Biodiversity Information Science and Standards最新文献

{"title":"FAIR but not Necessarily Open: Sensitive data in the domain of biodiversity","authors":"Patricia Mergen, S. Meeus, F. Leliaert","doi":"10.3897/biss.7.112296","DOIUrl":"https://doi.org/10.3897/biss.7.112296","url":null,"abstract":"In the framework of implementing the European Open Science Cloud (EOSC), there is still confusion between the concept of data FAIRness (Findable, Accessible, Interoperable and Re-usable, Wilkinson et al. 2016) and the idea of open and freely accessible data, which are not necessarily the same. Data can indeed comply with the requirements of FAIRness even if their access is moderated or behind a paywall. Therefore the motto of EOSC is actually “As open as possible, as closed as necessary”. This confusion or misinterpretation of definitions has raised concerns among potential data providers who fear being obligated to make sensitive data openly accessible and freely available, even if there are valid reasons for restrictions, or to forfeit any charges or hamper profit making if the data generate revenue. As a result, there has been some reluctance to fully engage in the activities related to FAIR data and the EOSC.\u0000 When addressing sensitive data, what comes to mind are personal data governed by the General Data Protection Regulation (GDPR), as well as clinical, security, military, or commercially valuable data protected by patents. In the domain of biodiversity or natural history collections, it is often reported that these issues surrounding sensitive data regulations have less impact, especially when contributors are properly cited and embargo periods are respected. However, there are cases in this domain where sensitive data must be considered for legal or ethical purposes. Examples include protected or endangered species, where the exact geographic coordinates might not be shared openly to avoid poaching; cases of Access and Benefit sharing (ABS), depending on the country of origin of the species; the respect of traditional knowledge; and a desire to limit the commercial exploitation of the data. The requirements of the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity, as well as the upcoming Digital Sequence Information regulations (DSI), play an important role here. The Digital Services Act (DSA) was recently adopted with the aim of the protection of the digital space against the spread of illegal content, which sets the interoperability requirements for operators of data spaces. This raises questions on the actual definition of data spaces and how they would be affected by this new European legislation but with a worldwide impact on widely used social media and content platforms such as Google or YouTube.\u0000 During the implementation and updating activities in projects and initiatives like Biodiversity Community Integrated Knowledge Library (BiCIKL), it became clear that there is a need to offer a secure data repository and management system that can deal with both open and non-open data in order to effectively include all potential data providers and mobilise their content while adhering to FAIR requirements.\u0000 In this talk, a","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"61 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76593348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integration of Ecosystem Services and Habitats into the Biodiversity Atlas Austria","authors":"Tanja Lumetsberger, Georg Neubauer, Reinhardt Wenzina","doi":"10.3897/biss.7.112315","DOIUrl":"https://doi.org/10.3897/biss.7.112315","url":null,"abstract":"The Biodiversity Atlas Austria (“Biodiversitäts-Atlas Österreich”) is a data portal to explore Austria’s biodiversity. It is based on the open-source infrastructure of the Atlas of Living Australia (ALA) and was launched with support of the Living Atlas (LA) community in late 2019 by the Biodiversity Hub of the University of Continuing Education Krems funded by the Government of Lower Austria. At present, it stores more than 8.5 million species occurrence records from various data partners and institutions and is available in both English and German. The Atlas is running on two virtual machines with 4 TB storage and is hosting many of the ALA-developed tools and services such as collectory, biocache, biodiversity information explorer, regions, spatial portal, sensitive data service, lists, images, and dashboard.\u0000 In the project “ÖKOLEITA” (2021-2023), two new tools were developed within the existing LA infrastructure and will be launched in late 2023 to allow users to deal with ecosystem services and habitat data.\u0000 The “ecosys”-tool will allow management, visualization, and analysis of ecosystem services by uploading different (raster or vector) TIFF files containing mapped ecosystem services to the geoserver. Users will be able to inspect various ecosystem services at a specific geolocation or compare different geolocations or a transect on their respective ecosystem service potential. The ecosystem service values are presented on the one hand as pictograms, where the value is transformed into quintiles, orienting on the work by Schreder et al. (2018), and as bar chart showing the true values.\u0000 The “habitat” tool will store and manage datasets of habitat mappings (shapefiles) and allow users to spatially explore those various habitat mappings on a map. Users will be able to search for specific habitats across all datasets or a specific one and get all occurrences of this habitat type returned. Through linkage to the biocache, a click on a specific area reveals the list of species found within that habitat recording, as well as all the species occurrences within that area stored in the database. A “habitat backbone” of the most used habitat classifications in Austria will allow dealing with habitat mappings that use different classifications.\u0000 Both tools are integrated into the Living Atlases infrastructure and communicate with the other tools and services of the Biodiversity Atlas Austria (Fig. 1). They share a common administration back-end but have different front-ends, where the users can explore the ecosystem services and habitats spatially and in connection with species occurrence records and other contextual information.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84171243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From the Shadows to the Spotlight: Unveiling Nepal's hidden kingdom of mushrooms and lichens through digitization","authors":"Shiva Devkota","doi":"10.3897/biss.7.112376","DOIUrl":"https://doi.org/10.3897/biss.7.112376","url":null,"abstract":"The digitization of herbarium collections has brought forth a transformative journey, transitioning Nepal's hidden kingdom of mushrooms and lichens from the shadows into the spotlight. Through a collaborative work within the framework of Global Biodiversity Information Facility's Biodiversity Information Fund for Asia (GBIF-BIFA), involving the herbaria (KATH: Nepal's National Herbarium and Plant Laboratories and TUCH: Natural History Museum, Tribhuvan University, Nepal), and the research institute, Global Institute for Interdisciplinary Studies (GIIS), a successful unveiling of Nepal's mycological treasures has been achieved through digital means. A comprehensive digitization effort has resulted in the complete digitization of 3,971 mushroom specimens and 2,462 lichen specimens, illuminating a wealth of information for researchers, citizen scientists, and the general public. GBIF and the online database maintained by Nepal's National Herbarium and Plant Laboratories, Department of Plant Resources, serve as the gateway to this work (KATH 2021). Prior to this work, the specimens resided in the shadows, lacking the recognition they deserved. Through meticulous collection management, sorting, curation, and labeling, their secrets were unveiled, and their stories brought to our fingertips. These previously obscured specimens now possess registered individual catalogue numbers, allowing the quantification of Nepal's fungal wealth within the participating institutions. This project serves as a testament to the vital role of capturing available field-level data, preserving specimens, and harnessing the power of digitization to showcase Nepal's mycological and lichenological wonders to a global audience. Meanwhile, it has also emphasized the significance of sharing this knowledge and fostering appreciation for the overlooked world of mushrooms and lichens.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91252599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Towards Improved Data Flows for the Management of Invasive Alien Species and Wildlife: A LIFE RIPARIAS use case","authors":"Lien Reyserhove, Pieter Huybrechts, J. Hillaert, T. Adriaens, B. D'hondt, Damiano Oldoni","doi":"10.3897/biss.7.112386","DOIUrl":"https://doi.org/10.3897/biss.7.112386","url":null,"abstract":"Invasive alien species (IAS) are recognised as a major threat to biodiversity. To prevent the introduction and spread of IAS, the European Union Regulation (EU) 1143/2014 imposes an obligation on Member States to both develop management strategies for IAS of Union Concern and report on those interventions. For this, we need to collect and combine management data and streamline management actions. This is still a major challenge: the landscape of IAS management is diverse and includes different authorities, managers, businesses and non-governmental organizations. Some organizations have developed their own specific software applications for recording management actions. For other organizations, such a software system is lacking. Their management data are scattered, not harmonized, and often not openly available. For EU reporting, a workflow is needed to centralize all information about the applied management method, management effort, cost, effectiveness and impact of the performed actions on other biota or the environment. At this moment, such a workflow is lacking in Belgium.\u0000 One of the aims of the LIFE RIPARIAS project is to set up a workflow for harmonizing IAS management data in Belgium. Based on the input from the IAS management community in Belgium, we were able to:\u0000 \u0000 \u0000 \u0000 draft a community-driven data model and exchange format called manIAS (MANagement of Invasive Alien Species, Reyserhove et al. 2022), and\u0000 \u0000 \u0000 identify the minimal requirements a software application should have for being successfully used in the field (Hillaert et al. 2022).\u0000 \u0000 \u0000 \u0000 draft a community-driven data model and exchange format called manIAS (MANagement of Invasive Alien Species, Reyserhove et al. 2022), and\u0000 identify the minimal requirements a software application should have for being successfully used in the field (Hillaert et al. 2022).\u0000 In this presentation, we will explore both outputs, the lessons learned and the way forward. With our work, we aim to facilitate coordination and transfer of information between the different actors involved in IAS and wildlife management, not only on a Belgian scale, but also within an international context.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85347480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EMODnet Biology: Unlocking European marine biodiversity data","authors":"Ruben Perez Perez, J. Beja, L. Vandepitte, Marina Lipizer, B. Weigel, B. Vanhoorne","doi":"10.3897/biss.7.112147","DOIUrl":"https://doi.org/10.3897/biss.7.112147","url":null,"abstract":"EMODnet Biology (hosted and coordinated by the Flanders Marine Institute (VLIZ)) is one of the seven themes within the European Marine Observation and Data network (EMODnet). The EMODnet Biology consortium aims to facilitate the accessibility and usage of marine biodiversity data. With the principle of \"collect once, use many times\" at its core, EMODnet Biology fosters collaboration across various sectors, including research, policy-making, industry, and individual citizens, to enhance knowledge sharing and inform decision-making.\u0000 EMODnet Biology focuses on providing free and open access to comprehensive historical and recent data on the occurrence of marine species and their traits in all European regional seas. It achieves this through partnerships and collaboration with diverse international initiatives, such as the World Register of Marine Species (WoRMS), Marine Regions and the European node of the Ocean Biodiversity Information System (EurOBIS) among others. By promoting the usage of the Darwin Core Standard (Wieczorek et al. 2012), EMODnet Biology fosters data interoperability and ensures seamless integration with wider networks such as the Global Biodiversity Information Facility (GBIF) and the Ocean Biodiversity Information System (OBIS), serving as a significant data provider of the latter, as it is responsible for most of its data generated in Europe.\u0000 Since its inception, EMODnet Biology has undertaken actions covering various areas, including\u0000 \u0000 \u0000 \u0000 providing access to marine biological data with spatio-temporal, taxonomic, environmental- and sampling-related information among others;\u0000 \u0000 \u0000 developing an exhaustive data quality control tool based on the Darwin Core standard, the British Oceanographic Data Centre and Natural Environment Research Council Vocabulary Server (BODC NVS2) parameters and other controlled vocabularies used;\u0000 \u0000 \u0000 creating and providing training courses to guide data providers;\u0000 \u0000 \u0000 performing gap analyses to identify data quality and coverage shortcomings;\u0000 \u0000 \u0000 creating and publishing marine biological distribution maps for various species or species groups; and\u0000 \u0000 \u0000 interacting with international and European initiatives, projects and organizations.\u0000 \u0000 \u0000 \u0000 providing access to marine biological data with spatio-temporal, taxonomic, environmental- and sampling-related information among others;\u0000 developing an exhaustive data quality control tool based on the Darwin Core standard, the British Oceanographic Data Centre and Natural Environment Research Council Vocabulary Server (BODC NVS2) parameters and other controlled vocabularies used;\u0000 creating and providing training courses to guide data providers;\u0000 performing gap analyses to identify data quality and coverage shortcomings;\u0000 creating and publishing marine biological distribution maps for various species or species groups; and\u0000 interacting with international and European initiatives, projects and organizations.\u0000 Furthermore, EMODnet Biology contributes to the ","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88483631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Role of the OLS Program in the Development of echinopscis (an Extensible Notebook for Open Science on Specimens)","authors":"Nicky Nicolson, Eve Lucas","doi":"10.3897/biss.7.112318","DOIUrl":"https://doi.org/10.3897/biss.7.112318","url":null,"abstract":"Starting in early 2022, biodiversity informatics researchers at Kew have been developing echinopscis: an \"extensible notebook for open science on specimens\". This aims to build on the early experiments that our community conducted with \"e-taxonomy\": the development of tools and techniques to enable taxonomic research to be conducted online. Early e-taxonomic tools (e.g., Scratchpads Smith et al. 2011) had to perform a wide range of functions, but in the past decade or so the move towards open science has built better support for generic functionality, such as reference management (Zotero) and document production (pandoc), skills development in automation and revision control to support reproducible science, as documented by the Turing Way (The Turing Way Community 2022), and an awareness of the importance of community building. We have developed echinopscis at Kew via a cross-departmental collaboration between researchers in biodiversity informatics and accelerated taxonomy. We have also benefitted from valuable input and advice from our many colleagues in associated projects and organisations around the world. \u0000 OLS (originally Open Life Sciences) is a training and mentoring program for Open Science leaders with a focus on community building. The name was recently (2023) made more generic—\"Open Seeds\"—whilst retaining their well-known acronym \"OLS\"*1. OLS is a 16-week cohort-based mentoring program. Participants apply to join a cohort with a project that is developed through the 16 weeks. Each week of the syllabus alternates between time with a dedicated Open Science mentor and cohort calls, which are used to develop skills in project design, community building, open development & licencing, and inclusivity. Over 500 practitioners, experts and learners have participated across the seven completed cohorts of OLS' Open Seeds training and mentoring. Through this programme, over 300 researchers and open leaders from across six continents have designed, lauched and supported 200 projects from different disciplines worldwide. The next cohort will run between September 2023 and January 2024, and will be the eighth iteration of the program. \u0000 This talk will briefly outline the work that we have done to setup and experiment with echinopscis, but will focus on the impact that the OLS program has had in its development. We will also include the use of techniques learned through OLS in other biodiversity informatics projects. OLS acknowledges that their program receives relatively few applications from project leads in biodiversity and we hope that this talk will be informative for Biodiversity Information Standards (TDWG) participants and can be used to build productive links between these communities.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77794142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GBIF-Compliant Data Pipeline for the Management and Publication of a Global Taxonomic Reference List of Pests in Natural History Collections","authors":"Carla Novoa Sepúlveda, Stephan Biebl, Nadja Pöllath, S. Seifert, Markus Weiss, Tanja Weibulat, Dagmar Triebel","doi":"10.3897/biss.7.112391","DOIUrl":"https://doi.org/10.3897/biss.7.112391","url":null,"abstract":"There is a growing demand for monitoring pests in natural history collections (NHCs) and establishing integrated pest management (IPM) solutions (Crossman and Ryde 2022). In this context, up-to-date taxonomic reference lists and controlled vocabularies following standard schemes are crucial and facilitate recording organisms detected in collections.\u0000 The data pipeline described here results in the publication of a taxon reference list based on information from online resources and standard IPM literature. Most of the over 140 pest taxa on species level and above are insects, the rest belong to other animal groups and fungi.\u0000 The complete taxon names, synonyms, English and German common names, and the hierarchical classification (parent-child relationships) are organised in a client-server installation of DiversityTaxonNames (DTN) at the Bavarian Natural History Collections (SNSB). DTN is a Microsoft Structured Query Language (MS SQL) database tool of the Diversity Workbench (DWB) framework with a published Entity Relation (ER) diagram (Hagedorn et al. 2019). The management is done using the Global Biodiversity Information Facility (GBIF) backbone taxonomy as external name resource, with linkage to the respective Wikidata Q item ID as a external persistent identifier (PID). Moreover, information on pest occurrence in NHCs is given, distinguishing the Consortium of European Taxonomic Facilities (CETAF) major NHC collection types affected (i.e., heritage sciences, life sciences and earth sciences) and the object categories, e.g., natural objects/specimens damaged. The data management in DTN enables the long-running curation, done by list curators.\u0000 The generic data pipeline for the management and publication of a Global Taxonomic Reference List of Pests in NHCs is based on the DTN taxon lists concept and architecture and described under About \"Taxon list of pest organisms for IPM at natural history collections compiled at the SNSB\". It includes four steps (A–D) with significant results for best practices of data processing (Fig. 1).\u0000 A. The data is managed and processed for publication by list curators in the database DiversityTaxonNames (DTN).\u0000 As a result, the list can be kept up-to-date and is—without transformation—ready to be used for IPM solutions at any NHC with a DiversityCollection installation and as part of the DWB cloud services.\u0000 B. The up-to-date data is publicly available via the DTN REST Webservice for Taxon Lists with machine-readable Application Programming Interface (API).\u0000 As a result, the dynamic list publication service can be used as a reference backbone for establishing IPM solutions for pest monitoring at any NHC.\u0000 C. The data is provided via the GBIF checklist data publication pipeline of the SNSB through GBIF validation tools and Darwin Core Archive in DwC-A (zip format) for GBIF.\u0000 As a result, the checklist information becomes part of the GBIF network with GBIF ChecklistBank and GBIF Global Taxonomy. This ensures future c","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84719431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Connecting the Dots: Aligning human capacity through networks toward a globally interoperable Digital Extended Specimen (DES) infrastructure","authors":"Elizabeth R. Ellwood, Wouter Addink, John Bates, Andrew Bentley, Jutta Buschbom, Alina Freire-Fierro, Jose Fortes, David Jennings, Kerstin Lehnert, Bertram Ludäscher, Keping Ma, James Macklin, Austin Mast, Joe Miller, Gil Nelson, Nicky Nicolson, Jyotsna Pandey, Deborah Paul, Sinlan Poo, Richard Rabeler, Pamela S. Soltis, Elycia Wallis, Michael Webster, Andrew Young, Breda Zimkus","doi":"10.3897/biss.7.112390","DOIUrl":"https://doi.org/10.3897/biss.7.112390","url":null,"abstract":"Thanks to substantial support for biodiversity data mobilization in recent decades, billions of occurrence records are openly available, documenting life on Earth and enabling timely research, awareness raising, and policy-making. Initiatives across local to global scales have been separately funded to serve different, yet often overlapping audiences of data users, and have developed a variety of platforms and infrastructures to meet the needs of these audiences. The independent progress of biodiversity data providers has led to innovations as well as challenges for the community at large as we move towards connecting and linking a diversity of information from disparate sources as Digital Extended Specimens (DES). Recognizing a need for deeper and more frequent opportunities for communication and collaboration across the globe, an ad-hoc group of representatives of various international, national, and regional organizations have been meeting virtually since 2020 to provide a forum for updates, announcements, and shared progress. This group is provisionally named International Partners for the Digital Extended Specimen (IPDES), and is guided by these four concepts: Biodiversity, Connection, Knowledge and Agency. Participants in IPDES include representatives of the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), American Institute of Biological Sciences (AIBS), Biodiversity Collections Network (BCoN), Natural Science Collections Alliance (NSCA), Distributed System of Scientific Collections (DiSSCo), Atlas of Living Australia (ALA), Biodiversity Information Standards (TDWG), Society for the Preservation of Natural History Collections (SPNHC), National Specimen Information Infrastructure of China (NSII), and South African National Biodiversity Institute (SANBI), as well as individuals involved with biodiversity informatics initiatives, natural science collections, museums, herbaria, and universities. Our global partners group strives to increase representation from around the globe as we aim to enable research that contributes to novel discoveries and addresses the societal challenges leading to the biodiversity crisis. Our overarching mission is to expand on the community-driven successes to connect biodiversity data and knowledge through coordination of a globally integrated network of stakeholders to enable an extensible technical and social infrastructure of data, tools, and working practices in support of our vision. The main work of our group thus far includes publishing a paper on the Digital Extended Specimen (Hardisty et al. 2022), organizing and hosting an array of activities at conferences, and asynchronous online work and forum-based exchanges. We aim to advance discussion on topics of broad interest to our community such as social and technical capacity building, broadening participation, expanding social and data networks, improving data models and building a backbone for the DES, and ide","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"13 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136299015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implementing CARE Principles to Link Noongar Language and Knowledge to Western Science through the Atlas of Living Australia","authors":"N. Raisbeck‐Brown, Denise Smith-Ali","doi":"10.3897/biss.7.112349","DOIUrl":"https://doi.org/10.3897/biss.7.112349","url":null,"abstract":"The Atlas of Living Australia (ALA), Australia's national online biodiversity database, is partnering with the Noongar Boodjar Language Centre (NBALC) to promote Indigenous language and knowledge by including Noongar names for plants and animals in the ALA. Names are included in the ALA species page for each plant and animal and knowledge is built into the Noongar Plant and Animal online Encyclopedia, hosted in the ALA. We demonstrate the use of CARE principles (Collective Benefit, Authority to Control, Responsibility, and Ethics (Carroll et al. 2020)) to engage, support, and deliver the project and outcomes to the Noongar people and communities working with us. \u0000 The ALA addresses the FAIR principles (Wilkinson et al. 2016) for data management and stewardship ensuring data are findable, accessable, interoperable, and reusable. The ALA is partnering with NBALC in Perth to ensure all sharing of Noongar data is on Noongar terms. NBALC and ALA have been working with Noongar-Wadjari, a southern clan from the Fitzgerald River area in Western Australia, to collect, protect and share their language and traditional knowledge for local species.*1\u0000 The Noongar Encyclopedia project exhibits Collective Benefit because it is a co-innovation project that was co-designed by NBALC and ALA. The project’s activities were designed by the Community-endorsed representatives, the Knowledge Holders. The aims and aspirations of the Community were included in the project design to ensure equitable outcomes. NBALC’s more than 25-year relationship with the Community, and as Noongar people themselves, meant they had a good understanding of what the Community might want from the project. These assumptions were tested and refined during the first Community consultation, before the project plan was finalised. The Community are keen for their traditional knowledge to be shared and freely available to their Community. The ALA only shared knowledge that has passed through strict consent processes. It is seen as a safe and stable digital environment for now and the future, and where the traditional knowledge can be accessed freely and easily. The link to western science knowledge is secondary to knowledge sharing for most of the Aboriginal and Torres Strait Islander Communities that the ALA are working with although the benefits of scientists having access to both knowledge systems is seen as a positive step in care for Country into the future.\u0000 The Noongar Encyclopedia project ensures Noongar Authority to Control these data because NBALC, as an Aboriginal organisation, led by Noongar people, understands the rights and interests of the Communities we are working with. Protection of these rights and inclusion of Community interests are written into the project methodology as part of the project co-design. It is important to ensure the project is working with the right people within the Community. NBALC facilitates this by finding people who hold traditional knowledge, and can trace","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85507465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bidirectional Linking: Benefits, challenges, pitfalls, and solutions","authors":"Guido Sautter, D. Agosti","doi":"10.3897/biss.7.112344","DOIUrl":"https://doi.org/10.3897/biss.7.112344","url":null,"abstract":"Taxonomy, and biodiversity science in general, mainly revolve around four types of entities, which are available digitally in ever increasing numbers from different services: (1) Physical specimens (kept in museums and other collections around the world) and observations are available digitally via the Global Biodiversity Information Facility (GBIF). (2) DNA sequences (often derived from preserved specimens) are available from the European Nucleotide Archive (ENA) and National Center for Biotechnology Information (NCBI), having accession numbers as their primary means of citation. (3) Taxa, identified by taxon names, are increasingly registered to nomenclatural reference databases (ZooBank, International Plant Names Index (IPNI)) and aggregated in the Catalogue of Life (CoL). (4) Taxonomic treatments combine the former three; they define taxa, express scientific opinions about existing taxa, based upon specimens as well as DNA sequences derived from themand coin respective names; they are available from TreatmentBank (as well as Zenodo/Biodiversity Literature Repository (BLR) and Swiss Institute of Bioinformatics Literature Services (SIBiLS), and GBIF).\u0000 Traditionally, treatments cite specimens, taxa, and other treatments in mainly human-centric ways, describing where to find the cited object, but they are not immediately actionable in a digital sense. Specimen citations use institution and collection codes and catalog numbers (often combined with geographical and environmental data). Taxon names are a type of self-citing entities, especially when given in combination with their (bibliographic) authorship, as they represent a historical approach to human-readable taxon identifiers. Citations of treatments are very similar to those of taxon names, adding (bibliographic) information of subsequent name usages as needed. Accession numbers for DNA sequences are the closest to modern digital identifiers. However, none of these means of citation, as usually found in literature, are readily machine actionable, which makes them hard to process at scale and analyze programmatically. Identifiers coined by the various data providers, in combination with APIs to resolve them, alleviate this problem and enable computational navigation of such links. However, this alone only defers the problem, as actionable identifiers (e.g., HTTP URIs) at some point still need to be inferred from the information given in the traditional means of citation where the latter occur in data.\u0000 Recent projects, like BiCIKL, aim to add machine navigable links to the various entities (or respective data records) at scale, in pursuit of (ideally) fully intermeshed records, connecting (1) treatments to subject taxon names and concepts, cited specimens and DNA sequences, as well as cited treatments (with explicit nomenclatorial implications, e.g., taxon name synonymies or rebuttals thereof), (2) (digital) specimens to assigned taxon names, citing treatments, and any derived DNA sequences,","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87815824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}