bluuebunny/crossref_metadata_2025 huggingface dataset:
Scaling Up Data Literacy and Computing Skills Training in Biodiversity Science, Lessons Learned from The Carpentries
Authors: Michonneau François , Paul Deborah
Published: June 2019

The expanding availability of access to data about museum specimens, species occurrences, trait data, genetics, and landscapes is revolutionizing biodiversity research. But mobilizing, evaluating, and synthesizing these data to address research questions requires domain-specific computing skills and knowledge.

The Carpentries is a global non-profit organization teaching researchers computational and data science skills for data management and analysis in all domains of research. The Carpentries' teaching practices are based on evidence from the science of learning. Current domain-specific lessons include life, physical, and social sciences. Hands-on exercises build on the existing knowledge of learners, quickly enabling them to apply skills learned to their research. The Carpentries' train-the-trainer model, its globally established community of ~2,000 instructors and its network of regional coordinators have allowed the organization to scale up rapidly, and over 40,000 learners have participated in Carpentries workshops since 2012.

The Carpentries assessment program evaluates the impact of attending a workshop on the participants' perception of their skills and confidence. After attending a Carpentries workshop, participants feel more confident in their ability to program and to overcome issues with their analysis. The Carpentries' mentoring program ensures that newly certified instructors receive support and guidance to successfully engage in leading and teaching workshops. Pairing new and experienced instructors, in combination with the development of local communities of instructors, have contributed to the success of The Carpentries workshops.

The Carpentries collaboratively seeks to develop new curricula to address the training needs of the biodiversity data community. Establishing training partnerships between The Carpentries and the various organizations involved in building biodiversity data science skills capacity would increase reach and efficacy. We seek to foster institutional and organizational collaborations that can support the establishment and growth of the infrastructure needed to provide the computational and data literacy skills needed to empower our stakeholders. These include those creating and mobilizing data (e.g., collectors, ecologists, conservationists, curators, collection/data managers), for all scientists, policy-makers, educators, and students who want to use biodiversity data.
Norwegian Taxonomy Initiative & Biodiversity Infrastructure
Authors: Skarp Liselott , Päivikki Kallioniemi Eveliina , Ertshus Mathisen Ingrid
Published: June 2019

Norwegian Biodiversity Information centre (NBIC) shares information about Norwegian species, habitats and ecosystems. One of the key tasks is to maintain an updated taxonomical and nomenclatural backbone “Norwegian Taxonomic backbone” (Artsnavnebase) for species. Launched in 2009, the backbone contains more than 185 000 scientific names, as well as 45 000 names in Norwegian (two languages) and Northern Sami. “Norwegian Taxonomic backbone” delivers names and taxonomic information to scientific institutions and museums across the country and is used for both management and research purposes as well as by general public. Additionally, the database has contributed more than 33500 names to the construction of the Global Biodiversity Information Facility (GBIF) taxonomy.

Another major task is the Norwegian Taxonomy Initiative (NTI) which was established in 2009 with the goal of improving knowledge about Norwegian biodiversity with special emphasis on poorly known species. In addition, the surveys provide information about distributions of species in Norway and their habitat requirements. NTI collaborates with Norwegian Barcode of Life (NorBOL) and contributes into building up a comprehensive library of standardized DNA sequences (DNA barcodes) and supports research school in biosystematics (ForBio). Swedish and Norwegian taxonomy initiatives work cooperatively to increase the collective knowledge on poorly known species, and as a result, more than 3 000 species new to the country in both Sweden and Norway has been found, of which about a third being new to science.

NBIC is in a process of developing and collating a trait database “Trait bank” (Egenskapsbank) for Norwegian species and habitats. Trait bank will describe and combine information about species traits on morphology, physiology and ecology etc. The aim is to also store information about Norwegian habitat types described based on Nature in Norway -system and establish the connections between habitats and species using them. Species trait data relevant for Norwegian species will be extracted from existing databases and other data sources. The first information from this work will be made available through 2020 and is going to be useful for research, conservation and area planning.
Mission: Implausible — Revealing rogue marine species in records across biodiversity data platforms
Authors: Nozères Claude , Kennedy Mary
Published: June 2019

Online biodiversity platforms publish datasets with graphic tools to help with quality control of submitted records, but more could be done to make the data robust for ecological analyses. Attention has focused mostly on automating tools for obvious errors, including misspelled names and synonyms, dates, or coordinates. However, a manual review of species identifications and distributions may uncover improbable records, such as a species reported in an area far from its usual range, or a rare species found in an area that has many more records of a related species. Examples are shown by constructing checklists in the Northwest Atlantic, using information from the World Register of Marine Species (WoRMS, http://www.marinespecies.org) and the Ocean Biogeographic Information System (OBIS, https://obis.org). Reviewing rare species records revealed some misidentifications, but in other instances, the rare species was valid while it was the commonly reported species that needed correction. Confirmations were obtained by comparing records from different regions, but also across platforms, including photos from observers on iNaturalist Canada (https://inaturalist.ca), genetic analyses on Barcode of Life Data systems (BOLD, http://www.boldsystems.org), and literature in the Biodiversity Heritage Library (BHL, https://www.biodiversitylibrary.org). While this exercise succeeded in validating the marine taxa of a region, it is an obvious candidate for automation in three areas: 1) flagging records of improbable taxa in a region, 2) comparing records with different types of information (e.g., specimen photos, genetic groupings, or literature records), and 3) updating users and providers when records get flagged as unusual or are modified. The first approach could be explored using online graphics tools or R software packages (rOpenSci, https://ropensci.org). The second toolset, comparing records across platforms, is partially realized with some linkages already operating between WoRMS, OBIS, BOLD, BHL, iNaturalist, and the Global Biodiversity Information Facility (GBIF, https://www.gbif.org). The third target will be the most difficult to implement, requiring reliable platform cross-linkages and specimen record identifiers to send notifications of changed status of records to both users and the original data source. Ongoing work is discussed on communicating the need to review records across platforms, with the hope that toolsets will be developed to make this task easier.
Automatic Pollen Species Image Identification
Authors: Polling Marcel , De Boer Hugo , Donders Timme , Verbeek Fons , Gravendeel Barbara
Published: June 2019

Recent data shows increasing numbers of hay fever patients, with approximately 10-30% of the population affected worldwide (Pawankar et al. 2011). This increase is most likely caused by prolonged and intensified pollen seasons which in turn have been linked to increased CO2 concentrations (Ziska et al. 2003, D'Amato et al. 2007, Albertine et al. 2014). Apart from this, especially in cities, the so-called ‘heat island effect’ enables exotic plant species to establish themselves there. In the Netherlands alone, six new species settle in cities on a yearly basis and some of these are severely allergenic (Denters 2004). Pollen concentrations in the air are currently monitored using pollen samplers that collect pollen on sticky traps. These are checked manually under the microscope, a process that requires highly trained specialists. Moreover, microscopic pollen identification rarely allows discrimination of pollen types at species or even genus level even though the allergenicity may be very different. While there has been progress in automating the microscope using machine learning, automatic microscopes have not been able to systematically identify pollen to the species level. We designed an automated approach identify a predefined set of pollen on microscopic pollen samples. We use 2D light microscope images and a confocal fluorescence microscope for 3D images to create a reference dataset of highly similar pollen species to train automated image recognition software, and compare the results. The most accurate method will be used to apply to a pollen sample time series (1970-present) to find trends in allergenic pollen species over time. Here I present the first results of this research and the challenges to overcome.
Introducing Nature 4.0: A sensor network for environmental monitoring in the Marburg Open Forest
Authors: Friess Nicolas , Bendix Jörg , Brändle Martin , Brandl Roland , Dahlke Stephan , Farwig Nina , Freisleben Bernd , Holzmann Hajo , Meyer Hanna , Müller Thomas , Opgenoorth Lars , Peter Carina , Quillfeldt Petra , Reudenbach Christoph , Seeger Bernhard , Steinmetz Ralf , Nauss Thomas
Published: June 2019

Successful conservation strategies require frequent observations and assessments of the landscape. Although expert surveys provide a great level of detail, the trade-off is the limited spatial coverage and repetition with which they are executed. Remote sensing technology can partially resolve these issues; nevertheless, it still requires experts’ experience to create conservation planning and reaction options. Nature 4.0 seeks to address these shortcomings by developing a prototype of a modular environmental monitoring system for high-resolution observation of species, habitats, and processes. The project combines expert surveys by nature conservationists, remote sensing, and a network of environmental sensors, which are integrated into stationary units as well as attached to unmanned aerial vehicles, rovers, or animals. By utilizing powerful data integration and analysis methods, Nature 4.0 will enable researchers to effectively observe landscapes through a set of diverse lenses. Time series data from the project will also inform the development of early warning indicators. Following the open-source principle, as much of the project as possible will be made publicly available, including, for instance, schematics for sensor units, algorithms for data integration or information on species occurrence. In summary, Nature 4.0 will establish new methods and protocols in the field of comprehensive environmental monitoring by combining traditional sampling, remote sensing, and automated measurement stations. The prototype system is being developed in the Marburg Open Forest, an open research, education, and development platform for environmental monitoring methods. The Marburg Open Forest brings a cross-disciplinary group of scientists together with nature conservation experts from the private sector and the state government, as well as local schools and private citizens to collaborate and bridge the gap between basic and applied environmental research. After one year, we will present the results of the initial phase and share our experience with developing Nature 4.0.
Phylogenetics Study of SalviaL. spp. Collections from the Botanical Garden of Medicinal Plants of Wroclaw Medical University
Authors: Pencakowski Bartosz , Bielecka Monika , Stafiniak Marta , Jakubowski Klemens , Matkowski Adam
Published: June 2019

Systematics of genusSalviaL. is still a field of discussion in taxonomic society. To this day, the position of certain genera fromLamiaceaeMartinov. family are considered as autonomic genera or incorporated in the genusSalviaL. as a subgenera (i.e.,PerovskiaKar.,RosmarinusL.). Moreover, some species are distinguished only by low-level differences in morphological traits and their geographic occurrence (Drew et al. 2017).

In this research, we focused on a molecular analysis of morphologically similarSalviaL. species with special attention paid toSalvia glutinosaL. andSalvia nubicolaWall. ex Sweet. All samples were collected from the Botanical Garden of Medicinal Plants of Wroclaw Medical University (http://www.obrl.umed.wroc.pl/index.html) and the Herbarium of Natural History Museum, Wroclaw University (http://www.muzeum-przyrodnicze.uni.wroc.pl/index.php).

Several DNA barcodes, includingmatK,rbcLa, ITS2 genes, andpsbA-trnH intergenic spacer, were used in maximal likelihood and Bayesian inference analyses. All sequences were amplified with Q5 High Fidelity DNA Polymerase (https://www.neb.com/) and universal primers. Amplicons were then sequenced by Sanger sequencing and analysed using the BLAST algorithm (Altschul et al. 1990). Subsequently, sequences were aligned using MAFFT v 7.409 (Katoh et al. 2005) software; poorly aligned sites were objectively eliminated with Gblocks v.0.91b (Talavera and Castresana 2007). ITS2 regions were extracted with ITSx (Bengtsson-Palme et al. 2013) software implemented on PlutoF web workbench (Abarenkov et al. 2010) to obtain ITS2 sequences without 5.8S and 26S fragments on both ends. Substitution models were identified utilizing jModelTest 2 software (Posada 2008) and basing on Bayesian information criterion (BIC) appropriate models were applied for further calculations. For maximum likelihood analyses and Bayesian inference, we implemented RAxML ver. 8.2.10 (Stamatakis et al. 2008) and MrBayes ver. 3.2.2 (Ronquist et al. 2012) respectively.

For the reconstruction of evolutionary relationship between study species, different DNA barcode combinations were applied (e.g.,matK+ITS2+psbA-trnH andrbcLa+matK+psbA-trnH). Consensus trees were compared and analysed using TreeGraph ver. 2.14 (Stöver and Müller 2010).
The Problem of Stratigraphical Time Grouping of Earth Science Data
Authors: Kröger Björn , Lintulaakso Kari
Published: June 2019

An essential aspect of earth science data is the age they represent. The age, in most cases, is not a simple time stamp measured in years, but often specified as a stratigraphic interval or unit. Numerous schemes exist for age attribution in geological data, referring to various methods of e.g. biostratigraphy, chronostratigraphy, sequence-stratigraphy, magnetostratigraphy. Furthermore, opinions about the relationships between the stratigraphical units differ from author to author and are in a steady historical flux. New stratigraphic units become established and old ones are abandoned. This is a challenge for databases that rely on fixed standards.

However, all stratigraphic schemes can be conceptualized as a system of unique names related by opinions and expressed in publications. A database (http://rnames.luomus.fi) linking the names of stratigraphic units with referenced (published) opinions would allow for the development of dynamic models for time grouping based on explicit algorithms. We will present and discuss our database approach to tackle this problem.
Considerable Progress in Russian GBIF Community
Authors: Shashkov Maxim , Ivanova Natalya
Published: June 2019

Russia is a huge gap on the open access global biodiversity map of the Global Biodiversity Information Facility (GBIF). National biodiversity data are stored in various sources including museums, herbaria, scientific literature and reports as well as in the private collections and local databases. The best known and largest of the Russian herbarium collections are the collections stored in Komarov Botanical Institute of the Russian Academy of Science (>6 M sheets) and Moscow University (>1 M sheets). The largest zoological collection is located in Zoological institute of the Russian Academy of Science, with >60 M specimens. But most of the national biodiversity data is not yet digitized. The national biodiversity portal as well as the list of Russian biodiversity data sources are still absent. Despite this, projects and other activities are implemented to mobilize a national data using international biodiversity data standards.

Currently Russia is not a GBIF member, but in the last 5 years, more than 1.6 M occurrences were published by Russian publishers through GBIF.org (69 datasets at the end of March 2019). The largest GBIF data provider in Russia is the Lomonosov Moscow State University. The Digital Moscow University Herbarium includes 971,732 specimens collected from Russia and many other countries. The Russian GBIF community is steadily expanding (Fig. 1); this is reflected in an increase in the number of publishers and published datasets. The current GBIF network infrastructure in Russia includes 5 IPT (Integrated Publishing Toolkit) installations in Saint Petersburg (two), Pushchino (Moscow region), Moscow, and Syktyvkar (Komi Republic).

Russian-language biodiversity informatics materials are collected and presented from an informal web site http://gbif.ru/ with three main sections:

data publishing through GBIF,

Russian GBIF activities, and

Russian biodiversity data sources.

data publishing through GBIF,

Russian GBIF activities, and

Russian biodiversity data sources.

Additional sections are dedicated to iNaturalist citizen science system and Russian Specify Software Project community. We provide technical helpdesk support not only for Russian publishers, but also for Russian speakers from the former USSR. The national mailing-list (via google groups) aims to provide a platform for news sharing. Now it includes >240 subscribers.

Since the end of 2014, regular biodiversity informatics events are being held in Russia. Last year, two data training courses, funded by GBIF (project ID Russia-02 - "GBIF.ru data mobilization activities") and ForBIO (Research school in biosystematics), were organized in Moscow and Irkutsk region with the participation of 29 Russian researchers. National biodiversity informatics conferences were held in Apatity (2017) and Irkutsk (2018).

We believe Russia already has a well established community that can become the basis for further development when Russia becomes a GBIF member.
Informatics in Support of Invasion Science and Policy
Authors: McGeoch Melodie
Published: June 2019

As one of the key components of biodiversity change and its associated negative consequences for society, biological invasion demands policy supported by a solid platform of data. These data must - like many other areas of evidence needed for policy - meet multiple criteria, such as effective integration across diverse data types and sources, the adoption of a broadly accepted vocabulary and mechanisms that smoothly enable the absorption, transfer and use of new data into policy reporting. With indicators of biological invasion as the endpoint of this process, the demand for such indicators has challenged the invasion science community to build and deliver such a process. Although still a work in progress, biodiversity data standards and data tools have been integral to the progress made towards delivering robust and sustainable indicators of biological invasion. They have also facilitated the integration of data that makes it possible to overcome a number of longstanding conceptual and analytical problems with estimating invasion trends. I will present some of the developments that demonstrate the advances that biodiversity informatics has enabled, connecting the science and policy on biological invasions.
Otobur™: A botanic garden data management system
Authors: Kanoglu Salih , Aydınkal Rasim
Published: June 2019

The main roles of botanic gardens are to undertake research, share information, and conserve plant biodiversity. Conservation can not only be thought of in terms of genetic resources, but also scientific knowledge and information about the plants.

There are different methods of recording data about living material in botanic gardens, ranging from the simple recording of information in handwritten books, to the use of sophisticated computer software programmes. In the case of electronically recorded information this can involve, complex construction of query sentences, that a majority of botanic garden staff are unable to write as they are not computer programmers, nor do they usually have any expertise of computer systems.

Although there are a few computer programs used to store information about plants in botanic gardens, Otobur™, is straight forward and easy to use with innovative features. Developed by us at the Nezahat Gökyiğit Botanik Bahçesi, it runs on a platform-independent online system and has an improved dashboard for real-time statistics as well as multi-language support. Its ‘just click’ query builder can readily create a detailed report and it can also send information by email to users. Example features include an estimated flowering calendar.

Otobur™ is an easy-to-use, open-source web application offering opportunities for adding other optional features.
E-learning in GBIF Capacity Activities
Authors: García Katia Cezón , Villaverde Cristina , Lujano Carmen , Russell Laura
Published: June 2019

E-learning is a training method increasingly used as it enhances opportunities for participation, allows active tracking of courses and enables wider flexibility for timetables and organization. The implementation of an e-learning platform managed by GBIF Spain was aimed at exploring other ways of creating capacity, reaching a broader audience and multiplying the impact of a well-consolidated training facility. The first platform, used by the Spanish node in 2012, was the open source tool ATutor, which was migrated to Chamilo in 2017 and is available at http://elearning.gbif.es. Since then, these platforms have hosted courses focused on biodiversity data mobilization and data use, addressing both users and data publishers. GBIF.es offers the platform to other organizations in the community so the entire GBIF network can benefit from this service, taking advantage of the already invested resources. Additionally, the GBIF Secretariat uses the platform for developing training activities in the Biodiversity Information for Development (BID) and Biodiversity Information for Asia (BIFA) programmes reaching participants in sub-Saharan Africa, the Caribbean and the Pacific, and has implemented the Biodiversity Data Mobilization course for use in other programmes such as Biodiversity Data Management Skills for Students (BioDATA) and Biodiversity Information Management and Reporting (BIMR), reaching communities in Eurasia and South-East Europe respectively. GBIF Argentina has also used it to offer a course on biodiversity data quality and publication. In this session, we will overview the GBIF.es e-learning platform, highlight some successful use cases of the virtual training tool and show how it helped GBIF Spain reach a broader community. We will also present plans for future expansion.
The Platform for Cybertaxonomy: Standards, services and tools
Authors: Güntsch Anton , Luther Katja , Müller Andreas , Kohlbecker Andreas , Plitzner Patrick , Kilian Norbert , Henning Tilo , von Mering Sabine , von Raab-Straube Eckhard , Kusber Wolf-Henning , Berendsohn Walter G.
Published: June 2019

The Platform for Cybertaxonomy (http://www.cybertaxonomy.org) is a standards-based open-source software framework covering the breadth of the taxonomic workflow, from fieldwork to publication (Ciardelli et al. 2009). It provides coupled tools for full, customized access to taxonomic data, editing and management, and collaborative team work. At the core of the platform is the Common Data Model (CDM, Müller et al. 2017), offering a comprehensive information model covering all relevant data domains: names and classifications, descriptive data (morphological and molecular), media, geographic information, literature, specimens, types, persons, and external resources.

Platform compliant software interacts via services and includes the following components:

CDM Server

Taxonomic Editor Rich Client

Web-based editors

Drupal-based and highly configurable portal software

Map services and map viewer

Xper2 descriptive data editor

Specimen search tool

Import and export modules

CDM Server

Taxonomic Editor Rich Client

Web-based editors

Drupal-based and highly configurable portal software

Map services and map viewer

Xper2 descriptive data editor

Specimen search tool

Import and export modules

Recent platform-based developments include software components for deriving formal species-level descriptions from measurements on individual specimens (Henning et al. 2018) as well as a registration system for nomenclatural acts of algae (Phycobank, https://www.phycobank.org/). Currently, about 30 portals with regional and taxonomic foci are using the Platform for Cybertaxonomy as their technical basis for capturing, managing, and publishing biodiversity data over the World Wide Web. Prominent examples are the Euro+Med Plantbase, the International Caryophyllales Network, and the Flora of Greece.
What's in this Collection Dataset? Semantic Annotation with GATE
Authors: Löffler Felicitas , König-Ries Birgitta
Published: June 2019

Semantic annotations of datasets are very useful to support quality assurance, discovery, interpretability, linking and integration of datasets. However, providing such annotations manually is often a time-consuming task . If the process is to be at least partially automated and still provide good semantic annotations, precise information extraction is needed. The recognition of entity names (e.g., person, organization, location) from textual resources is the first step before linking the identified term or phrase to other semantic resources such as concepts in ontologies. A multitude of tools and techniques have been developed for information extraction. One of the big players is the text mining framework GATE (Cunningham et al. 2013) that supports annotation rules, semantic techniques and machine learning approaches. We will run GATE's default ANNIE pipeline on collection datasets to automatically detect persons, locations and time. We will also present extensions to extract organisms (Naderi et al. 2011), environmental terms, data parameters and biological processes and how to link them to ontologies and LOD resources, e.g., DBPedia (Sateli and Witte 2015). We would like to discuss the results with the conference participants and welcome comments and feedbacks on the current solution. The audience is also welcome to provide their own datasets in preparation for this session.
Unexploited Biodiversity Data Sources: The case of airborne pollen
Authors: Ariño Arturo H. , González-Alonso Mónica , Pérez de Zabalza Anabel
Published: June 2019

With more than one billion primary biodiversity data records (PBR), the Global Biodiversity Information Facility (GBIF) is the largest and, arguably, most comprehensive and accurate resource about the biodiversity data on the planet. Yet, its gaps (taxonomical, geographical or chronological, among others) have often been brought to attention (Gaijy et al. 2013) and efforts are continuously made to ensure more uniform coverage. Especially as data obtained through this resource are increasingly being used for science, policy, and conservation (Ariño et al. 2018), drawing on every possible source of information to complement already existing data opens new opportunities for supplying the integrative knowledge required for global endeavors, such as understanding the global patterns of ecosystem and environment changes.

One such potential source that exists, but so far has experienced little integration, is the vast body of data acquired through airborne particle monitoring systems (for example, the European Aeroallergen Network, EAN). A large portion of pollen data is comprised of quantitative sampling of airborne pollen collected through semi-automated spore traps throughout the world. Its main use is clinical, as it forms the basis of the widespread allergen forecast bulletins. While geolocating the source of airborne pollen is fraught with obviously large uncertainty radii, the time and taxon components of the PBR remain highly precise and are therefore fit for many other uses (Hill et al. 2010). Presence data, and under certain circumstances, frequency data inferred from pollen counts have been often proposed as an excellent proxy for past climate change assessments as far back as the start of the Holocene (Mauri et al. 2015) and might therefore also be possibly used for current climate change detection.

We call for a concerted effort throughout the palynological community to first increase harmonizing, and then eventually standardizing, pollen data acquisition through the adoption of Darwin Core (DwC) and, eventually, DwC extensions to

mine current data and

pipeline future airborne pollen data as PBR.

mine current data and

pipeline future airborne pollen data as PBR.

Success in this endeavor may contribute to a better understanding of global change.
The Importance of Storing and Delivering Geochemical Data for Earth Science Collections
Authors: Miller Giles , Lehnert Kerstin
Published: June 2019

The composition and state of the earth’s lithosphere through time has had profound effect on past and present biodiversity and will continue to do so into the future. Environments ranging from deep sea hydrothermal vents to active continental volcanic centres provide a wide range of ecosystems that have shaped the planet we know. Catastrophic events relating to movements of the lithosphere and events deep in the mantle have also caused major biodiversity changes such as mass extinctions. Our museum collections contain rock and fossil specimens collected from many of these environments and suites of samples specifically collected in order to better understand the evolution of our planet. Requests to carry out geochemical investigations on these samples are common and a large amount of data is generated as a result. Currently there are no natural history collections management systems tailored towards recording and delivering these datasets and the result is that the data is recorded in various distributed systems and cannot be easily assessed and used. It is important for these analyses on our museum collections to be delivered in a standard way so that the importance and relevance of these collections can be demonstrated and large datasets generated to answer big questions regarding the geological evolution of our planet. Examples of these questions include “how and when will volcanic eruptions will occur?” and “what has been the role of volcanism during mass extinction?”. Other geochemical studies such as oxygen isotope studies have been carried out on museum collections in order to investigate past oceanic environments and the effects of changes in climate on our oceans. Geochemical data aggregators such as EarthChem have made great strides in working towards international data standards and providing portals for delivering this type of data. As we progress towards one European Collection (DiSSCo) it is vital that we recognise the importance of these natural history collections related geochemical datasets and include delivering them on the general roadmap.
The Catalogue of Life: Assembling data into a global taxonomic checklist
Authors: Ower Geoffrey , Roskov Yuri
Published: June 2019

Producing a global taxonomic checklist of all species is essential for indexing biodiversity data, and for providing the basic knowledge needed to study, manage, and conserve biological diversity. The Catalogue of Life (CoL) aims to provide a global taxonomic checklist of all species, and includes 1.9 million species names in the 2019 annual edition. The task of assembling data into CoL is complex and requires reformatting data, quality assurance testing, and collaborating with data providers to resolve detected taxonomic conflicts. Global Species Databases (GSDs) are submitted in a wide variety of data formats to CoL by hundreds of taxonomic experts and institutions. Submitted data are reformatted to a standard data submission format: CoL Standard Dataset (ACEF), DarwinCore, or CoLDP. A series of standardized data integrity checks are run to detect and resolve frequently occurring data quality problems including character encoding corruption, non-Latin characters in scientific names, missing parents, duplicated and homonymic names within the GSD and among other GSDs, split taxonomic groups that have been assigned to multiple parent taxa, and other issues. The process and challenges of assembling data into the Catalogue of Life, and future directions of the project in migrating to CoL+ infrastructure will be discussed.
Challenges of Integrating and Curating Nomenclatural and Taxonomic Data in the World Checklist of Vascular Plants
Authors: Turner Robert , Govaerts Rafaël
Published: June 2019

The World Checklist of Vascular Plants (WCVP) is the Royal Botanic Gardens (RBG) Kew’s global names and taxonomy output. The underlying data sources, the International Plant Names Index (IPNI), the World Checklist of Selected Plant Families (WCSP), and the World Checklist of Selected Plant Families – in Review (WCSP – In Review) are actively curated by a dedicated editorial team, who manage contributions from a wide range of international partners. WCVP is the intersection between IPNI and WCSP/WCSP-In Review and provides the names and taxonomy backbone for Plants of the World Online (POWO) – the web portal bringing Kew scientific data online. WCSP contains the peer reviewed taxonomic data covering about half of all vascular plant families. The taxonomy presented in WCSP is currently widely used, with most authoritative web resources on plants using the WCSP data either directly or indirectly. WCVP will bring this together with the remaining families currently in the ‘In-Review’ database. IPNI is a nomenclatural listing of all effectively published taxonomic acts for Plant Names (new species, new combinations, new names at rank of Family down to infraspecific). It is a project that has been continually compiling lists of new plant names since 1895. It provides the basis of many external plant names databases including Tropicos and GBIF and a point of contact for users to ask questions on plant nomenclature, with a public facing access to the nomenclatural expertise at Kew. The database is actively maintained, edited and added to daily.

This presentation will cover:

The integration of the resources and how the integrated product will be presented online

How the integrated product supports outputs like POWO

Experiences from the data integration process (the matching tools iteratively developed and tested in real world circumstances by dedicated staff)

The development of programmatic API access and names matching tools

The drafting of a data paper describing the WCVP (with access to a full download)

The integration of the resources and how the integrated product will be presented online

How the integrated product supports outputs like POWO

Experiences from the data integration process (the matching tools iteratively developed and tested in real world circumstances by dedicated staff)

The development of programmatic API access and names matching tools

The drafting of a data paper describing the WCVP (with access to a full download)
Making LTER Data FAIR: A workbench using DEIMS datasets and GBIF Tools
Authors: Pando Francisco , Bonet Francisco
Published: June 2019

DEIMS-SDR (Dynamic Ecological Information Management System - Site and dataset registry, Wohner et al. 2019) is one of the largest repositories of long-term ecological research (LTER) datasets. It provides sophisticated searching tools by metadata elements and identifiers for all the 930 contained datasets, most of them from European sites. Whereas datasets' metadata are highly structured and searchable, datasets themselves have little standardization in terms of content, identifiers or license, making data integration difficult or cumbersome. Adopting the data FAIR guiding principles(Wilkinson et al. 2016) for LTER data would result in better data integration and reutilization to support knowledge discovery and innovation in ecological research.

The Global Biodiversity Information Facility (GBIF 2019a). is the largest repository of species distribution data in the world, providing access to more than a billion records from over 43,000 datasets. GBIF is a good example of FAIR principles implementation: GBIF data is highly standardized, using Darwin Core (Wieczorek et al. 2012) for data and ecological metadata language (EML, Fegraus et al. 2005) for metadata, allowing record-level search; and has implemented globally unique and persistent identifiers for datasets and downloads. Relevant in this context is that GBIF has recently introduced a new data format intended for monitoring projects and sampling event protocols (GBIF 2019b).

In this presentation, we explore the suitability of GBIF data formats and workflows to serve LTER datasets, and the work it may take to transform typical LTER datasets into these formats. For this exercise, we use some datasets available via the DEIMS platform, corresponding to the same territory, (Sierra Nevada, Spain (e.g. Bonet 2016, Bonet 2018) and transform them into the GBIF's sample-based Event core publish them in the GBIF data network, and then perform an analysis to assess how the standardized datasets work in practice, both among themselves and also with typical “occurrence-based” GBIF datasets. Finally, we discuss our findings and make recommendations for the GBIF and LTER communities.
Actualité de l’approche sociotechnique
Authors: Michelot Christian , Ortsman Oscar
Published: June 2019

La question de l’autonomie est au cœur de l’approche sociotechnique de l’organisation. Cet article rappelle les grandes étapes et les principaux acquis scientifiques de ce courant avant d’en montrer l’actualité par la présentation d’une « opération miroir » dans une organisation non gouvernementale. Cette intervention autorise une hypothèse plus générale sur les soubassements des nouvelles formes d’organisation : elles ne sont plus portées par le modèle coopératif du mouvement ouvrier mais procèdent d’un infléchissement de la structure charismatique des entreprises.
D’un modèle de gouvernance classique aux modalités démocratiques de la SCOP : réalités cliniques de cette transition
Authors: Bétin Pascale , Bobillier-Chaumon Marc-Éric , Cuvillier Bruno
Published: June 2019

Cette contribution s’appuie sur l’observation en immersion d’un collectif d’ouvriers qui s’est engagé dans la lutte pour sauver son usine avec pour projet de la reprendre en scop . Cette lutte – et donc la période d’observation – aura duré onze mois (d’avril 2016 à mars 2017). Cette situation observée et analysée par le prisme des concepts et méthodologies de la clinique du travail a permis de révéler que ce passage d’un modèle à un autre n’est pas franc. Sous une apparente union collective, l’idéal démocratique visé ici – c’est-à-dire le modèle participatif de la scop  – n’est peut-être pas un objet d’union toujours suffisamment fort pour absorber d’emblée les défaillances du système classique dont on sort. Cet article propose l’analyse de ce phénomène et pose la question de l’accompagnement de ces collectifs en transition vers des modèles organisationnels plus démocratiques.
Le sens de l’entrepreneuriat de soi sur les places de marché numériques de bricolage
Authors: Dujarier Marie-Anne
Published: June 2019

Cet article porte sur les places de marché numériques saisies comme entreprises d’entrepreneurs de soi. Une enquête sociologique dans le secteur du bricolage, par analyse documentaire, observations et entretiens cliniques, détaille les caractéristiques et singularités de ce secteur. L’article montre ensuite le sens de cette pratique pour les travailleurs, alors que leurs conditions de travail, revenus et sécurité y sont défavorables. Selon leur trajectoire, leur place sur le marché du travail et leurs projets, cinq idéaux types apparaissent qui ont en commun la quête de revenus principaux, secondaires ou ponctuels, par l’achat de clientèle.
Faire l’expérience de la contribution. Une recherche-action sur l’intégration des nouveaux dans l’entreprise collaborative
Authors: Brugeilles Frédéric , Brochot Clément
Published: June 2019

Cet article vise à rendre compte de la façon dont s’opère l’intégration des nouveaux dans les entreprises collaboratives – à partir des résultats d’une recherche-action menée pour l’Agence nationale pour l’amélioration des conditions de travail auprès de cinq entreprises de conseil et de service, au sein d’un cluster d’entreprises. Pour les entreprises étudiées, l’intégration est un enjeu fort et qui présente certaines difficultés du fait d’un turnover important et de changements permanents à l’œuvre dans l’organisation. Ainsi, l’intégration des nouveaux s’opère plutôt de manière informelle, beaucoup dans l’oralité, avec peu de process d’accueil – ce qui correspond bien à la dynamique organisationnelle de ces entreprises, dans le changement. La contribution apparaît comme un enjeu central de ces organisations – au-delà du fait de participer à la vie de l’organisation, chacun est sollicité pour contribuer, quasiment personnellement, à développer et faire vivre le modèle. La contribution porte à la fois sur l’activité de travail et le mode de fonctionnement. Les nouveaux doivent aussi contribuer à alimenter le projet politique des organisations en partageant les valeurs de démocratie de l’économie sociale et solidaire et en se projetant parfois comme futurs associés de leurs entreprises. La contribution se réalise souvent malgré soi, dans la mesure où l’intégration des nouveaux est l’occasion pour les anciens d’expliciter, de réinventer et d’actualiser le modèle organisationnel et les pratiques. L’enjeu de l’intégration des nouveaux – et de l’intégration professionnelle en général – consiste à faire l’expérience ensemble d’une double dynamique de participation à une aventure collective et de contribution individuelle à ce collectif.
Les jeux du pouvoir dans l’entreprise libérée
Authors: Cultiaux John , Léon Xavier
Published: June 2019

L’entreprise libérée prétend concilier deux enjeux : accroître la productivité des travailleurs en les inscrivant dans une dynamique plus émancipatrice. De quelle manière et avec quelles limites cette pratique repensée de l’exercice du pouvoir se déploie-t-elle au quotidien ? Finalement, que devient le pouvoir et fait-il réellement barrage aux processus de domination organisationnels ? Sinon, sur quels obstacles prennent appui ces processus ? S’inscrivant dans le champ de la sociologie clinique, cet article propose d’investiguer ces questions à partir de deux recherches-interventions réalisées auprès d’une entreprise du secteur de la distribution et d’une association d’aide aux sans-abris. À rebours des prétentions émancipatrices annoncées, l’analyse exploratoire montre que cette recomposition peut, dans les conditions observées, contribuer au renforcement d’un pouvoir autoritaire et favoriser l’exercice d’un pouvoir « débridé ».
Bible et péché
Authors: Collange Jean-François
Published: June 2019

Résumé L’étude montre qu’à travers les multiples variations de l’usage des termes hébreux et grecs correspondant aux mots « péché/pécher » dans le Premier et le Nouveau Testaments se dégagent quelques traits caractéristiques : le péché n’est pas tant évoqué de façon culpabilisante que pour insister sur le pardon qu’apporte un Dieu miséricordieux ; il concerne moins des actes particuliers que la condition ou l’état général d’une humanité livrée au mal et au malheur, état dont elle se trouve largement responsable ; dès lors le « péché des péchés » revient à tenter d’échapper à cette responsabilité et à la rejeter sur autrui, brisant par là même la solidarité humaine, gage de toute vie apaisée et bonne.
Évolution du rendement du système de retraite entre générations
Authors: Dubois Yves , Marino Anthony
Published: June 2019

S’il constitue un indicateur naturel dans le cas d’un système en capitalisation, le niveau de rendement peut également être calculé s’agissant d’un système en répartition comme en France. Dans cette étude, nous calculons et comparons les taux de récupération dont bénéficient plusieurs générations (1950 à 1985). Cet indicateur de rendement est décomposé en deux sous-indicateurs, l’un de générosité (le taux de prestation), l’autre d’effort contributif (le taux de prélèvement). Ces trois indicateurs sont calculés sur le cycle de vie, c’est-à-dire en considérant les durées de carrière et de service et non pas la seule pension perçue à la liquidation. Pour expliquer la diminution du taux de récupération entre ces générations, nous examinons plus spécifiquement chacun de ses trois déterminants. Le premier correspond au financement du système de retraite, et notamment l’essor d’exonérations et de nouvelles recettes autres que les cotisations. Le deuxième déterminant est celui du taux de croissance économique, qui influe fortement sur le rendement et la soutenabilité du système de retraite. Cette dépendance nous amène d’ailleurs à nous interroger sur le choix de taux d’actualisation, crucial s’agissant d’indicateurs calculés sur le cycle de vie. Enfin, le dernier déterminant renvoie au partage de la vie entre périodes de scolarité, d’activité et de retraite, ce partage ayant été fortement modifié sous l’effet des réformes successives
Les nouveaux déterminants de la demande de sécurité sociale : le cas de la région d’Alger
Authors: Merouani Walid , Hammouda Nacer-Eddine , El Moudden Claire
Published: June 2019

L’objectif de cet article est de comprendre les raisons du déficit en couverture sociale de l’Algérie. Selon l’Office national des statistiques (ONS, 2013), 73 % de la population occupée du secteur privé ne possèdent pas de sécurité sociale. Ce système offre pourtant juridiquement une couverture contre tous les risques sociaux (maladie, maternité, maladie professionnelle, accident de travail, invalidité, décès et retraite). Il est obligatoire pour toutes les catégories de la population active occupée. Malgré cela, la demande d’assurance sociale reste faible. Pour expliquer ce phénomène, nous étudions tout d’abord, les fondements micro-économiques de la protection sociale qui nous fournissent les principales variables déterminantes de la demande d’assurance. Cela nous permet, dans un second temps, d’élaborer un questionnaire utilisant des méthodes expérimentales pour mesurer ces variables. Enfin, nous testons les effets de ces variables sur la demande d’assurance sociale en Algérie. Cet article présente ainsi les premiers résultats de notre enquête.