Knowledge Discovery in Biology and Biotechnology Texts: A Review of Techniques,Evaluation Strategies,and Applications

Abstract

Arguably, the richest source of knowledge (as opposed to fact and data collections) about biology and biotechnology is captured in natural-language documents such as technical reports, conference proceedings and research articles. The automatic exploitation of this rich knowledge base for decision making, hypothesis management (generation and testing) and knowledge discovery constitutes a formidable challenge. Recently, a set of technologies collectively referred to as knowledge discovery in text (KDT) has been advocated as a promising approach to tackle this challenge. KDT comprises three main tasks: information retrieval, information extraction and text mining. These tasks are the focus of much recent scientific research and many algorithms have been developed and applied to documents and text in biology and biotechnology. This article introduces the basic concepts of KDT, provides an overview of some of these efforts in the field of bioscience and biotechnology, and presents a framework of commonly used techniques for evaluating KDT methods, tools and systems.     

Knowledge networks in the age of the Semantic Web

The Web has become the major medium for various communities to share their knowledge. To this end, it provides an optimal environment for knowledge networks. The web offers global connectivity that is virtually instantaneous, and whose resources and documents can easily be indexed for easy searching. In the coupled realms of biomedical research and healthcare, this has become especially important where today many thousands of communities already exist that connect across academia, hospitals and industry. These communities also rely on several forms of knowledge assets, including publications, experimental data, domain-specific vocabularies and policies. Web-based communities will be one of the earlier beneficiaries of the emerging Semantic Web. With the new standards and technologies of the Semantic Web, effective utilization of knowledge networks will expand profoundly, fostering new levels of innovation and knowledge.     

Power/Knowledge,Power/Ignorance: Forest Fires and the State in Mexico

For over a century the Mexican state has justified its control of forests by claiming that rural people are ignorant and destructive fire setters, in the face of abundant evidence to the contrary. Academic and popular stereotypes of the state have tended to assume that official power and knowledge go hand in hand. In an institutional ethnography ofthe Mexican environment agency, SEMARNAP, I. show how official ignorance is deployed both within and outside state forestry institutions, and how ignorance and complicity may be as important as knowledge in asserting state power. Rather than internalizing official fire discourse, rural people in Mexico learn to mouth polite fictions in their encounters with officials. I argue that the scholarship on governmentality derived from Foucault has uncritically internalized the link between power and knowledge. A closer attention to the production and translation of knowledge within state institutions leads to a more nuancedunderstanding of various forms of obscurity and ignorance which accompany official knowledge claims. This paper is drawn from my fieldwork and archival research in Mexico in the summer of 1998 and between April 2000 and August 2001.     

学科前沿知识贯穿于微生物学教学过程的思考与实践——以反硝化作用教学为例

根据好氧反硝化作用机理研究进展和好氧反硝化细菌在污水脱氮处理工艺中的应用,结合微生物生态的教学内容,在提出教材重点教学内容与学科前沿知识优化整合方案的基础上,进一步阐述了在不增加课堂理论教学时数的前提下,如何通过学生课外自主学习环节进行好氧反硝化作用教学的做法,发现课外专题学习与课堂教学紧密结合是提高微生物学教学效果的有效方法,也是创新型应用型人才培养的有效途径。     

Time and Encoding Effects in the Concealed Knowledge Test

Although the traditional “lie detector” test is used frequently in forensic contexts, it has (like most test of deception) some limitations. The concealed knowledge test (CKT) focuses on participants’ recognition of privileged knowledge rather than lying per-se and has been studied extensively using a variety of measures. A “guilty” suspect’s interaction with and memory of crimescene items may vary. Furthermore, memory for crimescene items may diminish over time. The interaction of encoding quality and test delay on CKT efficiency has been previously implied, but not yet demonstrated. We used a response-time based CKT to detect concealed knowledge from shallow and deep study procedures after 10-min, 24-h, and 1-week delays. Results show that more elaborately encoded information afforded higher detection accuracy than poorly encoded items. Although classification accuracy following deep study was unaffected by delay, detection of poorly elaborated information was initially high, but compromised after 1 week. Thus, choosing optimal test items requires considering both test delay and initial encoding level.     

Public Knowledge of,and Attitudes to,Frogs in Colombia

ABSTRACT

People's response to the decline of biodiversity and their support for conservation measures depends on their knowledge of biodiversity and their attitudes to local species. This study is one of the first to investigate public knowledge of, and attitudes to, frogs in South America. We chose two study regions, the semi-urban region of Pensilvania and the rural region of Florencia. In spring 2011, 565 individuals completed a written questionnaire and a subsequent picture test. Overall, the public's attitudes to, and knowledge of frogs, were rather poor. Direct experiences and community elders were the major source of knowledge of frogs for participants in Florencia, whereas electronic media was the main source of knowledge in Pensilvania. Most participants felt that frogs are of high conservation value and important for medical and ecological purposes. The more strongly participants agreed that frogs are useful, of medicinal value, and beautiful, the more strongly they agreed that they should be conserved. Our results indicate that conservation education activities in schools and elsewhere are needed to improve people's knowledge of, and attitudes to, frogs. More positive attitudes toward local amphibian species might lead to an appreciation of their value and willingness to conserve them.     

Slovakian Pupils' Knowledge of,and Attitudes toward,Birds

ABSTRACT

As the world's biodiversity is being destroyed, costs for nature protection activities increase. One proposed way to increase people's pro-environmental attitudes is to increase their knowledge base. It has been suggested that knowledge and attitudes are related, but no consensus in this field yet exists. Thus, the investigation of the relationship between attitudes and knowledge has valuable implications for nature protection programs. In this paper, we investigated relationships between Slovakian grammar school pupils' attitudes to, and knowledge of, birds (n = 402 participants aged 10–19 years). We found that factual knowledge about birds was positively related to pupils' attitudes toward birds. Interestingly, younger pupils had better knowledge of birds than older pupils. Regarding attitudes, higher scores were registered for the Concern for Birds and Avoidance of Birds dimensions than the Interest in Birds dimension. Females showed more positive attitudes in the Avoidance of Birds dimension compared with males, and bird owners scored higher in the Interest in Birds dimension and lower in the Concern for Birds dimension compared with non-bird owners. Implications for nature protection programs are discussed.     

Amazon Forestry Tranformed: Integrating Knowledge for Smallholder Timber Managemet in Eastern Brazil

Recent discussions of local knowledge emphasize its dynamic nature invoking local peoples’ ability to effectively integrate traditional or local with science-based or “modern” knowledges. The smallholder timber industry of the Amazon’s estuarine floodplain provides an outstanding example of local patterns of resource management and economic activities transformed from within by smallholder farmers who participated in the industrial timber boom of the 1970s and 1980s. These farmers of eastern Amazonia have developed a vertically integrated local industry based on expertise reflecting profound locally developed knowledge of specific forests and management of ecological processes, individual observation and experimentation, as well as concepts and practices derived from temporary employment by large-scale industrial timber firms. At each stage of the smallholder forestry process—from managing natural regeneration to running small sawmills and marketing lumber—local managers apply an innovative set of practices reflecting their diverse experiences. This combination of technical, market, and ecological knowledge results in forests, timber markets, and economic patterns that do not correspond to many of the widely-held generalizations concerning either local or industrial tropical timber exploitation. This article uses data from 7 years of research in the Amazon floodplain.

Beyond Ground Truth: GIS and the Environmental Knowledge of Herders, Professional Foresters, and Other Traditional Communities

As a result of increasingly apparent and problematic effects of global information system and remote sensing technologies, there has been increased emphasis on demonstrating and incorporating indigenous environmental knowledges in land use and cover analysis. Such approaches, though ethnographically revealing and politically efficacious, tend to reproduce a model of difference between local and scientific knowledges that is epistemologically untenable. This paper demonstrates an alternative use of geographic information system and remotely sensed imagery to both demonstrate the partiality of mapping technology and show possibilities for critical usage of the tool. Using a case from India, the research shows a method to elicit and explore competing environmental knowledges, including and especially those of scientific experts. The analysis concludes that, for both local producers and expert managers, the cultural meaning of landscapes is dependent on their roles in regional production and resource politics.     

The Relationship Between Scientific Knowledge and Behaviour: An HIV/AIDS Case

Debates on the role of scientific knowledge to affect behaviour are continuing. The theory of planned behaviour suggests that behaviour is influenced by attitudes, subjective norms and perceived behavioural control and not by knowledge. However, a large body of knowledge argues that increased HIV/AIDS-related knowledge leads to the adoption of safe behavioural practices. The purpose of this non-experimental survey study, therefore, was to investigate the correlation between academic HIV/AIDS knowledge, functional HIV/AIDS knowledge and self-reported behavioural preferences of 300 biology and 243 non-biology students from nine South African schools. Results suggest a correlation between students’ understanding of academic and functional HIV/AIDS knowledge. The behavioural preferences of both biology and non-biology students were generally the same and safe. Among biology students, correlation was observed between academic HIV/AIDS knowledge and self-reported safe behavioural preferences, which was not the case for non-biology students, where functional HIV/AIDS knowledge correlated with self-reported safe behavioural preferences. Within schools, however, no correlation was found between both forms of HIV/AIDS knowledge and self-reported safe behavioural preferences. There were indications that context-specific local factors have a greater influence on behavioural preferences. These findings suggest that the type of knowledge that could influence behaviour is informed by context-specific dynamics.     

生物制氢——能源、资源、环境与经济可持续发展策略

人类面临能源危机、资源短缺、环境污染的严峻挑战,开发新的能源,合理利用资源并保护生态环境势在必行。氢能具有清洁、高效、可再生的特点,是未来重要的新能源物质。生物制氢技术利用可再生资源,特别是可利用工农业有机废弃物产氢,效率高,能耗低,污染少,成本低,具有巨大的发展潜力。本文简要阐述生物制氢技术及其发展状况,提出我国发展生物制氢技术,实现能源、资源、环境与经济可持续发展的政策建议。     

Endangered Forest, Endangered People: Environmentalist Representations of Indigenous Knowledge

Since 1987, Penan foragers in Malaysia have been increasingly affected by the activities of logging companies, and have protested this with blockades. Simultaneously, they have become the focus of a broad-based international environmental campaign. This paper examines the rhetoric of that campaign. In particular, I examine the ways in which Western environmentalists have constructed Penan land rights with reference to Penan knowledge of the landscape and of the biotic elements which exist there. Further, I consider how environmentalists have drawn on ethnographic accounts, and how those accounts are transformed in the process of generating images deployed in the campaign.     

Justice, Transaction, Translation: Blackfoot Tipi Transfers and WIPO's Search for the Facts of Traditional Knowledge Exchange

In this article, I examine the complexities and politics of enrolling one socially embedded form of transaction and knowledge into the terms or practices of another. I look at the correspondences and divergences in how the World Intellectual Property Organization (WIPO) transposed the "facts" of Blackfoot tipi-transfer practices in efforts to harmonize global intellectual property (IP) regimes and to achieve "justice" and "empowerment." WIPO's translation work is set against a case where Piikani Blackfoot tipi holders used relational transfer practices to effect a use arrangement, bypassing the means and ends of IP. I argue that looking at WIPO's practices helps us to see anthropology's own epistemological, instrumental, and political constraints, while looking at Piikani transfers helps us to conceive of alternatives. This has bearing across anthropology's disciplinary spectrum where problems of knowledge translation are commonplace.     

Ocean Tracking and Marine Species Protection in Australia and Canada: Science,Technology, and Knowledge Brokering

This article examines the promise and challenge of marine biotelemetry technologies, comparing the case of the Canadian Ocean Tracking Network (OTN) and the Australian Animal Tagging and Monitoring System (AATAMS). These technologies provide increased understanding of the marine environment and promise major advances in knowledge of species at risk. However, that utilization of marine biotelemetry raises challenges, including ensuring that knowledge obtained is translated into forms useful to and usable by decision makers. Knowledge brokering is a key to ensure that the advances seen in marine biotelemetry technologies lead to improved gover-nance of species at risk.     

Knowledge, Learning and the Evolution of Conservation Practice for Social-Ecological System Resilience

There are two broadly conceptualized ways in which conservation knowledge may evolve: the depletion crisis model and the ecological understanding model. The first one argues that developing conservation thought and practice depends on learning that resources are depletable. Such learning typically follows a resource crisis. The second mechanism emphasizes the development of conservation practices following the incremental elaboration of environmental knowledge by a group of people. These mechanisms may work together. Following a perturbation, a society can self-organize, learn and adapt. The self-organizing process, facilitated by knowledge development and learning, has the potential to increase the resilience (capability to absorb disturbance and reorganize while undergoing change) of resource use systems. Hence, conservation knowledge can develop through a combination of long-term ecological understanding and learning from crises and mistakes. It has survival value, as it increases the resilience of integrated social--ecological systems to deal with change in ways that continue to sustain both peoples and their environments.     

Animal Welfare Knowledge,Attitudes, and Practices of Stockpersons in Kenya

The stockpersons handling the transportation of animals between farms and slaughterhouses are rarely assessed for their animal welfare knowledge, attitudes, and practices (KAP). Thus, this investigation presents a unique opportunity to study these interactions. Herein, a cross-sectional survey was carried out among 266 stockpersons in 10 Kenyan livestock markets to determine their animal welfare KAP. The survey questionnaire was based on Kenya’s Regulations for Animal Transport (Act No: CAP. 360-L.N. 119/1984). Mean percentage scores for knowledge, attitudes, and practices were 78.0 ± 14.1, 75.6 ± 16.0, and 64.5 ± 17.6, respectively. From the responses to statements related to animal husbandry, practices of the housing of unfamiliar groups of animals, cooperation with other stakeholders, and stress caused to animals during handling, it was found that stockpersons’ animal welfare KAP was inadequate. Women aged > 50 years or having more than 10 years of experience had significantly higher levels of animal welfare KAP (p < 0.05). In conclusion, although Kenyan stockpersons may score adequately on the parameters of animal welfare knowledge and attitudes, their followed practices are poor, which may possibly be influenced by gender, age, or level of experience.     

Knowledge,place, and power: geographies of value in the bioeconomy

The idea that there is an emerging “bioeconomy” characterized by the capture of the latent value found in biological material (e.g. cells, tissues, plants, etc.) has become a popular policy agenda since the mid-2000s. A number of scholars have also written about this intersection between the life sciences and capitalism, often drawing on anthropological and sociological perspectives to conceptualize the new socialities, subjectivities, and identities brought about by new biotechnologies. While these studies are undoubtedly a fruitful academic enterprise, they have also left a gap in our understanding of the bioeconomy because they have not discussed knowledge or knowledge production. This article focuses on this immaterial side of the bioeconomy, exploring the geographies of value in the bioeconomy that are constituted by intangible and immaterial resources and labor. The core argument is that value in the bioeconomy is created from geographical processes that both embed immateriality in particular places and, at the same time, abstract it in global standards and regulations.     

Aromatic,Medicinal Plants and Vulnerability of Traditional Herbal Knowledge in a Berber Community of the High Atlas Mountains of Morocco

This article compliments the S18 session (transmission of traditional ecological knowledge and conservation of medicinal plants) at the 13th International Congress of Ethnobiology (ISE) in Montpellier, France (May 2012). The aim of the article is to provide an insight into the livelihoods of a Berber community, a village of the High Atlas Mountains of Morocco, of the local biodiversity and most importantly, the prevalent use of medicinal plants for primary health care. It seeks to demonstrate the value of traditional ecological and herbal knowledge for the subsistence of the community and emphasises the vital role that family and community connections play for the transmission of traditional herbal knowledge within the community.