Emerging semantics to link phenotype and environment

abstract: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.The final version of this article, as published in PeerJ, can be viewed online at: https://peerj.com/articles/1470

The Gene Ontology Handbook

bioinformatics; biotechnolog

A framework to support the annotation, discovery and evaluation of data in ecology, for a better visibility and reuse of data and an increased societal value gained from environmental projects

Die vorliegende Dissertationsschrift beschäftigt sich im Kern mit der Verwendung von Metadaten in alltäglichen, datenbezogenen Arbeitsabläufen von Ökologen. Die vorgelegte Arbeit befasst sich dabei mit der Erstellung eines Rahmenwerkes zur Unterstützung der Annotation ökologischer Daten, der effizienten Suche nach ökologischen Daten in Datenbanken und der Einbindung von Metadaten während der Datenanalyse. Weiterhin behandelt die Arbeit die Dokumentation von Analysen sowie die Auswertung von Metadaten zur Entwicklung von Werkzeugen für eine Aufbereitung von Informationen über ökologische Projekte. Diese Informationen können zur Evaluation und Maximierung des aus den Projekten gezogenen gesellschaftlichen Mehrwerts eingesetzt werden. Die vorliegende Arbeit ist als kumulative Dissertation in englischer Sprache abgefasst. Sie basiert auf zwei Veröffentlichungen als Erstautor und einem zur Einreichung vorbereiteten Manuskript

The sustainability of deep-sea fishing in Greenland from a benthic ecosystem perspective: the nature of habitats, impacts of trawling and the effectiveness of governance

The deep sea (>200 m) is the world’s least explored and largest biome, covering ~65% of the earth’s surface, it is increasingly subject to anthropogenic disturbance from fishing. The offshore Greenland halibut (Reinhardtius hippoglossoides) fishery, west Greenland, employs demersal trawl gear at depths of 800-1,400 m. Recent Marine Stewardship Council (MSC) certification of this fishery highlighted the paucity of knowledge of benthic habitats and trawling impacts. This interdisciplinary thesis employs a benthic video sled to investigate deep-sea habitats and trawling impacts and conducts a critical analysis of the fishery’s governance, with reference to the role of the MSC certification. The results provide new insights into this poorly known region of the Northwest Atlantic, including identifying four candidate vulnerable marine ecosystems (VMEs). Imagery obtained demonstrates that chronic trawling has had extensive impacts on the seafloor, which are significantly associated with the benthic communities observed. Further, trawling effort is shown to have a significant negative association with the abundance of some VME indicator taxa. The governance case study finds an effective system of state-led governance, supported by scientific, certification and industry actors. Outcomes directly attributable to engagement with the MSC certification include the introduction of a management plan and new benthic research programmes. However, questions are raised about the MSC certification, providing case study examples of existing criticisms. Assessments are weak with respect to benthic habitats and overreliant on the definitive, expert judgement of Conformity Assessment Bodies (CABs), whose independence is questioned. The assurance offered by the MSC certification in terms of the sustainability of trawling impacts on benthic ecosystems is found to seriously lack credibility. Findings are of direct relevance to the management of deep-sea fisheries in Greenland and elsewhere. Widely applicable critical insights into deep-sea fishery governance are presented, including into the role of eco-labels as a market-mechanism to promote sustainable fishery management

Biodiversity Databases

Computing and database management has shifted from cottage industry-style methods — the small independent researcher keeping records for a particular project — to state-of-the-art file storage systems, presentation, and distribution over the Internet. New and emerging techniques for recognition, compilation, and data management have made managing data a discipline in its own right. Covering all aspects of this data management, Biodiversity Databases: Techniques, Politics, and Applications brings together input from social scientists, programmers, database designers, and information specialists to delineate the political setting and give institutions platforms for the dissemination of taxonomic information. A practical and logical guide to complex issues, the book explores the changes and challenges of the information age. It discusses projects developed to provide better access to all available biodiversity information. The chapters make the case for the need for representation of concepts in taxonomic databases. They explore issues involved in connecting databases with different user interfaces, the technical demands of linking databases that are not entirely uniform in structure, and the problems of user access and the control of data quality. The book highlights different approaches to addressing concerns associated with the taxonomic impediment and the low reproducibility of taxonomic data. It provides an in-depth examination of the challenge of making taxonomic information more widely available to users in the wider scientific community, in government, and the general population

Semantic Domains in Akkadian Text

The article examines the possibilities offered by language technology for analyzing semantic fields in Akkadian. The corpus of data for our research group is the existing electronic corpora, Open richly annotated cuneiform corpus (ORACC). In addition to more traditional Assyriological methods, the article explores two language technological methods: Pointwise mutual information (PMI) and Word2vec.Peer reviewe

Knowledge visualization: From theory to practice

Visualizations have been known as efficient tools that can help users analyze com- plex data. However, understanding the displayed data and finding underlying knowl- edge is still difficult. In this work, a new approach is proposed based on understanding the definition of knowledge. Although there are many definitions used in different ar- eas, this work focuses on representing knowledge as a part of a visualization and showing the benefit of adopting knowledge representation. Specifically, this work be- gins with understanding interaction and reasoning in visual analytics systems, then a new definition of knowledge visualization and its underlying knowledge conversion processes are proposed. The definition of knowledge is differentiated as either explicit or tacit knowledge. Instead of directly representing data, the value of the explicit knowledge associated with the data is determined based on a cost/benefit analysis. In accordance to its importance, the knowledge is displayed to help the user under- stand the complex data through visual analytical reasoning and discovery