The protein information resource (PIR)

The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Sequence Database (JIPID). The expanded PIR WWW site allows sequence similarity and text searching of the Protein Sequence Database and auxiliary databases. Several new web-based search engines combine searches of sequence similarity and database annotation to facilitate the analysis and functional identification of proteins. New capabilities for searching the PIR sequence databases include annotation-sorted search, domain search, combined global and domain search, and interactive text searches. The PIR-International databases and search tools are accessible on the PIR WWW site at http://pir.georgetown.edu and at the MIPS WWW site at http://www. mips.biochem.mpg.de. The PIR-International Protein Sequence Database and other files are also available by FTP.     

Developing a regional environmental information system based on macro-level waste indicators

Waste information is necessary for proper management planning. However, data on waste generation and management are sometimes not reliable enough, do not exist or are not useful for the sector. This is due to the high number of waste types and flows, and actors (producers, managers and administrations), which make data collection and treatment difficult. Furthermore, data loss occurs because some waste flows have economic value and return to the second-hand markets without monitoring.The development of a waste information system for a region is more than just about establishing a routine data collection on waste. It is a way to support the challenges of decision-making on waste management. These challenges range from strategic issues of waste management in the national government to the basic challenges of running local governments.In the Cantabrian region, three indicator sets were defined to constitute the waste information system: (a) a Basic Indicator Set, which provides an overview of the status of the generation and management of the main waste streams, giving a national and international comparative analysis of the situation; (b) a Specific Indicator Set, which monitors the objectives of the different waste policies, and (c) a Transverse Indicator Set, which analyses the influence of different economic and social variables on the generation of specific waste streams.The Waste Information System of the Cantabrian Region has been created using a specific methodology for developing indicator sets with multiple objectives. This methodology consists of seven steps: (i) the synthesis, selection of the indicators sets; (ii) analysis of the system under study and data sources; (iii) evaluation of the indicators proposed; (iv) application and interpretation; (v) public review, dissemination and updating protocol; (vi) improvement of indicators sets using SWOT analysis; and (vii) aggregation of all indicators in an aggregated index.These indicator sets with a total of 27 indicators allow tracking the evolution of generation and management of waste streams and the achievement of the policy objectives, establishing a data record, evaluating the data and sources of data, monitoring proposed action and its effectiveness summarizing large amounts of data on waste in order to spread it to the public and finally, aggregate all information in a single index that allows the evaluation of the evolution of all waste sectors in time.     

The economic resource scarcity potential (ESP) for evaluating resource use based on life cycle assessment

Purpose

In life cycle assessment (LCA), resource availability is currently evaluated by means of models based on depletion time, surplus energy, etc. Economic aspects influencing the security of supply and affecting availability of resources for human use are neglected. The aim of this work is the development of a new model for the assessment of resource provision capability from an economic angle, complementing existing LCA models. The inclusion of criteria affecting the economic system enables an identification of potential supply risks associated with resource use. In step with actual practice, such an assessment provides added value compared to conventional (environmental) resource assessment within LCA. Analysis of resource availability including economic information is of major importance to sustain industrial production.

Methods

New impact categories and characterization models are developed for the assessment of economic resource availability based on existing LCA methodology and terminology. A single score result can be calculated providing information about the economic resource scarcity potential (ESP) of different resources. Based on a life cycle perspective, the supply risk associated with resource use can be assessed, and bottlenecks within the supply chain can be identified. The analysis can be conducted in connection with existing LCA procedures and in line with current resource assessment practice and facilitates easy implementation on an organizational level.

Results and discussion

A portfolio of 17 metals is assessed based on different impact categories. Different impact factors are calculated, enabling identification of high-risk metals. Furthermore, a comparison of ESP and abiotic depletion potential (ADP) is conducted. Availability of resources differs significantly when economic aspects are taken into account in addition to geologic availability. Resources assumed uncritical based on ADP results, such as rare earths, turn out to be associated with high supply risks.

Conclusions

The model developed in this work allows for a more realistic assessment of resource availability beyond geologic finiteness. The new impact categories provide organizations with a practical measure to identify supply risks associated with resources. The assessment delivers a basis for developing appropriate mitigation measures and for increasing resilience towards supply disruptions. By including an economic dimension into resource availability assessment, a contribution towards life cycle sustainability assessment (LCSA) is achieved.     

Information retrieval and knowledge discovery utilising a biomedical Semantic Web

Although various ontologies and knowledge sources have been developed in recent years to facilitate biomedical research, it is difficult to assimilate information from multiple knowledge sources. To enable researchers to easily gain understanding of a biomedical concept, a biomedical Semantic Web that seamlessly integrates knowledge from biomedical ontologies, publications and patents would be very helpful. In this paper, current research efforts in representing biomedical knowledge in Semantic Web languages are surveyed. Techniques are presented for information retrieval and knowledge discovery from the Semantic Web that extend traditional keyword search and database querying techniques. Finally, some of the challenges that have to be addressed to make the vision of a biomedical Semantic Web a reality are discussed.     

中国野生杜鹃花属植物名录与地理分布数据集

杜鹃花属(Rhododendron)植物分布广泛, 生存环境多样, 类群结构复杂, 深入分析其地理分布格局与特征, 可为种质资源保育和利用等提供依据。本文基于大量基础数据及文献资料, 更新了中国陆域分布的野生杜鹃花属植物物种名录, 统计了其物种多样性、组成成分等信息, 建立了中国野生杜鹃花属植物地理分布数据库, 旨在为种质资源调查及引种应用研究提供参考。截至2021年7月, 共记载7亚属720种(包括114变种、45亚种和2变型), 其中中国特有种450种。除宁夏和新疆干旱荒漠地带外, 中国其他各省区均有野生杜鹃花属分布, 其中云南省分布393种, 是省级尺度物种丰富度及特有性最高的区域; 其次为四川省(278种)及西藏自治区(271种)。县级尺度贡山独龙族怒族自治县与察隅县以134种并列物种丰富度第一, 其次是德钦县128种。     

Semantic Web Service provision: a realistic framework for Bioinformatics programmers

Several semantic Web Services clients for Bioinformatics have been released, but to date no support systems for service providers have been described. We have created a framework ('MobyServlet') that very simply allows an existing Java application to conform to the MOBY-S semantic Web Services protocol. Using an existing Java program for codon-pair bias determination as an example, we enumerate the steps required for MOBY-S compliance. With minimal programming effort, such a deployment has the advantages of: (1) wider exposure to the user community by automatic inclusion in all MOBY-S client programs and (2) automatic interoperability with other MOBY-S services for input and output. Complex on-line analysis will become easier for biologists as more developers adopt MOBY-S. AVAILABILITY: The framework and documentation are freely available from the Java developer's section of http://www.biomoby.org/.     

基于Global Forest Watch观察2000–2013年间中国森林变化

了解森林的变化,是评价生物多样性变化趋势和制订有效保护行动的基础,也是公共政策及广大公众普遍关心的议题,然而国内一直都没有可供空间分析的森林分布及变化的公开数据。Hansen等于2013年在Global Forest Watch网站上发布了基于Landsat数据的30 m分辨率的全球森林变化数据集,第一次提供给研究者一套高分辨率的公开数据。我们解读了2000–2013年的数据,并与已有的国家森林清查、China Cover、Globe Land30等数据集进行比较。结果表明,Global Forest Watch数据质量可靠,其与Globe Land30数据集的森林分布有较高的空间重合度,后者森林类别的生产者精度为87%,用户精度为89%。在大于20%的树木覆盖度下,估算出2000年森林面积为1,780,472 km2,与同期国家森林清查数据1,749,092 km2相近,解读结果表明2000–2010年间森林减少面积在37,551–42,031 km2之间,而同期其他几套数据显示森林面积增量为2,370–433,810 km2。森林面积年减少量最大值出现在2008年,以该年为拐点,森林每年减少面积的变化趋势在此之前为显著增加,在此之后为显著降低,林地变化最活跃的区域在广西、广东、福建、江西和云南等南方省份。到2013年底,占保护区总面积约60%以上的407个国家级保护区仅覆盖了森林面积的5.03%,对森林保护的面积覆盖有限,保护区对其内部的森林保护有成效,区内森林面积净减1.39%,低于全国平均水平(3.46%),相当于少毁林1,856 km2,但仍有1,200 km2的净减。     

DRUGSURV: a resource for repositioning of approved and experimental drugs in oncology based on patient survival information

The use of existing drugs for new therapeutic applications, commonly referred to as drug repositioning, is a way for fast and cost-efficient drug discovery. Drug repositioning in oncology is commonly initiated by in vitro experimental evidence that a drug exhibits anticancer cytotoxicity. Any independent verification that the observed effects in vitro may be valid in a clinical setting, and that the drug could potentially affect patient survival in vivo is of paramount importance. Despite considerable recent efforts in computational drug repositioning, none of the studies have considered patient survival information in modelling the potential of existing/new drugs in the management of cancer. Therefore, we have developed DRUGSURV; this is the first computational tool to estimate the potential effects of a drug using patient survival information derived from clinical cancer expression data sets. DRUGSURV provides statistical evidence that a drug can affect survival outcome in particular clinical conditions to justify further investigation of the drug anticancer potential and to guide clinical trial design. DRUGSURV covers both approved drugs (∼1700) as well as experimental drugs (∼5000) and is freely available at http://www.bioprofiling.de/drugsurv.     

褐飞虱EST资源的微卫星信息分析

表达序列标签（expressed sequence tags,ESTs）是开发微卫星标记的一个重要的资源。褐飞虱Nilaparvata lugens （Stål） EST序列的公布为开发EST-SSRs提供了宝贵的数据资源,本研究利用生物信息学对NCBI公共数据库中的37 398条褐飞虱ESTs序列进行EST-SSRs特征分析,得到全长为7 619 324 kb的无冗余EST 9 852条。按照3个不同的查找标准在这些序列中搜索SSR。查找结果显示：褐飞虱EST-SSRs主要重复基元以1～3碱基为主,占总EST-SSR的95％以上。在单碱基重复基元中,A/T是占优势的重复基元,在二相重复类型中,AG/CT重复基元出现的频率最多,而AAG/CTT是三相重复中占绝对优势的重复基元。在褐飞虱EST-SSRs中未查找到GC重复基元。以100 bp为参照,在3种查找标准下含有SSR的EST序列中两端侧翼序列均≥100 bp的序列分别为738,89和42个。通过分析褐飞虱EST-SSRs标记可以为褐飞虱和近缘种的SSR标记的开发提供信息,同时通过分析褐飞虱EST-SSRs的分布频率和分布特征可以为昆虫EST-SSRs的研究提供借鉴和参考。     

SILIC: A cross database framework for automatically extracting robust biodiversity information from soundscape recordings based on object detection and a tiny training dataset

• 1.Passive acoustic monitoring (PAM) offers many advantages comparing with other survey methods and gains an increasing use in terrestrial ecology, but the massive effort needed to extract species information from a large number of recordings limits its application. The convolutional neural network (CNN) has been demonstrated with its high performance and effectiveness in identifying sound sources automatically. However, requiring a large amount of training data still constitutes a challenge.
• 2.Object detection is used to detect multiple objects in photos or videos and is effective at detecting small objects in a complex context, such as animal sounds in a spectrogram and shows the opportunity to build a good performance model with a small training dataset. Therefore, we developed the Sound Identification and Labeling Intelligence for Creatures (SILIC), which integrates online animal sound databases, PAM databases and an object detection-based model, for extracting information on the sounds of multiple species from complex soundscape recordings.
• 3.We used the sounds of six owl species in Taiwan to demonstrate the effectiveness, efficiency and application potential of the SILIC framework. Using only 786 sound labels in 133 recordings, our model successfully identified the species' sounds from the recordings collected at five PAM stations, with a macro-average AUC of 0.89 and a mAP of 0.83. The model also provided the time and frequency information, such as the duration and bandwidth, of the sounds.
• 4.To our best knowledge, this is the first time that the object detection algorithm has been used to identify sounds of multiple wildlife species. With an online sound-labeling platform embedded and a novel data preprocessing approach (i.e., rainbow mapping) applied, the SILIC shows its good performance and high efficiency in identifying wildlife sounds and extracting robust species, time and frequency information from a massive amount of soundscape recordings based on a tiny training dataset acquired from existing animal sound databases. The SILIC can help expand the application of PAM as a tool to evaluate the state of and detect the change in biodiversity by, for example, providing high temporal resolution and continuous information on species presence across a monitoring network.