bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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.
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.
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.