Biodiversity Information Science and Standards最新文献

{"title":"Will a Local Portal using Global Data Encourage the Mainstreaming of Biodiversity Informatics in Asia? In Taiwan, We Say Yes","authors":"Jerome Chie-Jen Ko, Huiling Chang, Yihong Chang, You-Cheng Yu, Min-Hsuan Ni, Jun-Yi Wu, You Zhen Chen","doi":"10.3897/biss.7.112176","DOIUrl":"https://doi.org/10.3897/biss.7.112176","url":null,"abstract":"Five years ago, the value of biodiversity open data was scarcely recognized in Taiwan. This posed a significant challenge to the Taiwan Biodiversity Infomation Facility (TaiBIF), our national node of the Global Biodiversity Information Facility (GBIF), in its sustained efforts to enhance data publishing capacities. Notably, non-academic entities, both governmental and industrial, were reluctant to invest resources in data management and publication, questioning the benefits beyond purely research-oriented returns.\u0000 At the time, Taiwan had fewer than a million published records domestically, while GBIF held around 3 million occurrence records for Taiwan, largely unused by local users. We speculated that this discrepancy in data usage stemmed from three factors: (1) lack of species names in the local language within the occurrence data, (2) missing locally important species attributes, such as conservation status and national red list categories, and (3) absence of a culturally relatable local portal promoting biodiversity data usage.\u0000 To address these issues, we launched the Taiwan Biodiversity Network (TBN) website in 2018, localizing global data from GBIF and integrating missing information from local data sources. Collaborating with wildlife illustrators, we designed a user-friendly data interface to lessen the system's technical or academic barriers. This effort led to a doubling of website visitors and data download requests annually, and in recent years, biodiversity open data has become a vital component in environmental impact assessments. This upward trend heightened the recognition of the value of biodiversity open data, inciting organizations, such as initially data-conservative government agencies and private sectors with no obligatory data-sharing, to invest in data management and mobilization. This advancement also catalyzed the formation of the Taiwan Biodiversity Information Alliance (TBIA), actively promoting cross-organizational collaborations on data integration.\u0000 Today, Taiwan offers more than 19 million globally accessible occurrence records and data for more than 28,000 species. While the surge in data volume can certainly be credited to the active local citizen science community, we believe the expanded coverage of species and data types is a result of a growing community supportive of biodiversity open data. This was made possible by the establishment of a local portal that effectively bridged the gap between global data and local needs. We hope our experience will motivate other Asian countries to create analogous local portals using global open data sources like GBIF, illustrating the value of biodiversity open data to decision-makers and overcoming resource limitations that impede investments in biodiversity informatics.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74888548","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":"Measuring Habitat Restoration using the Darwin and \"Event\" Cores: Australian examples powered by BioCollect","authors":"Peter Brenton, Peggy Eby, Robert Stevenson, Elizabeth R. Ellwood","doi":"10.3897/biss.7.112083","DOIUrl":"https://doi.org/10.3897/biss.7.112083","url":null,"abstract":"Habitat decline and fragmentation are major factors in biodiversity loss across the globe and can be difficult to measure, particularly at landscape scale (Brooks et al. 2002, Fahrig 2003, Ritchie and Roser 2019). In Australia, rural, coastal and urban communities have been undertaking habitat restoration activities since the mid-1980s to protect and restore ecological balance on private land and in local shared and natural spaces. Much of the restoration effort has centered around hands-on activities as a mechanism for building community with environmental benefits. Over such a time span, thousands of locations throughout the country have been transformed from degraded and highly disturbed landscapes into resemblances of more-or-less natural areas. \u0000 However, collecting and analysing data for these activities was given little attention until quite recently, as governments, philanthropists and other investors have become increasingly interested in measuring the value and outcomes from investment. To measure the effectiveness of the restoration effort, it is essential to to benchmark the environmental state and species composition before the restoration begins, but surprisingly or unsurprisingly, this is rarely done (Hale et al. 2019).\u0000 Responding to this call for better documentation of restoration outcomes, over 30 groups have been using the Atlas of Living Australia’s BioCollect platform to capture complex information about current and past restoration work. The BioCollect platform enables each type of monitoring, establishment, and follow-up activity to have its own data collection schema and associated metadata structured around using a hierarchy of sampling events based on the Event class in the Darwin Core standard, which allows relationships between types of event records to be specified. When event records are created through use of an activity-based template, each occurrence of a species is also parsed and configured as a Darwin Core occurrence record. Standard templates have been created for a range of activities, such as benchmarking assessments, site establishment, follow-up interventions and monitoring over time, which are being used by many different groups over large areas of the landscape. This allows each group to operate independently, yet collect standardised data that can be easily aggregated at larger temporal and spatial scales, quantifying change over time. The relationships between occurrences and the event context in which they were collected is also preserved and navigable.\u0000 Here we present how Darwin Core and Event Core have been implemented in the BioCollect platform to enable this important data to be collected and stored in its full richness and resolution.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84158634","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":"Optimizing the Monitoring of Urban Fruit-Bearing Flora with Citizen Science: An Overview of the Pomar Urbano Initiative","authors":"Filipi Miranda Soares, Luís Ferreira Pires, Maria Carolina Garcia, A. D. de Carvalho, S. Koffler, N. Ghilardi-Lopes, Rubens Silva, Benildes Maculan, Ana Maria Bertolini, Gabriela Rigote, L. Coradin, U. Montedo, Debora P. Drucker, Raquel Santiago, Maria Clara de Carvalho, Ana Carolina da Silva Lima, Karoline Reis de Almeida, Stephanie Gabriele Mendonça de França, Hillary Dandara Elias Gabriel, Bárbara Junqueira dos Santos, A. Saraiva","doi":"10.3897/biss.7.112009","DOIUrl":"https://doi.org/10.3897/biss.7.112009","url":null,"abstract":"The \"Pomar Urbano\" (Urban Orchard) project focuses on the collaborative monitoring of fruit-bearing plant species in urban areas throughout Brazil.\u0000 The project collected a list of 411 fruit-bearing plant species (Soares et al. 2023), both native and exotic varieties found in Brazil. This list was selected from two main sources: the book Brazilian Fruits and Cultivated Exotics (Lorenzi et al. 2006) and the book series Plants for the Future, which includes volumes specifically dedicated to species of economic value in different regions of Brazil, namely the South (Coradin et al. 2011), Midwest (Vieira et al. 2016), Northeast (Coradin et al. 2018) and North (Coradin et al. 2022). To ensure broad geographic coverage, the project spans all 27 state capitals of Brazil. The data collection process relies on the iNaturalist Umbrella and Collection projects. Each state capital has a single collection project, including the fruit-bearing plant species list, and the locality restriction to that specific city. For example, the collection project Pomar Paulistano gathers data from the city of São Paulo. The Umbrella Project Urban Orchard was set to track data from all 27 collection projects.\u0000 We firmly believe that these fruit-bearing plant species possess multifaceted value that extends beyond mere consumption. As such, we have assembled a dynamic and multidisciplinary team comprising professionals from various institutions across Brazil in a collaborative effort that encompasses different dimensions of biodiversity value exploration and monitoring, especially phenological data.\u0000 One facet of our team is focused on creating products inspired by the diverse array of Brazilian fruit-bearing plants. Their work spans across sectors of the creative industry, including fashion, painting, and graphic design to infuse these natural elements into innovative and sustainable designs (Fig. 1 and Fig. 2).\u0000 A group of nutrition and health scientists in conjunction with communication and marketing professionals is working to produce engaging media content centered around food recipes that incorporate Brazilian fruits (Fig. 3). These recipes primarily feature the fruit-bearing plants most frequently observed on iNaturalist in the city of São Paulo, allowing us to showcase the local biodiversity while promoting culinary diversity. Some of these recipes are based on the book Brazilian Biodiversity: Flavors and Aromas (Santiago and Coradin 2018). This book is an extensive compendium of food recipes that use fruits derived from native Brazilian species.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"229 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84050439","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":"Promoting High-Quality Data in OBIS: Insights from the OBIS Data Quality Assessment and Enhancement Project Team ","authors":"Yi-Ming Gan, Ruben Perez Perez, Pieter Provoost, A. Benson, A. C. Peralta Brichtova, Elizabeth R. Lawrence, John Nicholls, Johnny Konjarla, Georgia Sarafidou, H. Saeedi, Dan Lear, Anke Penzlin, N. Wambiji, W. Appeltans","doi":"10.3897/biss.7.112018","DOIUrl":"https://doi.org/10.3897/biss.7.112018","url":null,"abstract":"The Ocean Biodiversity Information System (OBIS) (Klein et al. 2019) is a global database of marine biodiversity and associated environmental data, which provides critical information to researchers and policymakers worldwide. Ensuring the accuracy and consistency of the data in OBIS is essential for its usefulness and value, not only to the scientific community but also to the science-policy interface. The OBIS Data Quality Assessment and Enhancement Project Team (QCPT), formed in 2019 by the OBIS steering group, aims to assess and enhance data quality. It has been working on three categories of activities for this purpose:\u0000 \u0000 Data quality enhancement and management\u0000 \u0000 The OBIS QCPT organized data laundry events to identify and address data quality issues of published OBIS datasets. Furthermore, individual OBIS nodes were invited to give their data-processing presentations in the monthly meetings to foster knowledge sharing and collaborative problem-solving focused on data quality. Data quality issues and solutions highlighted in the presentations and data laundry events were documented in a dedicated GitHub repository as GitHub issues. The solutions for data quality issues and marine-specific pre-publication quality control tools, designed to identify the data quality issues, were provided as feedback to the OBIS Capacity Development Task Team. These inputs were used to create training resources (see OBIS manual, upcoming OBIS training course hosted on OceanTeacher Global Academy) aimed at preventing these issues.\u0000 \u0000 Standardization of OBIS data processing pipeline \u0000 \u0000 As OBIS uses the Darwin Core standard (Wieczorek et al. 2012), the use of standardized tests and assertions in the data processing pipeline is encouraged. To achieve this, the OBIS QCPT aligned OBIS quality checks with a subset of core tests and assertions (Chapman et al. 2020) developed by the Biodiversity Information Standards (TDWG) Biodiversity Data Quality (BDQ) Task Group 2 (TG2) (Chapman et al. 2020) as tracked in this GitHub issue. Not all default parameters of the core tests and assertions are optimal for marine biodiversity data. The OBIS QCPT met monthly to determine suitable parameters for customizing the tests. The pipeline produces a data quality report for each dataset with quality flags that indicate potential data quality issues, enabling node managers and data providers to review the flagged records.\u0000 \u0000 Community engagement\u0000 \u0000 The OBIS QCPT led a survey among data users to gather insights into OBIS data quality issues and bridge the gap between the current implementation and user expectations. The survey findings enabled OBIS to prioritize issues to be addressed, as summarized in Section 2.2.2 of the 11th OBIS Steering Group meeting report. In addition to engaging with data users, the OBIS QCPT also served as a platform to discuss questions related to the use of Darwin Core from the nodes and provided feedback for the term discussions. \u0000 In summary, the OBIS QCP","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85992377","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":"Growth and Evolution of the Symbiota Portal Network","authors":"Katie Pearson, E. Gilbert, K. S. Orellana, Greg Post, Lindsay Walker, Jenn Yost, Nico Franz","doi":"10.3897/biss.7.112028","DOIUrl":"https://doi.org/10.3897/biss.7.112028","url":null,"abstract":"Symbiota is empowering biodiversity collections communities across the globe to efficiently manage and mobilize their data. Beginning with only a handful of collections in two major portals in the early 2010s (Gries et al. 2014), Symbiota now acts as the primary content management system for over 1,000 collections in more than 50 portals. Over 1,800 collections share data through Symbiota portals, constituting over 90+ million records and 42+ million images. The iDigBio Symbiota Support Hub, a team and cyberinfrastructure based out of Arizona State University and supported by the United States (U.S.) National Science Foundation, hosts 52 Symbiota portals and provides daily help and resources to all Symbiota user communities. The Symbiota codebase is being actively developed in collaboration with several funded projects, including the U.S. National Ecological and Observatory Network (NEON), to support new data types and connections, such as between Symbiota portals and other collections management systems, and to other resources (e.g., Index Fungorum, Global Registry of Scientific Collections, Bionomia, Environmental Data Initiative). Because the Symbiota codebase is open source and shared among portals, new developments in any portal empower the entire network. Here we describe recent expansions of the Symbiota network, including new portals, collaborations, functionalities, and sustainability actions. We look forward to building further collaborations with diverse, international collections data communities.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84059322","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":"TaxonWorks in its 10th Year: What’s new, what’s next?","authors":"Deborah Paul, Matthew Yoder","doi":"10.3897/biss.7.112040","DOIUrl":"https://doi.org/10.3897/biss.7.112040","url":null,"abstract":"The Species File Group (SFG) endeavors to build tools and community structures that empower researchers and collections staff in their long-term collective efforts to gather, share, and learn from biodiversity data. One such tool is TaxonWorks, now in its 10th year of development. TaxonWorks provides a collaborative workbench where scientists, collection managers, students, and volunteers capture and build on the key data and concepts we use to Describe Life (TaxonWorks motto). It provides a growing number of ways to share descriptions, from Darwin Core Archives, to NeXML-formatted observations and keys, to checklists, and bibliographies.\u0000 \u0000 What’s New? \u0000 \u0000 We have expanded the data model of TaxonWorks, added new tools and functions, and some Companion software, that is, new stand-alone code-bases.\u0000 Two major additions, Unified Filters and Cached Maps, provide developers and users (and users who are developers) the ability to run complex queries across TaxonWorks' rich data model and to display quickly computed maps for datasets of notable size, 100K or more specimen and literature-based records. For example, Cached Maps can superimpose the asserted distribution and georeferenced literature and specimen records to create interactive searchable maps (Fig. 1). \u0000 In TaxonWorks, we aim to empower those working with the data with tools that help them visualize and curate information. To be able to model taxon concept relationships over time to reflect different taxonomic opinions, we added RCC-5 (Region Connection Calculus; Thau et al. 2008), which will make it possible to visualize these relationships. Similarly, we built a new visual editor (Fig. 2) for displaying, editing, and citing biological associations as recorded among specimens or taxa (or both).\u0000 Querying and enhancing data in a given database can be complex. We have worked on harmonizing the look-feel-function of the data filtering interfaces. With our Unified Filters, one can pass the results of one search to another filter (e.g., query for specimens for a given taxonomic group and then ask for the distinct collecting events for those specimens). Then, once you filter to a given dataset, you can use our new Stepwise tasks to enhance and edit that information en-masse.\u0000 Companions code-bases extend what one can do with the data in TaxonWorks, but are also available for use with other software. For example, using our new TaxonPages code, our users can produce their own web pages for taxa (Fig. 1). TaxonPages will be used by SFG groups to make available well over 100K pages this year. They include basic Bioschema integration, links to JSON-formatted data behind every panel, and the option to download any occurrence data present, expressed as Darwin Core attributes, formatted as a CSV file. TaxonPages can be set up in minutes and served on resources like GitHub pages and our user community can customize their content.\u0000 Finally, the TaxonWorks external API has added a huge number of new parame","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84278164","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":"Quality Control/Quality Assurance within the Integrated Taxonomic Information System (ITIS)","authors":"Thomas M. Orrell","doi":"10.3897/biss.7.112043","DOIUrl":"https://doi.org/10.3897/biss.7.112043","url":null,"abstract":"The Integrated Taxonomic Information System*1 (ITIS) and Species 2000*2 have worked together for two decades after signing an agreement to form the Catalogue of Life*3 (COL), striving to provide current and complete Global Species Databases (GSDs) from various sources. ITIS has provided many such GSDs to the COL.\u0000 In this presentation, we will demonstrate in detail the nine aspects of ITIS’ approach to quality assurance/quality control: People, Process, Rules, Standards, Automation, Control, Assurance, Publication, and Feedback. All of these aspects are important and deserve consideration in the creation/maintenance of ITIS’ high quality GSDs.\u0000 ITIS has also developed a new web-based ‘Taxonomic Workbench’ (TWB) that allows new levels of cooperative effort beyond what ITIS has been able to attain with a desktop version of the software, which has been used for twenty-five years. Some key aspects of these tools and what they will allow are discussed in the last half of the presentation.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87215297","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":"Ten Years and a Million Links: Building a global taxonomic library connecting persistent identifiers for names (LSIDs), publications (DOIs), and people (ORCIDs)","authors":"Roderic Page","doi":"10.3897/biss.7.112053","DOIUrl":"https://doi.org/10.3897/biss.7.112053","url":null,"abstract":"One thing the field of biodiversity informatics has been very good at is creating databases. However, this success in creation has not been matched by equivalent success in creating deep links between records in those databases. Instead, we create an ever growing number of silos. An obvious route to “silo-breaking” is the shared use of the same persistent identifiers for the same entities across those databases. For example, we have minted millions of Life Science Identifiers (LSIDs) for taxonomic names (which can be resolved at lsid.io), and a growing number of taxonomic papers have Digital Object Identifiers (DOIs), but we lack connections between these two identifiers. In this talk I describe work over the last decade to make these connections between LSIDs and DOIs across three large taxonomic databases: Index Fungorum, International Plant Names Index (IPNI), and the Index to Organism Names (ION) (Page 2023). Over a million names have been matched to DOIs or other persistent identifiers for taxonomic publications (Fig. 1 shows the coverage of publications for animal names). This represents approximately 36% of animal, plant or fungal names for which publication data is available.\u0000 The mappings between LSIDs and publication persistent identifiers (PIDs) such as DOIs and Wikidata item identifiers, are made available through ChecklistBank (datasets 129659, 164203, 128415), and also archived in Zenodo. By combining these LSID and DOI links with Open Researcher and Contributor ID (ORCIDs) for taxonomists, we can potentially gain insight into who is doing taxonomic research, where they work, and how they are funded. Possible applications of this data are discussed, including a tool to discover the citation for a species name (Species Cite, Fig. 2), using DOI to ORCIDs to discover who is doing taxonomic research, and creating a linked data version of the Catalogue of Life.","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"71 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86344658","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":"Improved Sharing and Linkage of Taxonomic Data with the Taxon Concept Standard (TCS)","authors":"Niels Klazenga","doi":"10.3897/biss.7.112045","DOIUrl":"https://doi.org/10.3897/biss.7.112045","url":null,"abstract":"The term ‘taxonomic backbone’ is often used to indicate the compromise taxonomies that form the taxonomic backbone of systems like the Global Biodiversity Information Facility (GBIF) and the Atlas of Living Australia (ALA). However, the term can also be seen in the broader sense as the entire expansive and continually evolving body of taxonomic work that underpins all biodiversity data and the linkage of all the different concepts that are used in various parts of the world and by various groups of people.\u0000 The Taxon Concept Schema (TCS; Hyam and Kennedy 2006), which was ratified as a TDWG standard in 2005, came forth from the need of providers of taxonomic information for a mechanism to exchange data with other providers and users. Additionally, there was the knowledge that taxon names make poor identifiers for taxa and that more than names are needed for effective sharing and linking of biodiversity data. The same name can be associated with multiple taxon concepts or definitions, especially when a name has been around for a long time or is used in a heavily revised group. In order for others to know what a name means, people who use a name should also indicate which concept of that name is being used. Traditionally, the Latin ‘sensu’ or `sec.` have been used for this purpose; in TCS, an ‘according to’ property is used. The taxon concept, along with a language to relate different concepts, which is also in TCS, was later introduced to a systematic audience in an article by Franz and Peet (2009).\u0000 Unfortunately, TCS has never enjoyed wide adoption and since Darwin Core (Wieczorek et al. 2012) was ratified in 2009, sharing of taxonomic information has mostly been done with the Darwin Core Taxon class. However, various issues with the Darwin Core Taxon class (e.g., Darwin Core and RDF/OWL Task Groups 2015) have made us look at TCS again and in 2020 the Taxonomic Names and Concepts Interest Group was formally renamed the TCS Maintenance Group. In 2021, a TCS 2 Task Group was established with the goal to update TCS to a Vocabulary Standard (like Darwin Core) that can be maintained under the TDWG Vocabulary Maintenance Specification (Vocabulary Maintenance Specification Task Group 2017).\u0000 As it currently stands, TCS 2 (TCS 2 Task Group 2023) has two classes for dealing with taxonomy, the Taxon Concept and Taxon Relationship classes, and two classes for dealing with nomenclature, the Taxon Name and Nomenclatural Type classes. TCS 2 describes objects that are present and known in the domain and uses terms that are used in the domain (e.g., Greuter et al. 2011, Hawksworth 2010), so is easily understood by practitioners in the domain and other users of taxonomic information, as well as data specialists and developers. At the same time, it is in accordance with the OpenBiodiv Ontology (Senderov et al. 2018) and the Simple Knowledge Organization System (SKOS; Miles and Bechhofer 2009).\u0000 TCS 2 can be used to mark up taxon concepts of any type, including tax","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86517208","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":"Mapping.bio: Piloting FAIR semantic mappings for biodiversity digital twins","authors":"Alexander Wolodkin, Claus Weiland, Jonas Grieb","doi":"10.3897/biss.7.111979","DOIUrl":"https://doi.org/10.3897/biss.7.111979","url":null,"abstract":"Biodiversity research has a strong focus on the links between environment and functional traits, e.g., to assess how anthropogenic drivers of change impact ecological systems (Díaz et al. 2013). Interoperable exchange and integration of such data is enabled through the use of ontologies that provide ”meaning” to data and enable downstream processing involving learning and inference over graph-structured models of these data (Kulmanov et al. 2020). However, the development of thematically similar semantic artifacts, e.g., the Environmental Ontology (ENVO, Buttigieg et al. 2016) and the Semantic Web for Earth and Environment Technology Ontology (SWEET, DiGiuseppe et al. 2014), in biodiversity-related disciplines (e.g., environmental genomics and earth observation) can introduce substantial conceptual overlaps, and highlights the need for bridging technologies to facilitate reuse of biodiversity data across those knowledge fields (Karam et al. 2020). \u0000 A recent design study, funded by the European Open Science Cloud (EOSC), proposes a framework to create, document and publish mappings and crosswalks linking different semantic artifacts within a particular scientific community and across scientific domains under the label of \"Flexible Semantic Mapping Framework\" (SEMAF, Broeder et al. 2021). SEMAF puts a strong emphasis on so-called pragmatic mappings, i.e., mappings that are driven by specific interoperability goals such as translations between specific observation measurements (e.g., sensor configurations) and metadata descriptions. Within the Horizon Europe Project “Biodiversity Digital Twin for Advanced Modelling, Simulation and Prediction Capabilities\" (BioDT), a mapping tool leveraging SEMAF is currently under development: Mapping.bio provides a lightweight web service to read semantic artifacts, visualize them, add mappings as graphical connections and store the mappings as FAIR (Findable, Accessible, Interoperable Reusable) Digital Objects (FDOs, De Smedt et al. 2020) in a repository. To foster reusability, sustainably and long-term availability of digital objects, mapping.bio features mappings compliant with the Simple Standard for Sharing Ontological Mappings (SSSOM, Matentzoglu et al. 2022), a machine-interpretable and extensible vocabulary enabling the self-contained exploration and processing of annotated mappings by machines (machine actionability, Jacobsen et al. 2020).","PeriodicalId":9011,"journal":{"name":"Biodiversity Information Science and Standards","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83194946","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}