EJT editorial standard for the semantic enhancement of specimen data in taxonomy literature

This paper describes a set of guidelines for the citation of zoological and botanical specimens in the European Journal of Taxonomy. The guidelines stipulate controlled vocabularies and precise formats for presenting the specimens examined within a taxonomic publication, which allow for the rich data associated with the primary research material to be harvested, distributed and interlinked online via international biodiversity data aggregators. Herein we explain how the EJT editorial standard was defined and how this initiative fits into the journal's project to semantically enhance its publications using the Plazi TaxPub DTD extension. By establishing a standardised format for the citation of taxonomic specimens, the journal intends to widen the distribution of and improve accessibility to the data it publishes. Authors who conform to these guidelines will benefit from higher visibility and new ways of visualising their work. In a wider context, we hope that other taxonomy journals will adopt this approach to their publications, adapting their working methods to enable domain-specific text mining to take place. If specimen data can be efficiently cited, harvested and linked to wider resources, we propose that there is also the potential to develop alternative metrics for assessing impact and productivity within the natural science

Enhancing Workflow with a Semantic Description of Scientific Intent

Peer reviewedPreprin

Towards a service-oriented e-infrastructure for multidisciplinary environmental research

Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures

Quality Flow : uma plataforma colaborativa orientada a qualidade para experimentos em eScience

Orientador: Claudia Maria Bauzer MedeirosDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Muitos procedimentos de pesquisa científica dependem da análise de dados obtidos de fontes de dados heterogêneas. A validade dos resultados de pesquisa depende, entre outros, da qualidade dos dados - um tópico recorrente na pesquisa em computação há décadas. Embora existam muitas propostas para a avaliação da qualidade de dados, ainda há problemas em aberto, como mecanismos flexíveis para a avaliação de qualidade e maneiras para derivar a qualidade dos dados. O objetivo desta dissertação é trabalhar nesses problemas. A principal contribuição da dissertação é a criação do QualityFlow: uma plataforma colaborativa para avaliação de qualidade para experimentos em eScience. As principais contribuições são: suportar à criação de workflows científicos com parâmetros de qualidade, permitindo a adição de atributos de qualidade a workflows, permitindo ao mesmo tempo que usuários disintos definam métricas de qualidade específicas para o mesmo workflow; permitir aos usuários manter o histórico de diferentes avaliações de qualidade para um mesmo processo, provendo assim melhor compreensão do real valor dos dados e workflows; e permitir aos cientistas customizar dimensões de qualidade de dados e métricas de qualidade colaborativamente. O QualityFlow foi desenvolvido como um protótipo web, e executado para dois experimentos ¿ um baseado em dados reais e o outro em um workflow de exemploAbstract: Many scientific research procedures rely upon the analysis of data obtained from heterogeneous sources. The validity of the research results depends, among others, on the quality of data. Data quality is a topic that has pervaded computer science research for decades. Though there are many proposals for data quality assessment, there are still open problems such as mechanisms to support flexible quality assessment and ways to derive data quality. The goal of this dissertation is to work on these issues. The main contribution of this dissertation is the proposal of QualityFlow: a quality-aware collaborative platform for experiments in eScience. The following contributions were accomplished: to support the creation of quality-aware scientific workflows, allowing the addition of quality attributes to workflows, while at the same time letting distinct users define their specific quality metrics for the same workflow; to allow users to keep track of different quality assessments for a given process, thereby providing insights into the actual value of data and workflow; and to allow scientists to customize data quality dimensions and quality metrics collaboratively. QualityFlow was developed as a web prototype, and executed in two experiments - one based upon a real problem and the other on a sample workflowMestradoCiência da ComputaçãoMestre em Ciência da Computaçã

2007 LNO Annual Report to the Executive Board

This report summarizes activities and accomplishments of the LTER Network Office (LNO) during the period March 1, 2006 until February 28, 2007. Along with the survey of sites administered by the Executive Board, this document will be used to facilitate the annual review of LNO performance. - Presented to the LTER Excutive Boar

Web-based interface for environmental niche modelling

Marine species are subject to anthropogenic impacts, such as noise pollution, marine litter, and direct impact collisions. While there are efforts in the marine community and crowd-sourcing to report the occurrence of marine species, not enough projects explore the prediction of where such animals may be. This dissertation analyzes the state of the art in species distribution model ing (SDM) systems, capable of reporting and predicting marine biodiversity. The proposal implements the algorithms for predicting species through publicly avail able repositories of data, provides means to ease the upload and management of occurrence points as well as methods for prediction analysis. A web-based user interface is proposed using Ecological Niche Modelling (ENM) as an automated alerting mechanism towards ecological awareness. Performed user studies evaluate marine biodiversity concerns from fisherman and whale-watching sea-vessels, assessing attitudes, threats, values, and motiva tion of both samples. Further, biologists and experts on ENMs will evaluate the workflow and interface, reviewing the proposal’s potential to enable ecologists to create solutions for their custom problems using simple protocols without the need for any third-party entities and extensive knowledge in programming.Espécies marinhas estão sujeitas a impactos antropogênicos, tais como poluição sonora, lixo marinho, e colisões com tráfego marinho. Apesar de existirem al guns esforços da comunidade marinha e crowdsourcing relativamente ao registo de ocorrências de biodiversidade marinha, não existem projeto suficientes que exploram as previsões de onde estas espécies poderão estar. Esta dissertação analisa o estado da arte em sistemas de modelação de dis tribuição de espécies, capazes de relatar e prever biodiversidade marinha. A pro posta implementa os algoritmos para prever espécies por meio de repositórios consolidados de dados disponíveis online, fornece meios para facilitar o carrega mento e gestão de pontos de ocorrência, bem como métodos para análise das previsões. Uma interface web de utilizador é proposta utilizando Ecological Niche Modeling como um mecanismo de alerta automatizado para incrementar a con sciência ecológica. Os estudos do sistema irão avaliar as preocupações relativas a biodiversi dade marinha de embarcações de pesca e navios de observação de baleias. Desta forma é possível determinar atitudes, ameaças, valores e motivação de ambas as amostras para com a biodiversidade marinha. Além disso, biólogos e espe cialistas nesta tipologia de sistemas, avaliarão o fluxo de trabalho e a inter face desenvolvida, avaliando o potencial do sistema, permitindo aos ecologistas criar soluções personalizados através de protocolos simples, sem a necessidade de quaisquer entidades terceirizadas e conhecimento em programação

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

2008 LNO Annual Report to the Executive Board

This report summarizes activities and accomplishments of the LTER Network Office (LNO) during the period March 1, 2007 until February 28, 2008. Along with the survey of sites administered by the Executive Board, this document will be used to facilitate the annual review of LNO performance

Digitization capacity and skills of academic librarians in Nigeria

In order to increase their global visibility and better performance in the web ranking of world universities, more Nigerian universities have been devising creative means of increasing their digital contents in the public domain resulting in more sharability of institutional resources. Digitization builds capacity for the university library system to realize its mandate of supporting learning, teaching and research activities of its parent institutions through the instrumentality of the emerging and evolving information and communications technologies (ICTs). However, certain skill sets and competencies are required by librarians in Nigerian universities to establish and maintain digital collections in their respective institutions. A questionnaire survey is conducted on this category of information professionals in ten selected private and public universities that have minimum ICT infrastructure required for digitization. The collected data are analyzed and results presented in simple descriptive statistics