bluuebunny/crossref_metadata_2025 huggingface dataset:
Orbital Migration of Interacting Stellar Mass Black Holes in Disks around Supermassive Black Holes
Authors: Secunda Amy , Bellovary Jillian , Low Mordecai-Mark Mac , Ford K. E. Saavik , McKernan Barry , Leigh Nathan W. C. , Lyra Wladimir , Sándor Zsolt
Published: June 2019

The merger rate of stellar-mass black hole binaries (sBHBs) inferred by the Advanced Laser Interferometer Gravitational-Wave Observatory (LIGO) suggests the need for an efficient source of sBHB formation. Active galactic nucleus (AGN) disks are a promising location for the formation of these sBHBs, as well as binaries of other compact objects, because of powerful torques exerted by the gas disk. These gas torques cause orbiting compact objects to migrate toward regions in the disk where inward and outward torques cancel, known as migration traps. We simulate the migration of stellar mass black holes in an example of a model AGN disk, using an augmented N-body code that includes analytic approximations to migration torques, stochastic gravitational forces exerted by turbulent density fluctuations in the disk, and inclination and eccentricity dampening produced by passages through the gas disk, in addition to the standard gravitational forces between objects. We find that sBHBs form rapidly in our model disk as stellar-mass black holes migrate toward the migration trap. These sBHBs are likely to subsequently merge on short timescales. The process continues, leading to the build-up of a population of over-massive stellar-mass black holes. The formation of sBHBs in AGN disks could contribute significantly to the sBHB merger rate inferred by LIGO.
The Relationship Between Quality of Sleep and Quality of Life of Patients in Medan, Indonesia
Authors: Mariani Dina , Muzasti Riri Andri , Thamrin Alwi
Published: June 2019

BACKGROUND: Hypertension is one of the most common diseases around the world, which is the most risk factor related to cardiovascular disease. The quality of life of hypertensive patients is influenced by various factors, namely age, sex, educational background, ethnicity and nutritional status. Another factor that is also important is the quality of sleep.AIM: We aimed the assessment of sleep quality using a PSQI questionnaire, and quality of life assessment with the SF-36 questionnaire.METHODS: This study was a cross-sectional study of 45 respondents at the H. Adam Malik Central General Hospital in Medan in 2018. Assessment of sleep quality was performed through the PSQI questionnaire (Pittsburgh Sleep Quality Index), and quality of life assessment was carried out with the SF-36 questionnaire.RESULTS: The prevalence of impaired sleep quality in hypertensive patients was 35.6%. Most patients have a good quality of life, with 71.1%. In this study, sleep quality was found to be related to the quality of life (p = 0.037). Furthermore, variables related to sleep quality were sex (gender) (p = 0.003) and education (p = 0.005). In multivariate analysis, the quality of life is predominantly influenced by sleep quality (p = 0.025).CONCLUSION: The quality of life of hypertensive patients is influenced by the quality of sleep.
High molecular diversity in the Carabus variolosus/nodulosus complex
Authors: Mossakowski Dietrich , Hejda Radek , Müller-Kroehling Stefan , Paill Wolfgang , Prunar Florin , Rapuzzi Ivan
Published: June 2019

Starting point of this study was the problem considering the status of Carabus variolous and C. nodulosus: French and some German authors classified them as species, most German authors as subspecies and Casale as semispecies.

We performed analyses of mitochondrial genes (COI-5', COI-3', ND5) as well as nuclear ones (ITS2, wingless) and analysed the DNA sequences using Seqotron, CLUSTALX (editing and alignment), MEGA, DNAML, SplitsTree (phylogeny and network), 4SALE (compensatory base changes), and BEAST (coalescence).

We could study specimens from all regions except the western most part of the distribution area (Massif Central and French Jura, France).

The mitochondrial DNA data resulted in a geographic pattern of high diversity within both taxa indicating a series of glacial refuges. In addition, a considerably large area was found were introgressive hybridisation took place in the past - at least two times by nodulosus of different regions into variolosus.

The nuclear DNA data show a clear and constant difference between both taxa.

In consequence, this complex of forms may be characterised as semispecies from an evolutionary viewpoint but taxonomically as one species because of hybridisation and the lack of compensatory bases changes.
An artisan approach to biodiversity software development
Authors: Noé Nico
Published: June 2019

In a discipline where interoperability is crucial, funding is limited and reinventing the wheel is frowned upon (and rightfully so), the development of data management tools and biodiversity data portals is generally approached in an industrial way: the same application - whose specifications are often written by a committee - is developed as a complex “one size fits all” tool to be used by various groups in different contexts.

While this approach generally makes sense, for the last 15 years the Belgian Biodiversity Platform has sometimes tried a complementary approach where an artisan-minded software developer is assigned to a specific “customer” and is given a direct communication channel and tons of freedom to develop a simple, made-to-measure application. This empirical experience has shown some unexpected advantages but also, as always, some new challenges. It takes inspiration in things as diverse as the Agile software manifesto and the apprenticeship model of medieval Europe.

This talk will present this unusual approach and reflect on this ongoing experience, hopefully extracting pieces of wisdom that is useful to the broader community. For example, the following questions will be discussed:

How does this method help mobilize biodiversity data? Can it “convert” scientists to Open Data?

Has it some effects on the team stability and developer retention?

Aren’t you writing the same code again and again, resulting in an unmaintainable mess?

Isn’t this an example of living in isolation? What about sharing data with global initiatives such as GBIF?

How does this method help mobilize biodiversity data? Can it “convert” scientists to Open Data?

Has it some effects on the team stability and developer retention?

Aren’t you writing the same code again and again, resulting in an unmaintainable mess?

Isn’t this an example of living in isolation? What about sharing data with global initiatives such as GBIF?
Semantic Interoperability Solutions for the Essential Variables: Focus on biodiversity
Authors: Buttigieg Pier Luigi , Walls Ramona , Thessen Anne
Published: June 2019

The Earth system is enduring multiple, interacting stressors causing immense and irreversible change to its biosphere. The unprecedented magnitude of human influence on the planet is a cause for much concern, but also an opportunity to mitigate undesirable impact by instituting socio-ecological management strategies and monitoring their effectiveness. To do so, local and global policy developers and decision makers must have access to clear and globally consistent information streams that serve as planetary diagnostics. This need is being addressed by several international, multi-agency networks which have developed sets of "Essential Variables" (EVs) to improve consistency in the observation of key phenomena within their domains of operation. For example, the implementation of the Essential Climate Variables (ECVs) led by the Global Climate Observing System (GCOS) has set an example being followed in the marine and biodiversity domains by, respectively, the Global Ocean Observing System's (GOOS) Essential Ocean Variables (EOVs) and the Group on Earth Observation Biodiversity Observation Network (GEO BON)'s Essential Biodiversity Variables (EBVs). Each of these EV collections has a subset dedicated to biological and ecological phenomena. This is greatly encouraging for biodiversity science at large, but also runs the risk of parallel and conflicting developments occuring in the EV communities addressing thecross-cutting theme of biodiversity. As a consequence, there is an urgent need for these systems, and the communities behind them, to pursue tight conceptual and technical interoperability in aid of a coherent treatment of biodiversity in planetary-scale monitoring.

In this contribution, we will describe our current research and implementation of a semantic interoperability layer for the EVs, with a focus on biology and ecology. Applying the best practices and core infrastructure of the Open Biological and Biomedical Ontology (OBO) Foundry and Library, we have leveraged both mature and emerging reference ontologies targeting the domains of ecosystems and environment, population and communities, and high-level ecological phenomena. This interoperable collection of ontologies constitutes a foundation for highly expressive EV knowledge representation and management through robust, FAIR-compliant technologies. Further, we are coordinating these efforts with semantic technology adopted by UN agencies, representing global directives and indicators of the UN Sustainable Development Agenda for 2030. With open editorial models behind each of these ontologies, we aim to offer a scalable and inclusive system to bridge data and information products across the EVs through machine-accessible knowledge representation.
FuTRES: Functional Trait Resource for Environmental Studies
Authors: Balk Meghan , Walls Ramona , Guralnick Robert , Davis Edward , Deck John , Emery Kitty , Bernor Raymond , Brenskelle Laura , Boileau Arianne
Published: June 2019

Functional traits are the features of organisms that directly interact with the environment. Studying change and variation in these traits across space, time, and taxonomy can inform how species have responded to environmental and climatic change, how communities are assembled, and other eco-evolutionary questions. Trait data are collected at the individual level; however, animal trait databases often report these data at the species level, undermining their value for researchers who want to look at variation within species and rendering trait data ambiguous when taxonomy is updated. Additionally, these data are often recorded in auxiliary fields, such as “field notes” or hidden in supplementary materials or published tables, making them difficult to recover by researchers. Furthermore, animal trait data from paleontological, zooarchaeological (from archaeological sites), and neontological specimens are typically curated in separate forums and formats that are not easily integrated to provide perspective across the entire range of time. We are developing a toolkit to overcome these challenges called FuTRES: Functional Trait Resource for Environmental Studies. We seek to make these data accessible, standardize trait descriptions across Vertebrata, and teach (future) scientists how to create FAIR (findable, accessible, interoperable, and reusable) trait datasets. To make data more FAIR, FuTRES employs ontologies, a logical framework for relating terms to search datasets and standardizing traits across datasets. FuTRES builds off existing ontologies and standards, such as UBERON for anatomical terms and PATO and OBA for trait terms, as well as create new terms that are general enough to be used for all vertebrates and multiple disciplines. This talk will showcase the semantic framework underpinning FuTRES, describe how we are linking diverse trait datasets to ontologies and, therefore, each other, and report the results of a preliminary analysis of integrated datasets.
Addressing Uncertainties in Machine Learning Predictions of Conservation Status
Authors: Walker Barnaby , Leão Tarciso , Bachman Steven , Lucas Eve , Nic Lughadha Eimear
Published: June 2019

Extinction risk assessments are increasingly important to many stakeholders (Bennun et al. 2017) but there remain large gaps in our knowledge about the status of many species. The IUCN Red List of Threatened Species (IUCN 2019, hereafter Red List) is the most comprehensive assessment of extinction risk. However, it includes assessments of just 7% of all vascular plants, while 18% of all assessed animals lack sufficient data to assign a conservation status. The wide availability of species occurrence information through digitised natural history collections and aggregators such as the Global Biodiversity Information Facility (GBIF), coupled with machine learning methods, provides an opportunity to fill these gaps in our knowledge. Machine learning approaches have already been proposed to guide conservation assessment efforts (Nic Lughadha et al. 2018), assign a conservation status to species with insufficient data for a full assessment (Bland et al. 2014), and predict the number of threatened species across the world (Pelletier et al. 2018).

The wide range in sources of species occurrence records can lead to data quality issues, such as missing, imprecise, or mistaken information. These data quality issues may be compounded in databases that aggregate information from multiple sources: many such records derive from field observations (78% for plant species in GBIF; Meyer et al. 2016) largely unsupported by voucher specimens that would allow confirmation or correction of their identification. Even where voucher specimens do exist, different taxonomic or geographic information can be held for a single collection event represented by duplicate specimens deposited in different natural history collections. Tools are available to help clean species occurrence data, but these cannot deal with problems like specimen misidentification, which previous work (Nic Lughadha et al. 2019) has shown to have a large impact on preliminary assessments of conservation status.

Machine learning models based on species occurrence records have been reported to predict with high accuracy the conservation status of species. However, given the black-box nature of some of the better machine learning models, it is unclear how well these accuracies apply beyond the data on which the models were trained. Practices for training machine learning models differ between studies, but more interrogation of these models is required if we are to know how much to trust their predictions.

To address these problems, we compare predictions made by a machine learning model when trained on specimen occurrence records that have benefitted from minimal or more thorough cleaning, with those based on records from an expert-curated database. We then explore different techniques to interrogate machine learning models and quantify the uncertainty in their predictions.
Access to Natural History Collections – from SYNTHESYS to DiSSCo
Authors: Knapp Sandra , Vincent Sarah , Arvanitidis Christos , Dixey Katherine , Mergen Patricia
Published: June 2019

Any one collection of objects never tells the whole story. Enabling access to natural history collections by users external to a given institution, has a long history–even that great stay-at-home, Linnaeus, relied on specimens in the hands of others. Neglecting collections outside one’s institution results in duplication and inefficiency, as can be seen in the history of synonymy. Physical access had always been the norm, but difficult for the single individual. A student in the late 20th century had to decide if money were better spent going to one collection or another, or if the sometimes rather fuzzy photographs really represented the taxon she was working with. Loans between institutions were a way to provide access, but came with their own risks. The very individualised–to users as well as institutions–system of access provisioning still operates today but has fundamentally changed in several respects. The SYNTHESYS (Synthesis of Systematic Resources) projects brought a set of European institutions into a consortium with one aim: to provide access to natural history collections in order to stimulate their use across communities. The SYNTHESYS Transnational Access (TA) programme provided access not only to the collections of participating institutions, but also to infrastructures such as laboratories and analytical facilities. The trajectory of TA has led to a change in thinking about natural history collections, along with access to them. Because access has been subsidised at both the individual and institutional levels, participating institutions began to function more as a collective; one infrastructure, albeit loosely dispersed. In the most recent iteration of the SYNTHESYS programme, SYNTHESYS+, access has changed yet again with the times. Technological advances in imaging permit high-quality surrogates of natural history specimens to be exchanged more freely, and Virtual Access (VA) forms an integral part of the SYNTHESYS+ access programme, alongside TA. Virtual access has been operating for some time in the natural history collections community, but like TA, with individual scientists requesting images/sequences/scans from individual institutions or curators. VA, as a centralised service, will be piloted in SYNTHESYS+ in order to establish the basis for community change in access provisioning. But what next? Will we continue to need physical access to specimens and facilities as VA becomes increasingly feasible? As European collections-based institutions coalesce into the DiSSCo (Distributed System of Systematics Collections) infrastructure, will the model established in SYNTHESYS+ continue to function in the absence of centralised funding? In this talk, we will explore the trajectory of access through SYNTHESYS and provide some scenarios for how access to natural history collections–both physical and virtual–may change as we transition to the broader infrastructure that DiSSCo represents.
Furthering Genomic Research Infrastructures: The Global Genome Biodiversity Network
Authors: Barker Katharine , Astrin Jonas , Droege Gabriele , Coddington Jonathan , Seberg Ole
Published: June 2019

Most successful research programs depend on easily accessible and standardized research infrastructures. Until recently, access to tissue or DNA samples with standardized metadata and of a sufficiently high quality, has been a major bottleneck for genomic research. The Global Geonome Biodiversity Network (GGBN) fills this critical gap by offering standardized, legal access to samples. Presently, GGBN’s core activity is enabling access to searchable DNA and tissue collections across natural history museums and botanic gardens. Activities are gradually being expanded to encompass all kinds of biodiversity biobanks such as culture collections, zoological gardens, aquaria, arboreta, and environmental biobanks. Broadly speaking, these collections all provide long-term storage and standardized public access to samples useful for molecular research. GGBN facilitates sample search and discovery for its distributed member collections through a single entry point. It stores standardized information on mostly geo-referenced, vouchered samples, their physical location, availability, quality, and the necessary legal information on over 50,000 species of Earth’s biodiversity, from unicellular to multicellular organisms. The GGBN Data Portal and the GGBN Data Standard are complementary to existing infrastructures such as the Global Biodiversity Information Facility (GBIF) and International Nucleotide Sequence Database (INSDC). Today, many well-known open-source collection management databases such as Arctos, Specify, and Symbiota, are implementing the GGBN data standard. GGBN continues to increase its collections strategically, based on the needs of the research community, adding over 1.3 million online records in 2018 alone, and today two million sample data are available through GGBN. Together with Consortium of European Taxonomic Facilities (CETAF), Society for the Preservation of Natural History Collections (SPNHC), Biodiversity Information Standards (TDWG), and Synthesis of Systematic Resources (SYNTHESYS+), GGBN provides best practices for biorepositories on meeting the requirements of the Nagoya Protocol on Access and Benefit Sharing (ABS). By collaboration with the Biodiversity Heritage Library (BHL), GGBN is exploring options for tagging publications that reference GGBN collections and associated specimens, made searchable through GGBN’s document library. Through its collaborative efforts, standards, and best practices GGBN aims at facilitating trust and transparency in the use of genetic resources.
The Additivity Project: Achieving additivity of structured taxonomic character data by persistently linking them to individual specimens
Authors: Plitzner Patrick , Henning Tilo , Müller Andreas , Güntsch Anton , Berendsohn Walter G. , Borsch Thomas , Kilian Norbert
Published: June 2019

Herbarium specimens have always played a central role in the classical disciplines of plant sciences and the global digitisation efforts now open new horizons. To make full use of the inherent possibilities of specimen based taxonomic descriptions corresponding workflows are needed. A crucial step in the comparative analyses of organisms is the preparation of a character matrix to record and compare the morphological variation of taxa on the basis of individual specimens.

This project focuses on the optimisation of the taxonomic research process with respect to delimitation and characterisation (“descriptions”) of taxa (Henning et al. 2018). The angiosperm order Caryophyllales provides exemplar use cases through cooperation with the Global Caryophyllales Initiative (Borsch et al. 2015). The workflow for sample data handling (Kilian et al. 2015), implemented on the EDIT Platform for Cybertaxonomy (http://www.cybertaxonomy.org, Ciardelli et al. 2009), has been extended to support additive characterisation of taxa via specimen character data.

The Common Data Model (CDM), already supporting persistent inter-linking of specimens and their metadata (Plitzner et al. 2017), has been adapted to facilitate specimen descriptions with characters constructed from the combination of structure and property terms and their corresponding states. Semantic web technology is used to establish and continuously elaborate expert community-coordinated exemplar vocabularies with term ontologies and explanations for characters and states (GFBio Terminology Service, Karam et al. 2016). Character data are recorded and stored in structured form in character state matrices for individual specimens instead of taxa, which allows generation of taxon characterisations by aggregating the data sets for the individual specimens included. Separating characters in structures and properties, which are based on concepts in public ontologies, guarantees a high visibility and instant re-usability of these character data. Taking into account that taxon concepts evolve during the iterative knowledge generation process in systematic biology, additivity of character data from specimen to taxon level therefore greatly facilitates the construction and reproducibility of taxon characterisations from changing specimen and character data sets.
Practical Tools for Collection Managers: Label designer, annotation tools and a QR code reader
Authors: Heikkinen Mikko , Riihikoski Ville-Matti , Kuusijärvi Anniina , Koivunen Anne , Lahti Kari , Schulman Leif
Published: June 2019

Kotka is a collection management system (CMS) developed by the Finnish Museum of Natural History (Luomus) and used by all major institutes with natural history collections in Finland. It is one of the primary data sources of the Finnish Biodiversity Information Facility through which the data managed in Kotka is distributed (species.fi). Kotka is designed to allow flexible development of new tools to support collection management practices. This paper describes some of the tools included in Kotka.

Label designer

Printed labels have traditionally been used to store and display data about specimens. In modern collection informatics their role in connecting specimens to electronic data and in collection and data curation is emphasised. Requirements for the labels are changing rapidly and different types of specimens have completely different label designs.

To give the collection managers an option to design suitable labels to meet their needs, we have created a WYSIWYG (What You See is What You Get) label designer (Fig. 1). It allows users to pick desired data fields and arrange them on the label, adjust styles and sizes, and generate HTTP-URI identifiers with QR Codes (Quick Response Codes).

The label designer can be used with a modern web browser or as a standalone desktop application, on both Windows and Mac. It is open source and can be integrated with other applications by using it as an Angular module or as an custom element to any site.

The label designer serves both scientific natural history collection managers and amateurs managing private collections. At Luomus the tool is used both in the Kotka CMS and in the Notebook system for species occurrence records.

Annotations

As collections are increasingly used and managed digitally, the traditional means of quality control and data improvement are no longer sufficient. We have developed tools which allow e.g. external researchers and citizen experts to review specimen data online at species.fi (species.fi), and annotate the data by evaluating its quality, propose and/or change species identifications and include comments. The annotations are delivered to collection managers who can then use them to update and improve the specimen data at the primary data source.

QR Code reader

Modern specimen labels often include specimen identifiers such as QR Codes or barcodes. To improve collection management efficiency, we have made a QR Code reader application, which allows collection managers to read these codes and display specimen data quickly on a handheld device (e.g. mobile phone) or a desktop computer with a web camera.

The application is open source and can be configured to connect to any system utilizing HTTP-URI identifiers.
Game of Tops: Trends in GBIF’s Community of Users
Authors: Escribano Nora , Galicia David , Ariño Arturo H.
Published: June 2019

Building on the development of Biodiversity Informatics, the Global Biodiversity Information Facility (GBIF) undertook the task of enabling access to the world’s wealth of biodiversity data via the Internet. To date, GBIF has become, in many respects, the most extensive biodiversity information exchange infrastructure in the world, opening up a full range of possibilities for science.

Science has benefited from such access to biodiversity data in research areas ranging from the effects of environmental change on biodiversity to the spread of invasive species, among many others. As of this writing, more than 7,000 published items (scientific papers, reviews, conference proceedings) have been indexed in the GBIF Secretariat’s literature tracking programme.

On the basis on this database, we will represent trends in GBIF in the users’ behaviour over time regarding openness, social structure, and other features associated to such scientific production: what is the measurable impact of research using GBIF data? How is the GBIF community of users growing? Is the science made with, and enabled by, open data, actually open? Mapping GBIF users’ choices will show how biodiversity research is evolving through time, synthesising past and current priorities of this community in an attempt to forecast whether summer—or winter—is coming.
Global Open Biodiversity Data: Future Vision of FAIR Biodiversity Data Access, Management, Use and Stewardship
Authors: De Prins Jurate
Published: June 2019

Major environmental–biodiversity changes and new developments in technology have changed the way we live, work and how we create our future. The main attention of biodiversity researchers nowadays is focused on the application of the developments of digital technology for fast, efficient and ethical solutions related to biodiversity data management and stewardship, so that everyone can benefit from better data, better science and better policies. Here the originally developed five point biodiversity data research and management programme is presented for your kind attention.

Open Biodiversity Data (OBD) which are usable, useful and used to promote the knowledge and the preservation of biodiversity.

Linking Open Biodiversity Data and making it useful for everybody. Knowledge of biodiversity for many and not for few.

The global web is our work platform. OBD creates an open community of contributors and users.

Open is FAIR. FAIR Guiding Principles for biodiversity data management and stewardship (EU Commission 2018)

Circular Open Biodiversity Data a high-value foundation for artificial intelligence.

Open Biodiversity Data (OBD) which are usable, useful and used to promote the knowledge and the preservation of biodiversity.

Linking Open Biodiversity Data and making it useful for everybody. Knowledge of biodiversity for many and not for few.

The global web is our work platform. OBD creates an open community of contributors and users.

Open is FAIR. FAIR Guiding Principles for biodiversity data management and stewardship (EU Commission 2018)

Circular Open Biodiversity Data a high-value foundation for artificial intelligence.

It is of great importance for society, communities and on a global scale to have unbiased and direct access to Open Biodiversity Data, as this maximises the impact on decision making and development of efficient solutions to tackle environmental problems (De Prins 2016, De Prins 2017, De Prins and De Prins 2019a, De Prins and De Prins 2019b, De Prins and Serna 2018, European Commission 2018). While embracing the latest developments of technology, in particular high resolution visual recognition tools, computer vision technologies to work with huge image galleries and link with other fields of biodiversity data (genetic sequences, distribution data) we are going to create an open international community of knowledgeable users, responsible for OBD. I suggest implementing FAIR guiding principles: Findability, Accessibility, Interoperability and Reusability. Following FAIR principles OBD become accessible to everybody, they are findable, visual, flexible, interchangeable in different formats, updated and reused for all biodiversity related questions. This kind of approach will ensure the use, and reuse of data in the most efficient way, so biodiversity knowledge and information are based on verified and clean data.
The European Journal of Taxonomy: Enhancing taxonomic publications for dynamic data exchange and navigation
Authors: Bénichou Laurence , Gerard Isabelle , Chester Chloé , Agosti Donat
Published: June 2019

The European Journal of Taxonomy (EJT) was initiated by a consortium of European natural history publishers to take advantage of the shift from paper to electronic-only publishing (Benichou et al. 2011). Whilst originally publishing in PDF format has been considered the state of the art, it became recently obvious that complementary dissemination channels help to disseminate taxonomic data - one of the pillars of Natural History institutions research - more widely and efficiently (Côtez et al. 2018). The adoption of semantic markup and assignment of persistent identifiers for content allow more comprehensive citations of the article, including elements therein, such as images, taxonomic treatments, and materials citation. It also allows more in-depth analyses and visualization of the contribution of collections, authors, or specimens to taxonomic output and third parties, such as the Global Biodiversity Information Facility, for reuse of the data or building the catalogue of life.

In this presentation, EJT will be used to outline the nature of natural history publishers and their technical set up. This is followed by a description of the post-publishing workflow using the Plazi workflow and dissemination via the Biodiversity Literature Repository (BLR) and TreatmentBank. It outlines switching the publishing workflow to an increased use of extended markup language (XML) and visualization of the output and concludes by publishing guidelines that enable more efficient text and data mining of the content of taxonomic publications.
Anatomy Knowledge Graphs: Toward FAIR morphological data
Authors: Vogt Lars
Published: June 2019

Most morphological data are still published as unstructured texts. This has far-reaching consequences for the Findability, Accessibility, Interoperability and Reusability of morphological data and thus for their FAIRness (Wilkinson et al. 2016). The lack of FAIR morphological data significantly affects their general usability within the life sciences. With the advent of the Semantic Web and an increasing amount of publicly accessible anatomy ontologies, technically feasible solutions to this linguistic problem of morphology have become available. After a brief introduction to the distinction between instance anatomy (anatomical data pertaining to instances, i.e. individuals) and canonical anatomy (generalized anatomical knowledge), between assertional statements (i.e., ABox expressions, statements about instances) and universal statements (i.e., TBox expressions, statements about kinds or classes), and between knowledge bases and ontologies, I compare two different approaches of representing anatomy through Resource Description Framework (RDF) based graphs (see Fig. 1): i) Semantic Phenotypes, which are class-based graphs that document anatomy purely as TBox expressions and ii) Semantic Instance Anatomy Knowledge Graphs (short: Anatomy Knowledge Graphs), which are instance-based graphs that document anatomy as a combination of ABox and TBox expressions, thereby limiting the portion of TBox expressions to a minimum. While both approaches provide solutions to the linguistic problem of morphology, they differ not only conceptually but also in their technical details. Because Anatomy Knowledge Graphs include ABox expressions, they allow the identification of any individually described part or property within the description through the part’s or property’s particular URI. This detail allows fragmentation of a morphological description into meaningful description fragments and reuse of these fragments in other contexts. Because Anatomy Knowledge Graphs limit TBox expressions to a minimum, they also perform better in many queries as querying ABox expressions is computationally less difficult than querying TBox expressions. These technical differences between the two approaches have substantial practical consequences that significantly affect the FAIRness of morphological data. Compared to Semantic Phenotypes, morphological data in the form of Anatomy Knowledge Graphs are overall more FAIR.
Using Wikibase as a Platform to Develop a Semantic TDWG Standard
Authors: Fichtmüller David , Reimeier Fabian , Güntsch Anton
Published: June 2019

In the ABCD 3.0 Project the ABCD (Access to Biological Collection Data) Standard (Access to Biological Collections Data task group 2007) was transformed from a classic XML Schema into an OWL (Web Ontology Language) ontology (along side an updated semantic-aware XML version). While it was initially planned to use the established TDWG Terms wiki as the editing and development platform for the ABCD ontology, the rise of Wikidata and its underlying platform Wikibase have caused us to reconsider this decision and switch to a Wikibase installation instead. This proved to be a crucial decision, as Wikibase turned out to be a well-suited platform to collaboratively import, develop and export this complex semantic standard. This experience is potentially of interest to maintainers of other Biodiversity Information Standards (TDWG) standards and the Technical Architecture Group.

In this presentation we will explain our technical setup and how we used Wikibase, alongside its related tools, to model the ABCD Ontology. We will introduce the tools we used for importing existing concepts from the previous ABCD versions, running maintenance queries (e.g. for checking the ontology for consistency or missing information about concepts), and exporting the ontology into the OWL/XML format. Finally we will discuss the lessons we learned and how our setup can be improved for future uses.
State of the Art in Computational Bioacoustics and Machine Learning: How far have we come?
Authors: Stowell Dan
Published: June 2019

Terrestrial bioacoustics, like many other domains, has recently witnessed some transformative results from the application of deep learning and big data (Stowell 2017, Mac Aodha et al. 2018, Fairbrass et al. 2018, Mercado III and Sturdy 2017). Generalising over specific projects, which bioacoustic tasks can we consider "solved"? What can we expect in the near future, and what remains hard to do? What does a bioacoustician need to understand about deep learning? This contribution will address these questions, giving the audience a concise summary of recent developments and ways forward. It builds on recent projects and evaluation campaigns led by the author (Stowell et al. 2015, Stowell et al. 2018), as well as broader developments in signal processing, machine learning and bioacoustic applications of these. We will discuss which type of deep learning networks are appropriate for audio data, how to address zoological/ecological applications which often have few available data, and issues in integrating deep learning predictions with existing workflows in statistical ecology.
Green Pioneers: Raising awareness of invasive plants for all ages
Authors: Bogaerts Ann , De Smedt Sofie , Meeus Sofie , Groom Quentin
Published: June 2019

When researchers and managers are asked to rank the issues that prevent adequate control of invasive species, lack of public awareness is at the top of the list (Dehnen‐Schmutz et al. 2018). It is therefore imperative to raise the general public's awareness of the potential risks of introducing alien species into the wild.

Green Pioneers, a citizen science project funded by the Flemish Government, (Fig. 1) aims to address this issue in Belgium, across age groups.

The project aims to

Create awareness on invasive species, highlighting how invasions can be avoided and how to mitigate their impact.

Improve communication between citizens and scientists on conservation and invasive plant species.

Augment the quality and quantity of data on invasive species.

Create awareness on invasive species, highlighting how invasions can be avoided and how to mitigate their impact.

Improve communication between citizens and scientists on conservation and invasive plant species.

Augment the quality and quantity of data on invasive species.

The project is developing three kinds of activity, specifically to attract a broad demographic:

- 'Young Pioneers', by developing tools for teachers in science, technology, engineering and mathemathics for school children from 12-15 years old.

- 'Online Pioneers', through our online citizen science platform DoeDat.be, by helping with the transcription of label information on herbarium specimens,

- and 'Visiteers', by inviting companies and working age people to help us in the collection and to inform them about invasive species.

Finally, we will be organizing a BioBlitz in spring 2020 at Meise Botanic Garden where we will celebrate plants and all our Green Pioneers, while also spreading the message of invasive plant awareness. During our 48 hour BioBlitz, scientists, volunteers and citizens are workig together to survey the biodiversity of our Botanic Garden.

Ultimately, Green Pioneers aim to encourage recording of alien species by amateur botanists and create a generation of responsible gardeners who understand the consequences of releasing invasive alien plants into the wild.
Auto-autorité et vouloir de création
Authors: Prades Jean-Luc
Published: June 2019

L’article tentera de montrer comment le dispositif institutionnel mis en œuvre par la sociopsychanalyse fait contrepoids aux divisions du travail qui aliènent les potentialités de ceux qui travaillent pour libérer leurs capacités créatives insoupçonnées. Pour ce faire, et préalablement, il mettra en parallèle les deux faces du travail salarié : son volet réifié (première partie : de l’aliénation à l’auto-autorité) et son volet créatif (deuxième partie : de la perruque au hacking) pour déboucher sur une proposition (troisième partie : un dispositif institutionnel au service de tous) visant à promouvoir, à l’intérieur même de l’organisation du travail pathogène actuelle, les potentialités créatrices toujours présentes de ceux qui travaillent.
Réinvention du caporalato : extension et développement de formes criminelles d’esclavage dans l’agriculture en Italie
Authors: Marcucci de Vincenti Antonella , Salinari Pietro
Published: June 2019

Dans le capitalisme globalisé, à côté de formes très avancées d’organisation du travail réapparaissent des formes archaïques d’exploitation. L’article analyse deux cas qui montrent, en Italie, l’exploitation de travailleurs démunis de la part de petites entreprises agricoles qui y ont recours pour baisser les coûts de production au niveau imposé par les grandes chaînes de distribution. «  Caporalato  » est le mot idiomatique utilisé pour désigner l’intermédiation illégale entre les entreprises et ceux que la Walk Free Foundation définit comme les esclaves modernes. Victimes de ce système sont en particulier les immigrés illégaux qui, comme les petits producteurs, constituent l’anneau le plus faible de la chaîne de production/distribution. Il existe donc un fil rouge qui lie l’exploitation du travail à la traite d’êtres humains par les filières globalisées de la criminalité internationale. L’article veut mettre en lumière le processus et les conséquences sociales de la traite d’êtres humains et de l’intermédiation illégale de la main-d’œuvre.
Couplage entre données objectives et points de vue du sujet : travail du négatif et intersubjectivité lors des appels d’urgence au SAMU centre 15
Authors: Montandon Christiane
Published: June 2019

Dans une recherche sur l’activité décisionnelle des médecins régulateurs des samu centre 15, l’intérêt de coupler données objectives et points de vue du sujet permet de faire émerger les non-dits sous-jacents à cette activité : par le recours à des entretiens d’explicitation, le médecin décrit son agir que le chercheur peut confronter au dire recueilli sur la bande audio lors de son échange avec l’appelant en situation d’urgence. Deux études de cas, paradigmatiques des rapports à la mort, mettent en évidence diverses catégories de non-dits : ce qui est tu, ce qui est occulté ou oublié, ce qui n’est pas perçu et reste subliminaire, ce qui n’est pas présent à la conscience mais agit inconsciemment dans cette situation intersubjective de l’appel d’urgence. La condition d’émergence à la conscience de ce travail du négatif réside dans la coconstruction d’une intersubjectivité.
Faire le travail autrement
Authors: Dromard Ingrid , Roth Tine
Published: June 2019

En tant qu’intervenantes en analyse du travail et chercheures, les auteures sont engagées dans des dispositifs d’évaluation des risques professionnels et d’accompagnement d’équipes de travail et de direction. Elles mettent en œuvre une démarche originale appelée « groupe de rencontres du travail ». Celle-ci propose de questionner, à partir d’une analyse de l’activité, les dimensions individuelles et collectives du travail qui permettent, ou empêchent, de travailler efficacement ensemble et en santé. À partir de leurs interventions dans le champ médico-social, l’article tente de montrer la nécessité d’échanger sur le travail afin de surpasser les obstacles physiques et psychiques inhérents à toute activité et organisation de travail.
Jean Calvin, François de Sales et la prophétie des ossements desséchés (Ez 37). 2 e partie : l’exégèse de François
Authors: Bossu Nicolas
Published: June 2019

Cet article fait suite à une présentation des interprétations de Calvin sur Ez 37. Nous confrontons son exégèse avec celle de François de Sales, pour montrer leur positionnement par rapport à l’exégèse médiévale des « quatre sens de l’Écriture », rejetée par le premier, pratiquée par le second. Cela permet d’illustrer l’écart qui s’est formé entre réforme protestante et contre-réforme catholique sur l’interprétation de l’Écriture.
Le chemin de la vie selon le Livre de la Sagesse
Authors: Leproux Alexis
Published: June 2019

Qu’est-ce que vivre ? Le Livre de la Sagesse répond à cette question. Sa lecture dévoile une cohérence dans le foisonnement des références bibliques et hellénistiques ; celui-ci n’efface pas les lignes de force. Attentif d’abord aux sujets des verbes qui disent la Sagesse, cet article décrypte les lieux et les temps de leur accomplissement. Ce n’est rien de moins qu’une promesse scripturaire toujours ouverte, autrement dit une mystique.
L’Action et « Histoire et dogme » de Maurice Blondel chez Joseph Malègue
Authors: Fontaine José
Published: June 2019

L’article montre, chose ignorée jusqu’ici, que Malègue recrée un passage capital de L’Action de Blondel – un « traité de la conversion » selon Aubert –, dans Augustin ou Le Maître est là , décidant de son sens entier . La réponse de Blondel à Loisy, « Histoire et dogme », nourrit l’action d’ Augustin , sans qu’il ne quitte le genre romanesque, devenant ainsi relecture créatrice profonde et mystique du modernisme, matrice intellectuelle du catholicisme contemporain.
Du Triangle dramatique de Karpman au Carré maléfique
Authors: Ide Pascal
Published: June 2019

L’article a pour objet un scénario psychologique d’une grande pertinence, le Triangle dramatique de Karpman (TDK), qui se déroule entre trois personnages : le Persécuteur, la Victime et le Sauveteur. Les interprétations psychologiques sont superficielles et surtout ambiguës. La philosophie permet d’interpréter le TDK à partir de la violence, de définir avec précision les trois personnages et de lever les ambivalences en dédoublant ceux-ci : Régulateur-Persécuteur ; Victime-Victimaire ; Sauveur-Sauveteur. Elle permet aussi de l’enrichir d’un quatrième personnage : le Justicier, qui est lui-même une caricature du Juge. Enfin, ce modèle des transactions violentes présente une pertinence scripturaire.
3. Retrouver le sens de la mesure pour de meilleures décisions collectives : vers une intelligence artificielle humaine à l’ère des données
Authors: Letouzé Emmanuel
Published: June 2019

Les données personnelles et institutionnelles récoltées de plus en plus massivement à l’échelle mondiale ouvrent la voie à de nouvelles façons de penser la prise de décision collective. Cet article présente les conditions d’un traitement de ces données tourné vers le développement humain, au travers du concept d’Intelligence Artificielle Humaine (IAH). Nous présentons à cet égard un exemple de projet destiné à appliquer ce concept dans plusieurs pays en développement.
9. La vie privée, un bien commun ?
Authors: Tubaro Paola
Published: June 2019

La vie privée s’est transformée sous l’effet des technologies numériques et des modèles d’affaires des plateformes. L’ancienne notion de privacy comme pénétration dans l’espace intime d’une personne a laissé place à une privacy « comme négociation », contextuelle et évolutive, dépendant de l’environnement social de chacun. Cette négociation doit être collective et associer les droits des usagers aux enjeux généraux de l’économie et du travail de la donnée.
Une brève histoire du péché
Authors: Euvé François
Published: June 2019

Résumé L’article déploie quelles ont été les grandes évolutions dans le traitement des péchés, en se référant principalement à la pratique du sacrement de pénitence. À la fois tribunal de la conscience et lieu de sa guérison, ce dernier a connu plusieurs périodes, depuis son appréhension collective dans les premières communautés chrétiennes jusqu’au retour de cette dimension à la suite du concile Vatican II, à travers les nombreux siècles marqués par la prééminence d’une pratique surtout individuelle. Ce parcours montre également une dialectique permanente entre l’aspect moral et l’aspect théologal du péché qui atteste du fait que le péché s’inscrit dans l’histoire, par nature toujours ouverte, de la relation vivante entre Dieu, les êtres humains et, plus largement, l’ensemble des créatures.