A biodiversity information system in an open data/metadatabase architecture

This thesis presents an overview of biological collections, their complexity and related bio-information management activities in the main institutes in the Amazon region

An entomological collections database model for INPA

The National Institute for Amazon Research, INPA, has more than 40 years tradition in studying the Amazon, the biggest region of biodiversity on this planet. Millions of organisms, collected from the rainforest and its rivers were deposited in the collections of the institute. They are divided into six botanical, four microorganismal and nineteen zoological collections, consisting of vertebrates and invertebrates. The majority of the invertebrates are insects, which comprise the entomological collection. The aim of this work is to present a database model for this entomological collection. Entomologists at INPA were interviewed and the results have been evaluated to determine the information scope. The models of the Association of Systematic Collections, the Ohio State University and the Museum for Vertebrate Zoology at the University of California, Berkeley, were used during the development of our model. The model presented here was constructed using concepts from the method Object Protocol Model (OPM). © Springer-Verlag Berlin Heidelberg 1998

OntoBio: Designing new features to improve modeling and implementation

OntoBio is a formal ontology developed in the scenario of biological collection and field data collection of biotic entities. Considering the complex and dynamic nature of biodiversity data and information, modeling and implementations decisions likely to be error prone, can happen. This paper presents OntoBio's limitations regarding conceptualization and implementational aspects and new features aiming to indicate accurate recommendations for OntoBio's evolution, by emphasizing several aspects that must be considered when designing a new version of the ontology

OntoBio: A biodiversity domain ontology for Amazonian biological collected objects

The use of ontology presents a novel data integration resource, when centred in semantic definitions and the need for interoperability. Results from previews works indicate that ontologies can drive knowledge acquisition processes for the purpose of comprehensive, transportable machine understanding and knowledge management. Applied to the biodiversity domain, ontologies can be a valuable resource for strategic planning and its contribution toward conservation of the Amazon region. This work presents a biodiversity domain ontology developed at the National Institute for Amazonian Research (INPA) using biological data as its object of study. © 2015 IEEE

Elicitation process and knowledge structuring: A conceptual framework for biodiversity

OntoBio is a formal ontology based on biodiversity concepts and applied for data integration and automatic system interoperability. Despite having reached a consistent stage of maturity, part of the experts' knowledge is still not represented in the ontology, and is thus lost. The knowledge (implicit-explicit) when modelled and made available on the Web, becomes essential in the process of generating of new knowledge. In this scope, questions are still open and research interests involve the representation of tacit knowledge, modelling and formalization. This work proposes a tacit knowledge formalization method to incorporate semantics and expressiveness in formal ontologies to support the generation of scientific knowledge. © 2015 IEEE

Elicitation taxonomy for acquiring biodiversity knowledge

Traditionally, knowledge is kept by individuals and not by institutions. This weakens an institution’s ability to survive and be competitive. Questions such as, how to maintain and manage knowledge of institutional interest regarding employee turn over and the information entropy problem, must be addressed. Evidence in the literature suggests gaps in the process of knowledge elicitation and acquisition. For a complex domain such as biodiversity, mechanisms are needed to acquire, record and manage knowledge with high level of expressiveness, which includes tacit knowledge. This paper presents techniques for eliciting tacit knowledge in the biodiversity domain to be used in a conceptual framework that integrates scientific knowledge. The main issues related to the knowledge elicitation process are presented, as well as the knowledge elicitation techniques used. As a case study, knowledge was elicited from INPA’s ichthyology group. © Springer International Publishing Switzerland 2016