Classical and quantum q-deformed physical systems

On the basis of the non-commutative q-calculus, we investigate a q-deformation of the classical Poisson bracket in order to formulate a generalized q-deformed dynamics in the classical regime. The obtained q-deformed Poisson bracket appears invariant under the action of the q-symplectic group of transformations. In this framework we introduce the q-deformed Hamilton's equations and we derive the evolution equation for some simple q-deformed mechanical systems governed by a scalar potential dependent only on the coordinate variable. It appears that the q-deformed Hamiltonian, which is the generator of the equation of motion, is generally not conserved in time but, in correspondence, a new constant of motion is generated. Finally, by following the standard canonical quantization rule, we compare the well known q-deformed Heisenberg algebra with the algebra generated by the q-deformed Poisson bracket.Comment: 9 pages, accepted for publication in "The European Physical Journal C

Towards an Ecological Trait-data Standard

Trait-based approaches are widespread throughout ecological research, offering great potential for trait data to deliver general and mechanistic conclusions. Accordingly, a wealth of trait data is available for many organism groups, but, due to a lack of standardisation, these data come in heterogeneous formats. We review current initiatives and infrastructures for standardising trait data and discuss the importance of standardisation for trait data hosted in distributed open-access repositories. In order to facilitate the standardisation and harmonisation of distributed trait datasets, we propose a general and simple vocabulary as well as a simple data structure for storing and sharing ecological trait data. Additionally, we provide an R-package that enables the transformation of any tabular dataset into the proposed format. This also allows trait datasets from heterogeneous sources to be harmonised and merged, thus facilitating data compilation for any particular research focus. With these decentralised tools for trait-data harmonisation, we intend to facilitate the exchange and analysis of trait data within ecological research and enable global syntheses of traits across a wide range of taxa and ecosystems

The Journey to a TDWG Mappings Task Group and its Plans for the Future

Some Biodiversity Information Standards (TDWG) standards have had mappings to other standards for years or even decades. However each standard is using its own approach to documenting those mappings, some are incomplete and often hard to find. There is no TDWG recommended approach for how mappings should be documented, like the Standards Documentation Standard (SDS) does for the standards themselves. During TDWG 2022 in Sofia, Bulgaria, the topic of mapping between standards was mentioned several times throughout the conference, which led to an impromptu discussion about standards mappings at the Unconference slot on the last conference day. Afterwards a dedicated Slack channel within the TDWG Slack workspace was added to continue the conversation (#mappings-between-standards). During further discussions, both within the Technical Architecture Group (TAG) of TDWG and during separate video conferences on the topic, it was decided to form a dedicated task group under the umbrella of the TAG. This task group is still in the process of formation. The goal of the group is to review the current state of mappings for TDWG standards, align approaches by the different standards to foster interoperability and give recommendations for current and future standards on how to specify mappings. Further work to define the strategy and scope for achieving these goals is needed, particularly to gain community input and acceptance. Consideration has been given to a range of possible types of mappings, which serve the different use cases and expectations for mappings such as machine actionability and improved documentation of the TDWG standards landscape to aid user understanding and implementation. In this talk we will show the work that has already been done, outline our planned steps and invite the community to give input on our process

Using Wikibase as a Platform to Develop a Semantic TDWG Standard

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

The ABCD/DwC Alignment Working Group: Presenting the results from the TDWG 2020 Workshop

ABCD (Access to Biological Collection Data, Holetschek et al. 2012) and DwC (Darwin Core, Wieczorek et al. 2012), are TDWG standards for documenting the occurrence of organisms in nature and/or collections, whether as specimens or observations (i.e., unit-level data), and are used for a wide range of applications. Since 2019, the working group has been investigating ways to enable a closer link and integration of these standards (Blum et al. 2019).This presentation will summarize the results of the September 2020 workshop of the ABCD/DwC Alignment Working Group as part of the TDWG 2020 Virtual Conference Working Sessions Week. Prior to the workshop, we will have collected use cases for the application of the standards, which will have been analysed and discussed in the workshop itself. On this basis, smaller working groups will have been formed to address technical, organisational, and sociological aspects relevant for an alignment and future maintenance of ABCD and DwC.The results of these working groups, as well as the general summary of the workshop and the planned next steps of the ABCD/DwC Alignment Working Group will be shown and discussed in this presentation

NFDI4Biodiversity: a German infrastructure for biodiversity data

Digital data have become an indispensable basis for biodiversity research. Sustainable curation, archiving, accessibility and integrability according to the FAIR principles ("Findable, Accessible, Interoperable and Reusable", Wilkinson et al. 2016) are essential for re-use to answer pressing questions in a rapidly changing environment.As part of the German multidisciplinary National Research Data Infrastructure (NFDI), the NFDI4Biodiversity consortium with 49 partners, spanning a broad spectrum from academia, to agencies, learned societies, and citizen science, has set itself the goal of providing a sustainable data infrastructure for biodiversity research. NFDI4Biodiversity builds on the German Federation for Biological Data (GFBio) project (2014–2021) and the GFBio e.V. founded in it, both organisationally and in the provision of services. These include a data submission and archiving system, support for the creation of data management plans and certification, portal functions with extensive data visualization and terminology services flanked by helpdesk, support and outreach activities*1 (Diepenbroek et al. 2014).Within the framework of NFDI4Biodiversity, these services will be expanded, based on (and calibrated by) the requirements of 23 concrete use cases from manifold biodiversity research domains. A central new component is the development of a capable multi-cloud platform, the "Research Data Commons" (RDC) where data can be aggregated, semantically linked and enriched with external services (Glöckner et al. 2020).Alongside the development of the services, the potential for joint use of standards and service components will be exploited through cooperation with existing data infrastructures. In addition to other NFDI consortia, international infrastructures and comparable national initiatives will play a special role; this process was already started with a symposium during the 2019 Biodiversity Next conference

State of the (Re-)Ratification of ABCD 2.06 and ABCD EFG under the SDS Guidelines

ABCD (Access to Biological Collection Data, Holetschek et al. 2012) 2.06 was ratified by Biodiversity Information Standards (TDWG) in September 2005. In 2017, TDWG ratified the Standards Documentation Standard (SDS, Vocabulary Maintenance Specification Task Group 2017), which is a set of regulations and guidelines on how TDWG standards should be structured and documented. Since then, ABCD has been classified with “2005 standards” on the TDWG standards website. However, with the planned ratifications of the ABCD Extension for Geoscience (ABCD EFG, Petersen et al. 2018) and the more semantic ABCD 3.0 (Fichtmueller et al. 2019), it became necessary to also ratify ABCD 2.06 under the SDS rules.In this talk, we will report on the progress of the ratification processes, both for ABCD 2.06 and ABCD EFG. In particular we want to address the specific challenges that arose from fitting existing XML schemas into the SDS structure and documenting them accordingly

Deliverable D1.3 Best practice manual for findability, re-use and accessibility of infrastructures

United and coordinated efforts of biodiversity data infrastructures are needed to bring together various data forms from many different scientific areas. Biodiversity data are considered of great importance and use when they form a network of knowledge that can be seamlessly integrated and presented to various audiences, promoting both research and education. The Biodiversity Community Integrated Knowledge Library (BiCIKL) project seeks to maximise the potential of integrated data sources by striving to connect fragmented data derived from biological, paleontological, and geological specimens and collections, as well as all derived information such as literature in the form of taxonomic treatments, research papers etc., taxonomic information and molecular sequences provided by these infrastructures, under the umbrella of common digital practices and policies in curation, data sharing and open data access over different scientific fields. One of the main goals of BiCIKL is to create bi-directional links between various data types, a process enabled by: a) the adoption of globally unique and persistent identifiers upon agreement among all stakeholders, that link to digital specimen objects, collections, taxonomic treatments, people, sequence data and taxa, and b) implementation of the best practices for the generation, management and curation of interlinked data by the host infrastructures. At the same time, infrastructures should be readily discoverable and accessible by end users, providing data that enable re-usability. In this manual we give an overview of the best practices and their associated recommendations for infrastructures on making the most out of their services and data, for establishing a network of knowledge with other infrastructures, for servicing researchers, data providers and other end users. These guidelines have been developed in collaboration with the infrastructures through Technical RI Forum meetings organised in the context of the BiCIKL project. Practices and recommendations were divided into six categories: 1) modalities of access, 2) building communities and trust, 3) technology and standards, 4) versioning of APIs and their data, 5) bi-directional linking between infrastructures and 6) API design patterns and naming conventions. A second division into three user groups (Infrastructures, Data providers, Users e.g. Researchers, Developers and Citizen scientists) is presented in Appendix I

European Taxonomists in Profile: A Data-Driven Approach

This presentation focuses on the service aspect of taxonomy in Europe, encompassing the description, identification, and nomenclature of taxa. This aspect of taxonomy supports all biological research, and working taxonomists contribute to it in different degrees (Dayrat 2005). Taxonomy also serves as a research discipline, emphasising the evolutionary aspects of biodiversity, but this study specifically investigates only the supply of taxonomists as a service and compares this with the demand for taxonomy, which arises from policy that requires information on European biodiversity for development or implementation.To profile taxonomists, we adopt an automated approach using OpenAlex, an open bibliography of scholarly publications, to extract comprehensive data on authors, their affiliated institutions, and their respective taxa of expertise. This automated approach avoids the well-known biases of self-reported questionnaires, thus ensuring robust coverage across all taxa, and minimising potential geographic, gender and demographic biases.In addition to analysing the current availability of taxonomic expertise (supply side), this study explores the gaps in taxonomic expertise by examining significant taxa from research and policy perspectives (demand side). Leveraging datasets such as the list of invasive species on the horizon for Europe (Roy et al. 2018), the Crop Wild Relative Data section of the U.S. National Plant Germplasm System (USDA 2023) and the International Union for Conservation of Nature's Red List of Threatened Species (IUCN 2022), we assess the demand for taxonomic expertise.A flow diagram (Fig. 1) illustrates our step-by-step methodology. Beginning with data extraction from OpenAlex, we categorised and analysed more than 650 taxonomic journals published over the past ten years. We filtered these for relevant papers only from European institutions. This resulted in a subset of 31 thousand publications from which we identified 44 thousand authors, and were able to map their taxonomic expertise and their geographic spread. This comprehensive workflow provides detailed demographic data directly derived from bibliographic information, extending on the Red List of Insect Taxonomists (Hochkirch et al. 2022) and enabling repeatable analyses to monitor trends and changes over time. For example, we can track the usage of ORCID identifers by European taxonomists, which we calculate is currently at 64%.By considering the demand side rather than assuming equal policy importance across all taxa, our study offers nuanced insights into the contribution of taxonomists in addressing conservation and policy needs in Europe. Furthermore, by highlighting impacts, challenges, and potential solutions, we underscore the significance of taxonomy as a vital service. The recommendations aim to prioritise taxonomy, enhance its contributions to biodiversity conservation efforts, and provide guidance to policymakers, researchers, and stakeholders invested in sustaining Europe's rich biodiversity

Deliverable D1.3 Best practice manual for findability, re-use and accessibility of infrastructures

United and coordinated efforts of biodiversity data infrastructures are needed to bring together various data forms from many different scientific areas. Biodiversity data are considered of great importance and use when they form a network of knowledge that can be seamlessly integrated and presented to various audiences, promoting both research and education. The Biodiversity Community Integrated Knowledge Library (BiCIKL) project seeks to maximise the potential of integrated data sources by striving to connect fragmented data derived from biological, paleontological, and geological specimens and collections, as well as all derived information such as literature in the form of taxonomic treatments, research papers etc., taxonomic information and molecular sequences provided by these infrastructures, under the umbrella of common digital practices and policies in curation, data sharing and open data access over different scientific fields. One of the main goals of BiCIKL is to create bi-directional links between various data types, a process enabled by: a) the adoption of globally unique and persistent identifiers upon agreement among all stakeholders, that link to digital specimen objects, collections, taxonomic treatments, people, sequence data and taxa, and b) implementation of the best practices for the generation, management and curation of interlinked data by the host infrastructures. At the same time, infrastructures should be readily discoverable and accessible by end users, providing data that enable re-usability. In this manual we give an overview of the best practices and their associated recommendations for infrastructures on making the most out of their services and data, for establishing a network of knowledge with other infrastructures, for servicing researchers, data providers and other end users. These guidelines have been developed in collaboration with the infrastructures through Technical RI Forum meetings organised in the context of the BiCIKL project. Practices and recommendations were divided into six categories: 1) modalities of access, 2) building communities and trust, 3) technology and standards, 4) versioning of APIs and their data, 5) bi-directional linking between infrastructures and 6) API design patterns and naming conventions. A second division into three user groups (Infrastructures, Data providers, Users e.g. Researchers, Developers and Citizen scientists) is presented in Appendix I