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Collections from Colonial Australia in Berlin's Museum für Naturkunde and the Challenges of Data Accessibility 柏林<s:1>自然博物馆的澳大利亚殖民地藏品和数据可访问性的挑战
Biodiversity Information Science and Standards Pub Date : 2023-09-01 DOI: 10.3897/biss.7.111980
Anja Schwarz, Fiona Möhrle, Sabine von Mering
{"title":"Collections from Colonial Australia in Berlin's Museum für Naturkunde and the Challenges of Data Accessibility","authors":"Anja Schwarz, Fiona Möhrle, Sabine von Mering","doi":"10.3897/biss.7.111980","DOIUrl":"https://doi.org/10.3897/biss.7.111980","url":null,"abstract":"German-speaking naturalists working in southeastern Australia in the mid-19th century relied heavily on the expertise of First Nations intermediaries who acted as guides, collectors, traders and translators (Clarke 2008, Olsen and Russell 2019). Many of these naturalists went to Australia because of the research opportunities offered by the British Empire at a time when the German nation states did not have colonies of their own. Others sought to escape political upheaval at home. They were welcome employees for colonial government agencies due to their training in the emerging research-oriented natural sciences that the reformed German universities offered at a time when British universities were still providing a broad general education (Home 1995, Kirchberger 2000).\u0000 Wilhelm von Blandowski (1822–1878 ) and Gerard Krefft (1830–1881 ), who both worked in colonial Victoria and New South Wales, are among this group. Throughout their work, they corresponded extensively with naturalists in Berlin, exchanging specimens and ideas. But the preserved Australian animals, plants and rock samples, as well as the written and drawn records of animals and landscapes now held at the Museum für Naturkunde Berlin (MfN), are much more than objects of scientific interest. They also contain information about Australia's First Nations. The collections provide evidence of their role in collecting as well as their knowledge of the natural world, which has long been overlooked and, at least in part deliberately, made invisible by Western knowledge systems (e.g., Das and Lowe 2018, Ashby 2020).\u0000 People data have been recognised as crucial for linking such collection objects with expeditions, publications, archival material and correspondence (Groom et al. 2020, Groom et al. 2022). It can thus potentially help reconstruct invisibilized Indigenous histories and knowledge. However, while the MfN keeps information about European collectors and other non-indigenous agents associated with their specimens in internal catalogues, databases and wikis, Indigenous actors remain largely absent from these repositories, which reproduce the colonial archive 'along the archival grain' (Stoler 2009).\u0000 With this in mind, we discuss in our presentation the complexities of using persistent identifiers and tools, such as Wikidata, to improve the integration and linkage of people data in the work currently being undertaken by the MfN and the Berlin's Australian Archive project to digitise and make accessible the museum’s collections. Drawing upon the guidance provided by the FAIR*1 and CARE*2 principles for data (Wilkinson et al. 2016, Carroll et al. 2020), and learning from the 2012 ATSILIRN Protocols for Libraries, Archives and Information Services*3, the 2019 Tandanya Adelaide Declaration and the 2020 AIATSIS Code of Ethics*4, we address the potential of these efforts in terms of collection accessibility, and also highlight the challenges and limitations of this approach in the context of","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89306401","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}
引用次数: 0
Building the Australian National Species List 建立澳大利亚国家物种名录
Biodiversity Information Science and Standards Pub Date : 2023-09-01 DOI: 10.3897/biss.7.111986
Endymion Cooper, G. Whitbread, Anne Fuchs
{"title":"Building the Australian National Species List","authors":"Endymion Cooper, G. Whitbread, Anne Fuchs","doi":"10.3897/biss.7.111986","DOIUrl":"https://doi.org/10.3897/biss.7.111986","url":null,"abstract":"The Australian National Species List (AuNSL) is a unified, nationally accepted, taxonomy for the native and naturalised biota of Australia. It is derived from a set of taxon-focussed resources including the Australian Plant Name Index and Australian Plant Census, the Australian Faunal Directory, and similar lists of fungi, lichens and bryophytes. These resources share a common infrastructure, contribute to the single national taxonomy (AuNSL), but retain their independent curation practices and online presentation. The AuNSL is now the core national infrastructure providing names and taxonomy for significant biodiversity data infrastructures including the Atlas of Living Australia, the Terrestrial Ecosystem Research Network, the Biodiversity Data Repository, and the Species Profile and Threats Database.\u0000 As the go-to resource for names and taxonomy for Australia’s unique biodiversity, the AuNSL must be constantly updated to reflect taxonomic and nomenclatural change. For some taxonomic groups, the AuNSL is substantially complete, and the incorporation of new taxa and other novelties occurs with little time lag. For other taxonomic groups the data are patchy and updates sporadic. Like similar projects, the AuNSL would benefit from improvements to taxonomic data publishing and sharing. Such improvements have the potential to enable automated, real-time ingestion for new taxonomic and nomenclatural data, allowing curator time to be re-directed to backfilling the historical data from a dispersed and complex literature. Ideally, the AuNSL will be able to benefit from advances in automated approaches to processing the historical data, including via the sharing of standardised representations of such data.\u0000 Here we outline the AuNSL data model, editor functionality, and describe our approach to sharing our data via existing and emerging standards such as Darwin Core and Taxon Concept Schema (TCS2). We then describe what we, as consumers of taxonomic data from published works, really need from publishers of new, and reprocessed historical data. In brief, we need structured taxonomic data conforming to an adequate standard.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91274161","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}
引用次数: 0
Systema Dipterorum
Biodiversity Information Science and Standards Pub Date : 2023-09-01 DOI: 10.3897/biss.7.111959
Thomas Pape, Neal Evenhuis
{"title":"Systema Dipterorum","authors":"Thomas Pape, Neal Evenhuis","doi":"10.3897/biss.7.111959","DOIUrl":"https://doi.org/10.3897/biss.7.111959","url":null,"abstract":"From its birth as the ‘Biosystematic Database of World Diptera’ in 1984, the ‘Systema Dipterorum’ (Evenhuis and Pape 2023) has grown into one of the largest databases currently maintained for the taxonomy and nomenclature of a single order of insects. Systema Dipterorum covers all two-winged insects (Diptera), and with almost a quarter of a million names representing more than 170,000 valid species distributed in some 13,000 valid genera, we cover about 10% of the described and named Animalia. About 1,000 new nominal species are described annually within Diptera. Data are entered in FileMaker Pro (database) and served through an online portal*1 with an updated version currently provided every two months. Names are harvested and reviewed through a four-tier quality assurance hierarchy with entries eventually reaching taxonomic and nomenclatural standards equivalent to being published online. The nomenclatural status of each name is shown using 50 different codes, and at this moment a published authority source is linked to more than 70% of the entries. Universal Unique Identifiers (UUIDs) are automatically generated for every record of names and the more than 35,000 references. Names are made available for the Catalogue of Life, and we envision a web portal for seamless harvesting of new names and literature as well as for updating of both nomenclature and taxonomy by making changes and correcting errors with explicit reference to published authority sources. We envision the future for Systema Dipterorum to be a one-stop website, where clicking on a name resulting from a search may call up links to, e.g., its nomenclatural registry in ZooBank, the original description through the Biodiversity Heritage Library, taxonomic treatments from Plazi, images from Morphbank, occurrence data through the Global Biodiversity Information Facility (GBIF), molecular sequence data from GenBank, Barcode Index Numbers (BINs) from Barcode of Life, and additional data from many other sources.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"85 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81194395","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}
引用次数: 9
FAIR Principles and TDWG Standards: The case of morphological description of taxa and specimens FAIR原则与TDWG标准:分类群与标本形态描述案例
Biodiversity Information Science and Standards Pub Date : 2023-08-31 DOI: 10.3897/biss.7.111859
Régine Vignes Lebbe
{"title":"FAIR Principles and TDWG Standards: The case of morphological description of taxa and specimens","authors":"Régine Vignes Lebbe","doi":"10.3897/biss.7.111859","DOIUrl":"https://doi.org/10.3897/biss.7.111859","url":null,"abstract":"Sharing data is crucial in biodiversity research as well as in all scientific domains. Biodiversity Information Standards (TDWG) validates and makes available a set of standards to facilitate the sharing of biodiversity data. Of the 23 standards listed in alphabetical order, each has a status, a category, and a short description. But these standards are designed for very different purposes, which we will discuss by linking them to the FAIR principles (Findable, Accessible, Interoperable, and Reusable) .\u0000 The FAIR principles (Wilkinson et al. 2016) focus on the ability of machines to automatically find and use the digital data. It is therefore crucial that software for editing, acquiring and using data, shares defined standards that are made available to all. TDWG has been working in this direction for over 30 years. Pioneers in biodiversity informatics, such as Richard Pankhust (Pankhurst 1970), Mike Dallwitz (Dallwitz 1974, Dallwitz 1980) and Jacques Lebbe (Lebbe et al. 1987) worked specifically on taxon identification with computers and how to represent morphological descriptions of taxa and specimens.\u0000 Some TDWG standards, such as ABCD (Access to Biological Collection Data; Access to Biological Collections Data Task Group 2005), TCS (Taxonomic Concept Transfer Schema; Taxonomic Names Subgroup 2006) or SDD (Structured Descriptive Data; Structure of Descriptive Data (SDD) Subgroup 2006) are expressed by an XML schema covering a formal data model. Other standards, as Floristic Regions of the World (Takhtajan 1986), or Vocabulary Maintenance Standard (VMS; Vocabulary Maintenance Specification Task Group 2017) concern vocabularies or a collection of standardized terms. The Plant Occurrence and Status Scheme (POSS; World Conservation Monitoring Centre 1995) provides both, a list of accepted terms, and a data model (list of fields). In case of morpho-anatomical data describing taxa or specimens, TDWG offers two standards: DELTA (DEscription Language for TAxonomy, Dallwitz 2006) and SDD (Structured Descriptive Data, Hagedorn 2007).\u0000 In order to further the discussion on morphological description data sharing, we would like to clarify what is meant by the term standard. We'll be looking at the concepts of guidelines, rules, defined format, referential list of terms, data schema, model, metamodel, protocols, which are all terms linked to this notion of standard and FAIR principles. Perhaps this reflection will lead us to propose criteria for better classifying TDWG standards.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76053342","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}
引用次数: 0
Japan Biodiversity Information Initiative (JBIF)'s Efforts to Collect and Publish Biodiversity Information from Japan 日本生物多样性信息倡议(JBIF)收集和发布日本生物多样性信息的努力
Biodiversity Information Science and Standards Pub Date : 2023-08-31 DOI: 10.3897/biss.7.111893
Showtaro Kakizoe, Aino T. Ota, T. Hosoya, U. Jinbo
{"title":"Japan Biodiversity Information Initiative (JBIF)'s Efforts to Collect and Publish Biodiversity Information from Japan","authors":"Showtaro Kakizoe, Aino T. Ota, T. Hosoya, U. Jinbo","doi":"10.3897/biss.7.111893","DOIUrl":"https://doi.org/10.3897/biss.7.111893","url":null,"abstract":"The Japan Biodiversity Information Initiative (JBIF) was originally established in 2007 as the Global Biodiversity Information Facility (GBIF) Japan National Node to aggregate biodiversity data in Japan and conduct publications through GBIF. JBIF was later renamed after Japan became a GBIF observer, but activities including data publication through GBIF have continued to the present. JBIF operates with the support of the National BioResource Project (NBRP) by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), with collaboration from three institutions: the National Institute of Genetics (NIG), the National Institute for Environmental Studies (NIES), and the National Museum of Nature and Science (NMNS). The NBRP is a project that focuses on the collection, preservation, provision, and enhancement of bioresources.\u0000 JBIF collects both observation and specimen data and publishes them through GBIF. For domestic data use, a search system for data published by JBIF is available on the JBIF website. Moreover, NMNS managed a museum network called the Science Museum Net (S-Net), and bilingual (Japanese and English) specimen data collected by S-Net is also available via the S-Net portal site. We are working to promote the biodiversity informatics field in Japan through a translation of the GBIF resources, including the website, important documents such as the GBIF Science Review, as well as organize workshops and conferences, primarily targeting students, researchers, museum curators, and local government officials, to facilitate the sharing of information and exchange of opinions on biodiversity information.\u0000 To date, Japan has published 564 datasets and over 12 million occurrences to GBIF, making it the third-largest contributor of data to GBIF in Asia, following India and Taiwan. Moreover, regarding specimen-based occurrence data, Japan is the largest contributor in Asia.\u0000 In this presentation, we will introduce JBIF's initiatives and future activities.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"589 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78940555","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}
引用次数: 0
An Excel Template Generator for Darwin Core 一个Excel模板生成器为达尔文核心
Biodiversity Information Science and Standards Pub Date : 2023-08-31 DOI: 10.3897/biss.7.111907
L. Marsden, O. Schneider
{"title":"An Excel Template Generator for Darwin Core","authors":"L. Marsden, O. Schneider","doi":"10.3897/biss.7.111907","DOIUrl":"https://doi.org/10.3897/biss.7.111907","url":null,"abstract":"Scientific data is diverse and can be complex, potentially including biotic or abiotic measurements, material samples, DNA derived data and more. Especially for researchers who are new to the Darwin Core standard (Darwin Core Task Group 2009), it is not always obvious what the best practice is for creating a Darwin Core Archive (GBIF 2021) for their data. Which core and extensions should they select? Which Darwin Core terms*1 should they include? We present the 'Learnings from Nansen Legacy template generator' (Marsden and Schneider 2023), a spreadsheet template generator to simplify the creation of Darwin Core Archives. It enables users to create a single Microsoft Excel file that includes one sheet per core or extension using a graphical user interface. The user can select from a complete list Darwin Core terms to use as column headers. There are requirements and recommendations for which terms are selected for each core and extension. Descriptions for all terms are displayed when one hovers over a Darwin Core term, and are stored as notes in the template when one select a relevant cell. The generated template includes cell restrictions to prevent one from inputting data in an incorrect format. A separate configuration is also available to aid researchers in creating CF-NetCDF*2 files for physical data, which are also compliant with the FAIR (Findable, Accessible, Interoperable, Resuable)*3 data management principles.\u0000 The Learnings from Nansen Legacy template generator is published (Marsden and Schneider 2023) and can be installed for use on your website or computer by following the instructions on the software's GitHub repository*4. The template generator can be tested where it is currently hosted, by SIOS*5 (Svalbard Integrated Arctic Earth Observing System). One can also refer to a YouTube tutorial*6 on how the template generator works.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"53 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85584577","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}
引用次数: 0
Towards FAIR Principles in Biodiversity Research: Enabling computable taxonomic descriptions and ecological data with Phenoscript 迈向生物多样性研究的公平原则:利用Phenoscript实现可计算的分类描述和生态数据
Biodiversity Information Science and Standards Pub Date : 2023-08-30 DOI: 10.3897/biss.7.111862
S. Tarasov, G. Montanaro, Federica Losacco, D. Porto
{"title":"Towards FAIR Principles in Biodiversity Research: Enabling computable taxonomic descriptions and ecological data with Phenoscript","authors":"S. Tarasov, G. Montanaro, Federica Losacco, D. Porto","doi":"10.3897/biss.7.111862","DOIUrl":"https://doi.org/10.3897/biss.7.111862","url":null,"abstract":"Taxonomic descriptions hold immense phenotypic data, but their natural language (NL) format poses challenges for computer analysis. In this talk, we will present Phenoscript, a user-friendly computer language enabling computer-readable species descriptions and automated phenotype comparisons, in accordance with FAIR (Findable, Accessible, Interoperable, Reusable) principles.\u0000 Phenoscript facilitates the creation of semantic species descriptions that represent a knowledge graph composed of terms from predefined biological ontologies. A Phenoscript description resembles a NL description, but follows a specific language grammar. We have developed the Phenospy package: a Python-based Phenoscript toolkit. Phenospy converts Phenoscript descriptions into both NL format, facilitating scientific publication, and the Web Ontology Language (OWL) format, enabling downstream analysis and computable phenotypic comparisons. OWL is a standard for sharing semantic data on the Web. While initially designed for phenotypes, Phenoscript can be extended to create semantic ecological data, encompassing environmental traits, functional traits, and species interactions. We will discuss the integration of species and ecological traits encoded in Phenoscript into downstream analysis, highlighting its potential for phenomic-level research in biology.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"69 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84910661","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}
引用次数: 0
Improving FAIRness of eDNA and Metabarcoding Data: Standards and tools for European Nucleotide Archive data deposition 提高eDNA和元条形码数据的公平性:欧洲核苷酸档案数据沉积的标准和工具
Biodiversity Information Science and Standards Pub Date : 2023-08-30 DOI: 10.3897/biss.7.111835
J. Paupério, Vikas Gupta, Josephine Burgin, Suran Jayathilaka, J. Lanfear, K. Abarenkov, U. Kõljalg, L. Penev, G. Cochrane
{"title":"Improving FAIRness of eDNA and Metabarcoding Data: Standards and tools for European Nucleotide Archive data deposition","authors":"J. Paupério, Vikas Gupta, Josephine Burgin, Suran Jayathilaka, J. Lanfear, K. Abarenkov, U. Kõljalg, L. Penev, G. Cochrane","doi":"10.3897/biss.7.111835","DOIUrl":"https://doi.org/10.3897/biss.7.111835","url":null,"abstract":"The advancements in sequencing technologies have promoted the generation of molecular data for cataloguing and describing biodiversity. The analysis of environmental DNA (eDNA) through the application of metabarcoding techniques enables comprehensive descriptions of communities and their function, being fundamental for understanding and preserving biodiversity. Metabarcoding is becoming widely used and standard methods are being generated for a growing range of applications with high scalability. The generated data can be made available in its unprocessed form, as raw data (the sequenced reads) or as interpreted data, including sets of sequences derived after bioinformatics processing (Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs)) and occurrence tables (tables that describe the occurrences and abundances of species or OTUs/ASVs). However, for this data to be Findable, Accessible, Interoperable and Reusable (FAIR), and therefore fully available for meaningful interpretation, it needs to be deposited in public repositories together with enriched sample metadata, protocols and analysis workflows (ten Hoopen et al. 2017). \u0000 Metabarcoding raw data and associated sample metadata is often stored and made available through the International Nucleotide Sequence Database Collaboration (INSDC) archives (Arita et al. 2020), of which the European Nucleotide Archive (ENA, Burgin et al. 2022) is its European database, but it is often deposited with minimal information, which hinders data reusability. \u0000 Within the scope of the Horizon 2020 project, Biodiversity Community Integrated Knowledge Library (BiCIKL), which is building a community of interconnected data for biodiversity research (Penev et al. 2022), we are working towards improving the standards for molecular ecology data sharing, developing tools to facilitate data deposition and retrieval, and linking between data types. \u0000 Here we will present the ENA data model, showcasing how metabarcoding data can be shared, while providing enriched metadata, and how this data is linked with existing data in other research infrastructures in the biodiversity domain, such as the Global Biodiversity Information Facility (GBIF), where data is deposited following the guidelines published in Abarenkov et al. (2023). We will also present the results of our recent discussions on standards for this data type and discuss future plans towards continuing to improve data sharing and interoperability for molecular ecology.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76347338","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}
引用次数: 0
Building Software for Hierarchical Events in Biodiversity Informatics 生物多样性信息学中的分层事件构建软件
Biodiversity Information Science and Standards Pub Date : 2023-08-29 DOI: 10.3897/biss.7.111770
P. Newman, David Martin, J. Molina
{"title":"Building Software for Hierarchical Events in Biodiversity Informatics","authors":"P. Newman, David Martin, J. Molina","doi":"10.3897/biss.7.111770","DOIUrl":"https://doi.org/10.3897/biss.7.111770","url":null,"abstract":"In 2019, the Atlas of Living Australia (ALA) ran a national consultation, clarifying a long-held suspicion that while simple occurrence records provide invaluable discoverability and analysis for biodiversity data, the lack of contextual information on data collection methodology and protocols limits its usefulness for species abundance estimation and time-series analysis. The consultation recognised that the ALA has strong leadership in biodiversity standards and development, and that our 12-year history and investment in projects and engagement demonstrates a clear capacity to transition to a repository capable of capturing and aggregating the monitoring and survey data required for conservation efforts (Daly 2019). \u0000 Around the same time, the larger data landscape was undergoing change in a similar direction, both internationally through the Global Biodiversity Information Facility’s (GBIF) Unified Model engagements, and nationally through the development of the Australian Biodiversity Information Standard (ABIS), an ontology for describing environmental data (Anonymous 2021). We embarked on a project to examine existing data standards and practices, extend our own occurrence model, and build software that could ingest event-based datasets and make them discoverable and interoperable.\u0000 Initially we focused on well-structured surveys, both marine and terrestrial, to develop the system and user interface (UI). During the project, we restructured and modeled other exemplar datasets, collaborating with GBIF to develop event terms, vocabularies, and user interface components. Seeking interoperability with existing standards, we integrated concepts from both ABIS and the Ocean Biodiversity Information System’s (OBIS) ENV-DATA model (De Pooter et al. 2017) into a standardised yet flexible implementation of Event Core, navigable via a friendly user interface. \u0000 The initial software release is comprised of an ingestion pipeline for events in parallel to occurrences, an index capable of handling nested data structures, and a user interface. The UI guides the user to explore and filter datasets; includes visualisations for data structures, taxonomic scope, repeat location surveys, extended measurements or facts; and links out to child occurrence records. Users can download filtered original and interpreted datasets with Digital Object Identifiers (DOI), in compressed files that comply simultaneously with Darwin Core Archive and Frictionless Data Package specifications.\u0000 On release, we will present a range of datasets covering different event-based scenarios. The model has serendipitously provided the flexibility to encapsulate complex seed bank data. During the project, we developed a draft extension, which we used to service a new data portal for the Australian Seed Bank Partnership, a testament to the model’s serviceability for novel use cases. \u0000 The ALA has taken innovative steps beyond simple collection of complex data types and worked with our local","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78903435","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}
引用次数: 0
Restricted Access Species Data Systems: A starting point 限制获取物种数据系统:一个起点
Biodiversity Information Science and Standards Pub Date : 2023-08-29 DOI: 10.3897/biss.7.111746
Piers Higgs, Cameron Slatyer
{"title":"Restricted Access Species Data Systems: A starting point","authors":"Piers Higgs, Cameron Slatyer","doi":"10.3897/biss.7.111746","DOIUrl":"https://doi.org/10.3897/biss.7.111746","url":null,"abstract":"Restricted access species data requires constrained shared access to meet conservation, legal and legislative requirements. Access to this data is essential for better evidenced-based decision-making; reduced regulatory timeframes and improved environmental and research outcomes. The Restricted Access Species Data Service (RASDS)*1 was developed to accept, track and manage data use requests, passing enquiries to data custodians, and providing a conduit for data and legal agreements between custodians and requesters. For those data custodians who wish to delegate queries to the RASDS, the service will ensure that datasets are transformed, attributed, and Digital Object Identifiers and metadata are applied. The data service will also manage reporting on data use. In this presentation we will demonstrate the RASDS, and discuss the future roadmap for the system. This abstract sets the scene for the rest of workshop and provides a starting point for the futher talks and discussions.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81965050","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}
引用次数: 0
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