The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

An Ontology-Based Recommender System with an Application to the Star Trek Television Franchise

Collaborative filtering based recommender systems have proven to be extremely successful in settings where user preference data on items is abundant. However, collaborative filtering algorithms are hindered by their weakness against the item cold-start problem and general lack of interpretability. Ontology-based recommender systems exploit hierarchical organizations of users and items to enhance browsing, recommendation, and profile construction. While ontology-based approaches address the shortcomings of their collaborative filtering counterparts, ontological organizations of items can be difficult to obtain for items that mostly belong to the same category (e.g., television series episodes). In this paper, we present an ontology-based recommender system that integrates the knowledge represented in a large ontology of literary themes to produce fiction content recommendations. The main novelty of this work is an ontology-based method for computing similarities between items and its integration with the classical Item-KNN (K-nearest neighbors) algorithm. As a study case, we evaluated the proposed method against other approaches by performing the classical rating prediction task on a collection of Star Trek television series episodes in an item cold-start scenario. This transverse evaluation provides insights into the utility of different information resources and methods for the initial stages of recommender system development. We found our proposed method to be a convenient alternative to collaborative filtering approaches for collections of mostly similar items, particularly when other content-based approaches are not applicable or otherwise unavailable. Aside from the new methods, this paper contributes a testbed for future research and an online framework to collaboratively extend the ontology of literary themes to cover other narrative content.Comment: 25 pages, 6 figures, 5 tables, minor revision

Open Science principles for accelerating trait-based science across the Tree of Life.

Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges

Building essential biodiversity variables (EBVs) of species distribution and abundance at a global scale

Much biodiversity data is collected worldwide, but it remains challenging to assemble the scattered knowledge for assessing biodiversity status and trends. The concept of Essential Biodiversity Variables (EBVs) was introduced to structure biodiversity monitoring globally, and to harmonize and standardize biodiversity data from disparate sources to capture a minimum set of critical variables required to study, report and manage biodiversity change. Here, we assess the challenges of a ‘Big Data’ approach to building global EBV data products across taxa and spatiotemporal scales, focusing on species distribution and abundance. The majority of currently available data on species distributions derives from incidentally reported observations or from surveys where presence-only or presence–absence data are sampled repeatedly with standardized protocols. Most abundance data come from opportunistic population counts or from population time series using standardized protocols (e.g. repeated surveys of the same population from single or multiple sites). Enormous complexity exists in integrating these heterogeneous, multi-source data sets across space, time, taxa and different sampling methods. Integration of such data into global EBV data products requires correcting biases introduced by imperfect detection and varying sampling effort, dealing with different spatial resolution and extents, harmonizing measurement units from different data sources or sampling methods, applying statistical tools and models for spatial inter- or extrapolation, and quantifying sources of uncertainty and errors in data and models. To support the development of EBVs by the Group on Earth Observations Biodiversity Observation Network (GEO BON), we identify 11 key workflow steps that will operationalize the process of building EBV data products within and across research infrastructures worldwide. These workflow steps take multiple sequential activities into account, including identification and aggregation of various raw data sources, data quality control, taxonomic name matching and statistical modelling of integrated data. We illustrate these steps with concrete examples from existing citizen science and professional monitoring projects, including eBird, the Tropical Ecology Assessment and Monitoring network, the Living Planet Index and the Baltic Sea zooplankton monitoring. The identified workflow steps are applicable to both terrestrial and aquatic systems and a broad range of spatial, temporal and taxonomic scales. They depend on clear, findable and accessible metadata, and we provide an overview of current data and metadata standards. Several challenges remain to be solved for building global EBV data products: (i) developing tools and models for combining heterogeneous, multi-source data sets and filling data gaps in geographic, temporal and taxonomic coverage, (ii) integrating emerging methods and technologies for data collection such as citizen science, sensor networks, DNA-based techniques and satellite remote sensing, (iii) solving major technical issues related to data product structure, data storage, execution of workflows and the production process/cycle as well as approaching technical interoperability among research infrastructures, (iv) allowing semantic interoperability by developing and adopting standards and tools for capturing consistent data and metadata, and (v) ensuring legal interoperability by endorsing open data or data that are free from restrictions on use, modification and sharing. Addressing these challenges is critical for biodiversity research and for assessing progress towards conservation policy targets and sustainable development goals

Proceedings of the 10th International Conference on Ecological Informatics: translating ecological data into knowledge and decisions in a rapidly changing world: ICEI 2018

The Conference Proceedings are an impressive display of the current scope of Ecological Informatics. Whilst Data Management, Analysis, Synthesis and Forecasting have been lasting popular themes over the past nine biannual ICEI conferences, ICEI 2018 addresses distinctively novel developments in Data Acquisition enabled by cutting edge in situ and remote sensing technology. The here presented ICEI 2018 abstracts captures well current trends and challenges of Ecological Informatics towards: • regional, continental and global sharing of ecological data, • thorough integration of complementing monitoring technologies including DNA-barcoding, • sophisticated pattern recognition by deep learning, • advanced exploration of valuable information in ‘big data’ by means of machine learning and process modelling, • decision-informing solutions for biodiversity conservation and sustainable ecosystem management in light of global changes

A FOUNDATION FOR OPEN INFORMATION ENVIRONMENTS

Traditionally, information systems were developed within organizations for use by known audiences for known purposes. Advances in information technology have changed this landscape dramatically. The reach of information systems frequntly extends beyond organizational boundaries for use by unknown audiences and for purposes not originally anticipated. Individuals and informal communities can generate and use information in ways previously restricted to formal organizations. We term applications with these characteristics open information environments (OIEs). OIEs are marked by diversity of information available, flexibility in accommodating new sources, users and uses, and information management with minimal controls on structure, content, and access. This creates opportunities to generate new information and use it in unexpected ways. However, OIEs also come with challenges in managing the semantic diversity, flexibility of use, and information quality issus arising from the range of users and lack of controls. In this paper, we propose a set of principles for managing OIEs effectively. We outline a research program to examine the potential of OIEs, the challenges they present, and how to design OIEs to realize the benefits while mitigating the challenges. We highlight our ongoing research in this area, and conclude with a call for more research on this important phenomenon

Proceedings of the 10th International Conference on Ecological Informatics: translating ecological data into knowledge and decisions in a rapidly changing world: ICEI 2018

The Conference Proceedings are an impressive display of the current scope of Ecological Informatics. Whilst Data Management, Analysis, Synthesis and Forecasting have been lasting popular themes over the past nine biannual ICEI conferences, ICEI 2018 addresses distinctively novel developments in Data Acquisition enabled by cutting edge in situ and remote sensing technology. The here presented ICEI 2018 abstracts captures well current trends and challenges of Ecological Informatics towards: • regional, continental and global sharing of ecological data, • thorough integration of complementing monitoring technologies including DNA-barcoding, • sophisticated pattern recognition by deep learning, • advanced exploration of valuable information in ‘big data’ by means of machine learning and process modelling, • decision-informing solutions for biodiversity conservation and sustainable ecosystem management in light of global changes

Conservation GIS: Ontology and spatial reasoning for commonsense knowledge.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.Geographic information available from multiple sources are moving beyond their local context and widening the semantic difference. The major challenge emerged with ubiquity of geographic information, evolving geospatial technology and location-aware service is to deal with the semantic interoperability. Although the use of ontology aims at capturing shared conceptualization of geospatial information, human perception of world view is not adequately addressed in geospatial ontology. This study proposes ‘Conservation GIS Ontology’ that comprises spatial knowledge of non-expert conservationists in the context of Chitwan National Park, Nepal. The discussion is presented in four parts: exploration of commonsense spatial knowledge about conservation; development of conceptual ontology to conceptualize domain knowledge; formal representation of conceptualization in Web Ontology Language (OWL); and quality assessment of the ontology development tasks. Elicitation of commonsense spatial knowledge is performed with the notion of cognitive view of semantic. Emphasis is given to investigate the observation of wildlife movement and habitat change scenarios. Conceptualization is carried out by providing the foundation of the top-level ontology- ‘DOLCE’ and geospatial ontologies. Protégé 4.1 ontology editor is employed for ontology engineering tasks. Quality assessment is accomplished based on the intrinsic approach of ontology evaluation.(...