin-based fissure sealants on permanent teeth: An update of systematic review evidence

Background

The 1980s marked the occasion when Geographical Information System (GIS) technology was broadly introduced into the geo-spatial community through the establishment of a strong GIS industry. This technology quickly disseminated across many countries, and has now become established as an important research, planning and commercial tool for a wider community that includes organisations in the public and private health sectors. The broad acceptance of GIS technology and the nature of its functionality have meant that numerous datasets have been created over the past three decades. Most of these datasets have been created independently, and without any structured documentation systems in place. However, search and retrieval systems can only work if there is a mechanism for datasets existence to be discovered and this is where proper metadata creation and management can greatly help. This situation must be addressed through support mechanisms such as Web-based portal technologies, metadata editor tools, automation, metadata standards and guidelines and collaborative efforts with relevant individuals and organisations. Engagement with data developers or administrators should also include a strategy of identifying the benefits associated with metadata creation and publication.

Findings

The establishment of numerous Spatial Data Infrastructures (SDIs), and other Internet resources, is a testament to the recognition of the importance of supporting good data management and sharing practices across the geographic information community. These resources extend to health informatics in support of research, public services and teaching and learning. This paper identifies many of these resources available to the UK academic health informatics community. It also reveals the reluctance of many spatial data creators across the wider UK academic community to use these resources to create and publish metadata, or deposit their data in repositories for sharing. The Go-Geo! service is introduced as an SDI developed to provide UK academia with the necessary resources to address the concerns surrounding metadata creation and data sharing. The Go-Geo! portal, Geodoc metadata editor tool, ShareGeo spatial data repository, and a range of other support resources, are described in detail.

Conclusions

This paper describes a variety of resources available for the health research and public health sector to use for managing and sharing their data. The Go-Geo! service is one resource which offers an SDI for the eclectic range of disciplines using GIS in UK academia, including health informatics. The benefits of data management and sharing are immense, and in these times of cost restraints, these resources can be seen as solutions to find cost savings which can be reinvested in more research.     

Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics

Background  

Academic social tagging systems, such as Connotea and CiteULike, provide researchers with a means to organize personal collections of online references with keywords (tags) and to share these collections with others. One of the side-effects of the operation of these systems is the generation of large, publicly accessible metadata repositories describing the resources in the collections. In light of the well-known expansion of information in the life sciences and the need for metadata to enhance its value, these repositories present a potentially valuable new resource for application developers. Here we characterize the current contents of two scientifically relevant metadata repositories created through social tagging. This investigation helps to establish how such socially constructed metadata might be used as it stands currently and to suggest ways that new social tagging systems might be designed that would yield better aggregate products.