Model Framework for Development of Biodiversity Information Systems (original) (raw)
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Biodiversity knowledge organization system: Proposed architecture
2012
Summary This document provides a proposed architecture for the new Knowledge Organization System (KOS) for biodiversity information resources to be hosted by GBIF. The proposed KOS architecture includes the following key components:“Vocabulary of Terms”(1),“Term Browser”(2),“Extensions and Code lists for the Darwin Core Archives”(3), domain Ontologies (4), and a “Resources Repository”(5). This document presents the overall architecture and how these conceptual building blocks are linked together.
BIODIVERSITY DATA MODEL (BiDaM) USING OBJECT RELATIONAL APPROACH: CONCEPTUAL FRAMEWORK
The extensive research has been performed on plant biodiversity and even on mangrove area recent years; managing plant biodiversity data with database system still poses many challenges. Plant biodiversity is the variety of different types of plants species that growth in various landscape. There are phenomenal growths in the area of biodiversity studies, largely motivated by its economic and humanitarian. Various data models, query languages and techniques have been proposed by many researchers. Traditional database systems (built on relational hierarchical and network models) which are widely used for commercial applications such as banking fail to meet the modeling and processing requirements of the biodiversity data.
1 BIODIVERSITY DATA MODEL (BiDaM) USING OBJECT RELATIONAL APPROACH: CONCEPTUAL FRAMEWORK
2015
The extensive research has been performed on plant biodiversity and even on mangrove area recent years; managing plant biodiversity data with database system still poses many challenges. Plant biodiversity is the variety of different types of plants species that growth in various landscape. There are phenomenal growths in the area of biodiversity studies, largely motivated by its economic and humanitarian. Various data models, query languages and techniques have been proposed by many researchers. Traditional database systems (built on relational hierarchical and network models) which are widely used for commercial applications such as banking fail to meet the modeling and processing requirements of the biodiversity data. Recently developed BODHI (Biodiversity Object Database arcHItecture) data model which is designed based on Indian plant biodiversity and only support spatial data. Integration between plant Bio-diversity data (BODHI) and geographical data with event-based approach c...
Information System Design in Support of Albanian Biodiversity Conservation
2018
The conservation of biodiversity is one of the challenges of ecologists. The collection and monitoring of biodiversity knowledge is the first step in the conservation of biodiversity. Technological developments and their implementation in the field of biodiversity are thought to turn the WWW into a giant global information system on biodiversity. Biodiversity data in Albania are distributed. It would be very helpful for students and researchers to integrate these data as it would facilitate teaching and research. The aim of this paper is to model and implement the database for Albanian biodiversity knowledge in ODONATA species and to design and an information system that will facilitate access to biodiversity data. The system is implemented for ODONATA species and their habitats in Albania.
Open Biodiversity Knowledge Management System, PhD Project
Background This is a Research Presentation paper, one of the novel article formats developed for the Research Ideas and Outcomes (RIO) journal and aimed at representing brief research outcomes. In this paper we publish and discuss our webinar presentation for the Integrated Digitized Biocollections (iDigBio) audience on two novel publishing workflows for biodiversity data: (1) automatic import of specimen records into manuscripts, and (2) automatic generation of data paper manuscripts from Ecological Metadata Language (EML) metadata. New information Information on occurrences of species and information on the specimens that are evidence for these occurrences (specimen records) is stored in different biodiversity databases. These databases expose the information via public REST API's. We focused on the Global Biodiversity Information Facility (GBIF), Barcode of Life Data Systems (BOLD), iDigBio, ‡ § ‡
A digital library framework for biodiversity information systems
International Journal on Digital Libraries, 2006
Biodiversity Information Systems (BISs) involve all kinds of heterogeneous data, which include ecological and geographical features. However, available information systems offer very limited support for managing these kinds of data in an integrated fashion. Furthermore, such systems do not fully support image content (e.g., photos of landscapes or living organisms) management, a requirement of many BIS end-users. In order to meet their needs, these users—e.g., biologists, environmental experts—often have to alternate between separate biodiversity and image information systems to combine information extracted from them. This hampers the addition of new data sources, as well as cooperation among scientists. The approach provided in this paper to meet these issues is based on taking advantage of advances in digital library innovations to integrate networked collections of heterogeneous data. It focuses on creating the basis for a next-generation BIS, combining new techniques of content-based image retrieval and database query processing mechanisms. This paper shows the use of this component-based architecture to support the creation of two tailored BIS systems dealing with fish specimen identification using search techniques. Experimental results suggest that this new approach improves the effectiveness of the fish identification process, when compared to the traditional key-based method.
Biodiversity information platforms: From standards to interoperability
ZooKeys, 2011
One of the most serious bottlenecks in the scientific workflows of biodiversity sciences is the need to integrate data from different sources, software applications, and services for analysis, visualisation and publication. For more than a quarter of a century the TDWG Biodiversity Information Standards organisation has a central role in defining and promoting data standards and protocols supporting interoperability between disparate and locally distributed systems. Although often not sufficiently recognized, TDWG standards are the foundation of many popular Biodiversity Informatics applications and infrastructures ranging from small desktop software solutions to large scale international data networks. However, individual scientists and groups of collaborating scientist have difficulties in fully exploiting the potential of standards that are often notoriously complex, lack non-technical documentations, and use different representations and underlying technologies. In the last few years, a series of initiatives such as Scratchpads, the EDIT Platform for Cybertaxonomy, and biowikifarm have started to implement and set up virtual work platforms for biodiversity sciences which shield their users from the complexity of the underlying standards. Apart from being practical work-horses for numerous working processes related to biodiversity sciences, they can be seen as information brokers mediating information between multiple data standards and protocols. The ViBRANT project will further strengthen the flexibility and power of virtual biodiversity working platforms by building software interfaces between them, thus facilitating essential information flows needed for comprehensive data exchange, data indexing, web-publication, and versioning. This work will make an important contribution to the shaping of an international, interoperable, and user-oriented biodiversity information infrastructure.
2005
The Science Environment for Ecological Knowledge (SEEK) [1] is an information technology project designed to address the many challenges associated with data accessibility and integration of large-scale biocomplexity data in the ecological sciences. The SEEK project is creating cyberinfrastructure encompassing three integrated systems: EcoGrid, a Semantic Mediation System (SMS) and an Analysis and Modeling System (AMS). SEEK enables ecologists to efficiently capture, organize and search for data and analytical processes (i.e., scientific workflows) from their desktop in a user friendly interface --ultimately providing access to global data and analytical resources typically out of reach for many ecologists. The prototype application is ecological niche modeling.