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Journal articles on the topic 'Darwin Core mapping'

Author: Grafiati

Published: 5 June 2025

Last updated: 16 July 2025

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1

Wieczorek, John, Paul J. Morris, James Hanken, et al. "Darwin Cloud: Mapping real-world data to Darwin Core." Biodiversity Information Science and Standards 1 (August 21, 2017): e20486. https://doi.org/10.3897/tdwgproceedings.1.20486.

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Since its ratification as a TDWG standard in 2009, data publishers have had to struggle with the essential step of mapping fields in working databases to the terms in Darwin Core Wieczorek et al. 2012 in order to publish and share data using that standard. Doing so requires a good understanding of both the data set and Darwin Core. The accumulated knowledge about these mappings constitutes what we call the "Darwin Cloud." We will explore the nature of data mapping challenges and the potential for semi-automated solutions to them. Specifically, we will look at the "Darwinizer" actor and its usa

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Wieczorek, John, Paul J. Morris, James Hanken, et al. "Darwin Cloud: Mapping real-world data to Darwin Core." Proceedings of TDWG 1 (August 21, 2017): e20486. http://dx.doi.org/10.3897/tdwgproceedings.1.20486.

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3

Hall, Kathryn, Matt Andrews, Keeva Connolly, et al. "The Australian Reference Genome Atlas (ARGA): Finding, sharing and reusing Australian genomics data in an occurrence-driven context." Biodiversity Information Science and Standards 7 (September 6, 2023): e112129. https://doi.org/10.3897/biss.7.112129.

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Fundamental to the capacity of Australia's 15,000 biosciences researchers to answer questions in taxonomy, phylogeny, evolution, conservation, and applied fields like crop improvement and biosecurity, is access to trusted genomics (and genetics) datasets. Historically, researchers turned to single points of origin, like GenBank (part of the United States' National Center for Biotechnology Information), to find the reference or comparative data they needed, but the rapidity of data generation using next-gen methods, and the enormous size and diversity of datasets derived from next-gen sequencin

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4

Meyer, Raïssa, Pier Buttigieg, John Wieczorek, et al. "Aligning Standards Communities: Sustainable Darwin Core MIxS Interoperability." Biodiversity Information Science and Standards 5 (September 1, 2021): e73775. https://doi.org/10.3897/biss.5.73775.

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Biodiversity is increasingly being assessed using omic technologies (e.g. metagenomics or metatranscriptomics); however, the metadata generated by omic investigations is not fully harmonised with that of the broader biodiversity community. There are two major communities developing metadata standards specifications relevant to omic biodiversity data: TDWG, through its Darwin Core (DwC) standard, and the Genomic Standard Consortium (GSC), through its Minimum Information about any (x) Sequence (MIxS) checklists. To prevent these specifications leading to silos between the communities using them

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Strong, Mieke, and Piers Higgs. "Mapping between Darwin Core and the Australian Biodiversity Information Standard: A linked data example." Biodiversity Information Science and Standards 7 (September 15, 2023): e112722. https://doi.org/10.3897/biss.7.112722.

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The Australian Biodiversity Information Standard (ABIS) is a data standard that has been developed to represent and exchange biodiversity data expressed using the Resource Description Framework (RDF). ABIS has the TERN ontology at its core, which is a conceptual information model that represents plot-based ecological surveys. The RDF-linked data structure is self-describing, composed of "triples". This format is quite different from tabular data. During the Australian federal government Biodiversity Data Repository pilot project, occurrence data in tabular Darwin Core format was converted into

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Klazenga, Niels, and Johan Liljeblad. "Expressing Circumscription in the Taxon Concept Schema (TCS)." Biodiversity Information Science and Standards 8 (November 1, 2024): e140738. https://doi.org/10.3897/biss.8.140738.

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The Taxon Concept Schema (TCS, Biodiversity Information Standards (TDWG) 2005) is the TDWG standard for sharing taxonomic data. TCS has never enjoyed widespread use and most taxonomic data is exchanged using the Darwin Core (Wieczorek et al. 2012) Taxon class or non-standard terms. For the last three years, the TCS 2 Task Group has been working on a major new version, which will take TCS out of its XML Schema and convert it to a vocabulary standard of terms and definitions that does not dictate a data format and can be maintained under the TDWG Vocabulary Maintenance Standard (Vocabulary Maint

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Meyer, Raïssa, Ward Appeltans, William Duncan, et al. "Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability." Biodiversity Data Journal 11 (October 3, 2023): e112420. https://doi.org/10.3897/BDJ.11.e112420.

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The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, and knowledge generation. However, the biodiversity and omics communities, converging on omics biodiversity data, have historically developed and adopted their own distinct standards, hindering effective (meta)data integration and collaboration.In response to this challenge, the Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic S

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Desmet, Peter, Hoey Stijn Van, Lien Reyserhove, Dimitri Brosens, Damiano Oldoni, and Tanja Milotic. "Standardizing Biologging Data for LifeWatch: Camera Traps, Acoustic Telemetry and GPS Tracking." Biodiversity Information Science and Standards 3 (June 26, 2019): e37413. https://doi.org/10.3897/biss.3.37413.

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The Research Institute for Nature and Forest (INBO) is co-managing three biologging networks as part of a terrestrial and freshwater observatory for LifeWatch Belgium. The networks are a GPS tracking network for large birds, an acoustic receiver network for fish, and a camera trap network for mammals. As part of our mission at the Open science lab for biodiversity, we are publishing the machine observations these networks generate as standardized, open data. One of the challenges however, is finding the appropriate standards and platforms to do so. In this talk, we will present the three netwo

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Salim, José Augusto, and Antonio Saraiva. "A Google Sheet Add-on for Biodiversity Data Standardization and Sharing." Biodiversity Information Science and Standards 4 (October 2, 2020): e59228. https://doi.org/10.3897/biss.4.59228.

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For those biologists and biodiversity data managers who are unfamiliar with information science data practices of data standardization, the use of complex software to assist in the creation of standardized datasets can be a barrier to sharing data.Since the ratification of the Darwin Core Standard (DwC) (Darwin Core Task Group 2009) by the Biodiversity Information Standards (TDWG) in 2009, many datasets have been published and shared through a variety of data portals. In the early stages of biodiversity data sharing, the protocol Distributed Generic Information Retrieval (DiGIR), progenitor of

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Frøslev, Tobias, Thomas Jeppesen, Tim Robertson, and Dmitry Schigel. "eDNA Metabarcoding Data in the Global Biodiversity Information Facility (GBIF)." Biodiversity Information Science and Standards 7 (August 7, 2023): e110672. https://doi.org/10.3897/biss.7.110672.

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The Global Biodiversity Information Facility (GBIF) is an international network and data infrastructure that provides free and open access to biodiversity data from around the world, enabling scientists, policymakers, and the public to explore and analyze information about the Earth's living organisms. Originally developing at a distance from GBIF, metabarcoding of DNA has become a standard tool for detecting species in bulk samples or environmental samples such as soil, water, and air. Raw sequence data (fastq files) are often shared and deposited in dedicated repositories. Seen from a biodiv

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Sica, Yanina, and Paula Zermoglio. "Unlocking Inventory Data Capture, Sharing and Reuse: The Humboldt Extension to Darwin Core." Biodiversity Information Science and Standards 5 (September 13, 2021): e74275. https://doi.org/10.3897/biss.5.74275.

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Biodiversity inventories, i.e., recording multiple species at a specific place and time, are routinely performed and offer high-quality data for characterizing biodiversity and its change. Digitization, sharing and reuse of incidental point records (i.e., records that are not readily associated with systematic sampling or monitoring, typically museum specimens and many observations from citizen science projects) has been the focus for many years in the biodiversity data community. Only more recently, attention has been directed towards mobilizing data from both new and longstanding inventories

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Ettema, Thijs J. G., та Siv G. E. Andersson. "The α-proteobacteria: the Darwin finches of the bacterial world". Biology Letters 5, № 3 (2009): 429–32. http://dx.doi.org/10.1098/rsbl.2008.0793.

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The α-proteobacteria represent one of the most diverse bacterial subdivisions, displaying extreme variations in lifestyle, geographical distribution and genome size. Species for which genome data are available have been classified into a species tree based on a conserved set of vertically inherited core genes. By mapping the variation in gene content onto the species tree, genomic changes can be associated with adaptations to specific growth niches. Genes for adaptive traits are mostly located in ‘plasticity zones’ in the bacterial genome, which also contain mobile elements and are highly vari

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Edelstein, Susan, and Ben Norton. "Semantic Mapping of the Geologic Time Scale: A temporal reference." Biodiversity Information Science and Standards 7 (September 7, 2023): e112232. https://doi.org/10.3897/biss.7.112232.

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The Geologic Time Scale is an ordered hierarchical set of terms representing specific time intervals in Earth's history. The hierarchical structure is correlated to the geologic record and major geologic events in Earth's history (Gradstein et al. 2020). In the absence of quantitative numeric age values from absolute dating methods, the relative time intervals in the geologic time scale provide us with the vocabulary needed for deciphering Earth's history and chronological reconstruction. This temporal frame of reference is critical to establishing correlations between specimens and how they f

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Woodburn, Matt, Jutta Buschbom, Sharon Grant, et al. "No Pain No Gain: Standards mapping in Latimer Core development." Biodiversity Information Science and Standards 7 (September 21, 2023): e113053. https://doi.org/10.3897/biss.7.113053.

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Latimer Core (LtC) is a new proposed Biodiversity Information Standards (TDWG) data standard that supports the representation and discovery of natural science collections by structuring data about the groups of objects that those collections and their subcomponents encompass (Woodburn et al. 2022). It is designed to be applicable to a range of use cases that include high level collection registries, rich textual narratives and semantic networks of collections, as well as more granular, quantitative breakdowns of collections to aid collection discovery and digitisation planning.As a standard th

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Leeflang, Sam, and Wouter Addink. "Harmonised Data is Actionable Data: DiSSCo's solution to data mapping." Biodiversity Information Science and Standards 7 (September 6, 2023): e112137. https://doi.org/10.3897/biss.7.112137.

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Predictability is one of the core requirements for creating machine actionable data. The better predictable the data, the more generic the service acting on the data can be. The more generic the service, the easier we can exchange ideas, collaborate on initiatives and leverage machines to do the work. It is essential for implementing the FAIR Principles (Findable, Accessible, Interoperable, Reproducible), as it provides the "I" for Interoperability (Jacobsen et al. 2020). The FAIR principles emphasise machine actionability because the amount of data generated is far too large for humans to han

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Bentley, Andrew. "Management and GGBN publishing of tissue and DNA extract data through Specify software." Biodiversity Information Science and Standards 2 (July 5, 2018): e26749. http://dx.doi.org/10.3897/biss.2.26749.

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Due to the recent establishment of the Global Genome Biodiversity Network (GGBN) data portal, we have extended Specify collections management software (http://www.sustain.specifysoftware.org/) to more effectively manage, publish, and integrate tissue and DNA extract data by adding support for the GGBN data schema. Specify’s database design now includes a number of data fields and tables proscribed in GGBN standard vocabularies. We also realigned some of the underlying table relationships to address the needs of specimen curation and collection transactions for extract and tissue samples. Speci

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Bentley, Andrew. "Management and GGBN publishing of tissue and DNA extract data through Specify software." Biodiversity Information Science and Standards 2 (July 5, 2018): e26749. https://doi.org/10.3897/biss.2.26749.

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Due to the recent establishment of the Global Genome Biodiversity Network (GGBN) data portal, we have extended Specify collections management software (http://www.sustain.specifysoftware.org/) to more effectively manage, publish, and integrate tissue and DNA extract data by adding support for the GGBN data schema. Specify's database design now includes a number of data fields and tables proscribed in GGBN standard vocabularies. We also realigned some of the underlying table relationships to address the needs of specimen curation and collection transactions for extract and tissue samples. Speci

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18

Haston, Elspeth, Mathias Dillen, Sam Leeflang, et al. "Mapping across Standards to Calculate the MIDS Level of Digitisation of Natural Science Collections." Biodiversity Information Science and Standards 7 (September 14, 2023): e112672. https://doi.org/10.3897/biss.7.112672.

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The Minimum Information about a Digital Specimen (MIDS) standard is being developed within Biodiversity Information Standards (TDWG) to provide a framework for organisations, communities and infrastructures to define, measure, monitor and prioritise the digitisation of specimen data to achieve increased accessibility and scientific use. MIDS levels indicate different levels of completeness in digitisation and range from Level 0: not yet meeting minimal required information needs for scientific use to Level 3: fulfilling the requirements for Digital Extended Specimens (Hardisty et al. 2022) by

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Salim, José Augusto, Katja Seltmann, Jorrit Poelen, and Antonio Saraiva. "Indexing Biotic Interactions in GBIF data." Biodiversity Information Science and Standards 6 (August 23, 2022): e93565. https://doi.org/10.3897/biss.6.93565.

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The Global Biodiversity Information Facility (GBIF 2022a) has indexed more than 2 billion occurrence records from 70,147 datasets. These datasets often include "hidden" biotic interaction data because biodiversity communities use the Darwin Core standard (DwC, Wieczorek et al. 2012) in different ways to document biotic interactions. In this study, we extracted biotic interactions from GBIF data using an approach similar to that employed in the Global Biotic Interactions (GloBI; Poelen et al. 2014) and summarized the results. Here we aim to present an estimation of the interaction data availabl

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Haston, Elspeth, Mathias Dillen, Sam Leeflang, and Cat Chapman. "Completing the Completeness Measure: the MIDS Specification." Biodiversity Information Science and Standards 8 (September 24, 2024): e137717. https://doi.org/10.3897/biss.8.137717.

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The need to rapidly digitise millions of specimens in natural history collections has seen the development of a staged approach for data capture by institutions that have been carrying out mass digitisation projects. The cost and difficulty of transcribing labels associated with specimens has necessitated an approach that prioritises parts of the data based on research and curatorial requirements as well as ease of transcription and methodology available. This approach means that there is currently a wide variation in the completeness of data capture and imaging of specimens within and between

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Rowswell, David, (Lipsen) Linda Jennings, and Nicolas Bailly. "Beaty Biodiversity Museum Collection and Observation Databases: Towards a single search interface." Biodiversity Information Science and Standards 3 (July 2, 2019): e37675. https://doi.org/10.3897/biss.3.37675.

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The Beaty Biodiversity Museum (BBM), at the University of British Columbia, houses over two million biological research specimens, with nearly 40% of the specimen records digitized into databases, unlocking a wealth of information for research and teaching (Table 1). However, these collection databases were neither available nor unified for users. Even museum and collections staff could not digitally access each other's collections. With a total of 6 collections (in different colors in Fig. 1) in 13 separate databases in differing stages of development, across several varying interfaces and sy

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Martínez, de la Riva Santiago. "The Registry component of Atlas of Living Australia." Biodiversity Information Science and Standards 1 (July 25, 2017): e19802. https://doi.org/10.3897/tdwgproceedings.1.19802.

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Atlas of Living Australia (ALA)*1 is a Biodiversity Information System that has been developed to support the Biodiversity community. It offers access to open data allowing queries, downloads and interoperability. It uses standards to show and make accessible the information: JSON*2, Darwin Core Archive*3 and OGC*4. And users can see the data, have access to the metadata at different levels (occurrence, dataset, collection, institution, data provider...) ALA is developed on an architecture based on RESTFUL*5 web services and it is composed of several components that interact with each other us

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Jomier, Remy, Paula Zermoglio, and John Wieczorek. "Building community-specific standards and vocabularies: prospects and challenges for linking to the broader community - The SINP Case." Biodiversity Information Science and Standards 1 (August 14, 2017): e20297. https://doi.org/10.3897/tdwgproceedings.1.20297.

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Biodiversity data may come from myriad sources. From data capture in the field through digitization processes, each source may choose distinctive ways to capture data. When it comes to sharing data more broadly at national or regional levels, it is imperative that data is presented in ways that encourage understanding both by humans and machines, allowing aggregation and serving the data back to the community. This implies two levels of agreement, one at a structural level, where data is organized under certain terms or fields, and another related to the actual values contained in such fields.

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Claudel, Morgane, Emilie Lerigoleur, Cécile Brun, and Sylvie Guillerme. "Geohistorical dataset of ten plant species introduced into Occitania (France)." Biodiversity Data Journal 10 (March 28, 2022): e76283. https://doi.org/10.3897/BDJ.10.e76283.

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The original dataset presented here is the result of the first near-exhaustive analysis performed on historical data concerning ten plant species introduced in and around Occitania (south-western France) since 1651. Research was carried out on the following species: <i>Alnus incana</i>, <i>Buddleja davidii</i>, <i>Castanea sativa</i>, <i>Helianthus tuberosus</i>, <i>Impatiens glandulifera</i>, <i>Prunus cerasifera</i>, <i>Prunus laurocerasus</i>, <i>Reynoutria japonica</i>, <i>Robinia pseudoacacia</i> and <i>Spiraea japonica</i>.The data file contains 199 occurrence data exclusively based on h

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Van Hoey, Stijn, and Peter Desmet. "Whip: Communicate and Test What to Expect from Data." Biodiversity Information Science and Standards 2 (May 18, 2018): e25317. http://dx.doi.org/10.3897/biss.2.25317.

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The ability to communicate and assess the quality and fitness for use of data is crucial to ensure maximum utility and re-use. Data consumers have certain requirements for the data they seek and need to be able to check if a data set conforms with these requirements. Data publishers aim to provide data with the highest possible quality and need to be able to identify potential errors that can be addressed with the available information at hand. The development and adoption of data publication guidelines is one approach to define and meet those requirements. However, the use of a guideline, the

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Van, Hoey Stijn, and Peter Desmet. "Whip: Communicate and Test What to Expect from Data." Biodiversity Information Science and Standards 2 (May 18, 2018): e25317. https://doi.org/10.3897/biss.2.25317.

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The ability to communicate and assess the quality and fitness for use of data is crucial to ensure maximum utility and re-use. Data consumers have certain requirements for the data they seek and need to be able to check if a data set conforms with these requirements. Data publishers aim to provide data with the highest possible quality and need to be able to identify potential errors that can be addressed with the available information at hand. The development and adoption of data publication guidelines is one approach to define and meet those requirements. However, the use of a guideline, the

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Svenningsen, Cecilie, Marcos Gonzalez, and Tim Robertson. "GBIF's Vocabulary Server: A Tool to Create, Manage and Apply Controlled Vocabularies for Biodiversity." Biodiversity Information Science and Standards 8 (September 26, 2024): e137853. https://doi.org/10.3897/biss.8.137853.

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Global Biodiversity Information Facility's (GBIF) global index of primary biodiversity data is based on contributions from more than 2,200 publishing institutions and over 100,000 datasets. Data originate from a broad variety of fields, from research to citizen science, from eDNA through specimen collections to observations and monitoring projects, across all taxonomic groups, and with a wide range of datasets and data types. Equally variable is the underlying motivation and focus for data collection and digitization. Even within commonly used domain concepts like Kingdom or OccurrenceStatus,

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Dillen, Mathias, Pieter Huybrechts, Quentin Groom, and Lynn Delgat. "Calculating the Digitization Level of Specimens with the Minimum Information about a Digital Specimen (MIDS) Standard." Biodiversity Information Science and Standards 6 (August 1, 2022): e90879. https://doi.org/10.3897/biss.6.90879.

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Natural history specimens constitute physical evidence for past observations of nature. They hold further value as the backbone of taxonomy and as historical samples that can be subjected to further analysis. Yet, as physical objects scattered across collections around the world, their scientific use cases are limited by an overall lack of FAIRness, i.e. not easily Findable, Accessible, Interoperable or Reusable. Digitization of these specimens through imaging and categorical metadata capture can improve this FAIRness and has been done to some extent for decades already, but only recently have

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Meyke, Evgeniy. "When Data Management Meets Project Management." Biodiversity Information Science and Standards 3 (June 19, 2019): e37224. https://doi.org/10.3897/biss.3.37224.

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Complex projects that collect, curate and analyse biodiversity data are often presented with the challenge of accommodating diverse data types, various curation and output workflows, and evolving project logistics that require rapid changes in the applications and data structures. At the same time, sustainability concerns and maintenance overheads pose a risk to the long term viability of such projects. We advocate the use of flexible, multiplatform tools that adapt to operational, day-to-day challenges while providing a robust, cost efficient, and maintainable framework that serves the needs

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Müller, Andreas, Raab-Straube Eckhard von, and Walter G. Berendsohn. "A Taxonomic Concept Mapping Service for Taxonomic Information Aggregators." Biodiversity Information Science and Standards 8 (September 2, 2024): e136016. https://doi.org/10.3897/biss.8.136016.

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Linking local taxon-related information to global (or larger area) aggregators of taxonomic information is in ever growing demand. However, linking local taxon-related data to global information systems faces various obstacles. Apart from technical problems, there are specific taxonomic issues to solve. Not only do taxon names need to be matched if written in different ways (e.g., <em>Abies alba</em> Mill. and <em>Abies alba</em> Miller), but also taxonomic concepts have to be compared and mapped. A taxonomic concept is here understood to circumscribe the taxon, i.e., it determines to which ta

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Rapalai, Boikhutso Lerato, Kudzai Mafuwe, Laban Njoroge, and Balsama Rajemison. "Towards Insect Digital Collections and Data Publishing: A journey for the GBIF-funded African Insect Atlas Collaborative Project." Biodiversity Information Science and Standards 1 (August 15, 2017): e20274. https://doi.org/10.3897/tdwgproceedings.1.20274.

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Museums from six African countries (Botswana, Kenya, Zimbabwe, South Africa, Madagascar, Mozambique), with support from the California Academy of Sciences, are currently collaborating on the GBIF funded project: African Insect Atlas: unleashing the potential of insects in conservation and sustainability research in Africa (BID-AF2015-0134-REG). This project was initiated to move biodiversity knowledge out of insect collections into the hands of a new generation of global biodiversity researchers interested in direct outcomes. The project acknowledges that insects are the glue that hold ecosyst

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Islam, Sharif, Gordillo Julian Lopez, Dag Endresen, and Carrie Andrew. "Bridging Data Standards and FAIR Principles in Biodiversity Digital Twinning: Prototyping, Challenges, Lessons Learned, and Future Plans." Biodiversity Information Science and Standards 8 (August 7, 2024): e133089. https://doi.org/10.3897/biss.8.133089.

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Digital twins combine modelling, domain knowledge, computing power, and multiple datasets to offer the potential to unlock new insights into biodiversity (de Koning et al. 2023). The Biodiversity Digital Twin (BioDT) project pioneers this approach to aid in understanding biodiversity through prototyping digital twins (Golivets et al. 2024). However, working with biodiversity data presents challenges due to their dynamic and diverse nature as well as the need for having to deal with incompleteness, uncertainties (Rocchini et al. 2011), disproportionate representation patterns in global studies

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Little, Holly, Christina Byrd, Talia Karim, Erica Krimmel, and Ben Norton. "Extinct Taxa in an Extant World: Working towards better fossil taxonomic representation." Biodiversity Information Science and Standards 6 (September 7, 2022): e94417. https://doi.org/10.3897/biss.6.94417.

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Paleontology collections face many similar challenges mobilizing taxonomic data as extant collections disciplines: from complex nomenclatural histories to incomplete taxonomic authorities to questionable specimen identifications. These challenges exist within the information management of an individual institution and are amplified at the level of data aggregation, where a minor misspelling of authorship or a historic name can completely erase the discoverability of a specimen. In addition to those challenges shared with extant taxonomy, fossil taxonomy must also address uncertainty in far mor

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Lewers, Kristen "Kit." "Comparative Methods for Building Chatbots: Open Source, Hybrid, and Fully Integrated Large Language Models." Biodiversity Information Science and Standards 8 (November 29, 2024): e143032. https://doi.org/10.3897/biss.8.143032.

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In the complex and dynamic realm of biodiversity informatics, the accessibility and comprehension of standards and vocabularies are pivotal for, but not limited to, effective data management, research, policy, regulation, and education. Biodiversity Information Standards (TDWG) provides a suite of standards crucial for the interoperability and consistency of biodiversity data applied to petabytes of data aggregated at GBIF (Global Biodiversity Information Facility). Among these, Darwin Core (DwC; Darwin Core Task Group 2009) and its extensions, stand out as foundational frameworks that guide t

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Koivula, Hanna, Christoph Wohner, Barbara Magagna, Acquaviva d'Aragona Paolo Tagliolato, and Alessandro Oggioni. "Mobilising Long-Term Natural Environment and Biodiversity Data and Exposing it for Federated, Semantic Queries." Biodiversity Information Science and Standards 7 (September 7, 2023): e112221. https://doi.org/10.3897/biss.7.112221.

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Biodiversity and ecosystems cannot be studied without assessing the impacts of changing environmental conditions. Since the 1980s, the U.S. National Science Foundation's Long Term Ecological Research (LTER) Network has been a major force in the field of ecology to better understand ecosystems. In Europe, the LTER developments are led by the the Integrated European Long-Term Ecosystem, critical zone and socio-ecological system Research Infrastructure (eLTER RI), a currently project-based infrastructure initiative with the aim to facilitate high impact research and catalyse new insights about th

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Ariño, Arturo, Daniel Noesgaard, Angel Hjarding, and Dmitry Schigel. "Biodiversity Information Services: A (not-so-) little knowledge that acts." Biodiversity Information Science and Standards 2 (May 22, 2018): e25738. http://dx.doi.org/10.3897/biss.2.25738.

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Standards set up by Biodiversity Information Standards-Taxonomic Databases Working Group (TDWG), initially developed as a way to share taxonomical data, greatly facilitated the establishment of the Global Biodiversity Information Facility (GBIF) as the largest index to digitally-accessible primary biodiversity information records (PBR) held by many institutions around the world. The level of detail and coverage of the body of standards that later became the Darwin Core terms enabled increasingly precise retrieval of relevant records useful for increased digitally-accessible knowledge (DAK) whi

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Ariño, Arturo, Daniel Noesgaard, Angel Hjarding, and Dmitry Schigel. "Biodiversity Information Services: A (not-so-) little knowledge that acts." Biodiversity Information Science and Standards 2 (May 22, 2018): e25738. https://doi.org/10.3897/biss.2.25738.

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Standards set up by Biodiversity Information Standards-Taxonomic Databases Working Group (TDWG), initially developed as a way to share taxonomical data, greatly facilitated the establishment of the Global Biodiversity Information Facility (GBIF) as the largest index to digitally-accessible primary biodiversity information records (PBR) held by many institutions around the world. The level of detail and coverage of the body of standards that later became the Darwin Core terms enabled increasingly precise retrieval of relevant records useful for increased digitally-accessible knowledge (DAK) whi

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Addink, Wouter, Sam Leeflang, and Sharif Islam. "A Simple Recipe for Cooking your AI-assisted Dish to Serve it in the International Digital Specimen Architecture." Biodiversity Information Science and Standards 7 (September 14, 2023): e112678. https://doi.org/10.3897/biss.7.112678.

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With the rise of Artificial Intelligence (AI), a large set of new tools and services is emerging that supports specimen data mapping, standards alignment, quality enhancement and enrichment of the data. These tools currently operate in isolation, targeted to individual collections, collection management systems and institutional datasets. To address this challenge, DiSSCo, the Distributed System of Scientific Collections, is developing a new infrastructure for digital specimens, transforming them into actionable information objects. This infrastructure incorporates a framework for annotation a

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Suominen, Tommi, Joonas Kesäniemi, and Hanna Koivula. "Making Schemas and Mappings Available and FAIR: A metadata and schema crosswalk registry from the FAIRCORE4EOSC project." Biodiversity Information Science and Standards 7 (September 7, 2023): e112223. https://doi.org/10.3897/biss.7.112223.

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Community standards like the Darwin Core (Darwin Core Task Group 2009) together with semantic artefacts (controlled vocabularies, ontologies, thesauri, and other knowledge organisation systems) are key building blocks for the implementation of the FAIR (Findable, Accessible, Interoperable, Reusable) principles (Wilkinson et al. 2016), specifically as emphasized in the Interoperability principle I2 "(Meta)data use vocabularies that follow FAIR principles". However, most of these artefacts are actually not FAIR themselves (Le Franc et al. 2020). To address this, the FAIRCORE4EOSC project (2022-2

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Buschbom, Jutta, Ben Collier, Matt Woodburn, et al. "Simple Models, Complex Vocabularies: Developing Controlled Vocabularies for an Interdisciplinary Collection Management System in RECODE." Biodiversity Information Science and Standards 8 (August 22, 2024): e135228. https://doi.org/10.3897/biss.8.135228.

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Situated at the intersection of distinct stakeholder communities and their objectives, collection management systems (CMS) need to integrate and mediate a wide range of demands to provide functionality, user experience, and data fit for purpose. While metadata standards, (e.g., Biodiversity Information Standards (TDWG) Darwin Core (Darwin Core Task Group 2009) and its Latimer Core (Grant et al. 2024), and Pinian Core (Plinian Core Task Group 2021) extensions) and ontologies, (e.g., the World Wide Web Consortium (W3C) Provenance Ontology (Lebo et al. 2013) or the W3C Open Digital Rights Languag

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Oldoni, Damiano, Quentin Groom, and Peter Desmet. "Occurrence Cubes: A new way of aggregating heterogeneous species occurrence data." Biodiversity Information Science and Standards 4 (September 30, 2020): e59154. https://doi.org/10.3897/biss.4.59154.

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The digital era has brought about an impressive increase in the volume of published species occurrence data. Research infrastructures such as the Global Biodiversity Information Facility (GBIF), the digitization of legacy data, and the use of mobile applications have all played a role in this transition. More data implies, unavoidably, more heterogeneity at multiple levels as a result of the different methods and standards used to collect data. Data standardization and aggregation help to reduce this heterogeneity. Furthermore, intermediate data products that can be used for activities such as

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Salim, José Augusto, Paula Zermoglio, Debora Drucker, et al. "Plant-pollinator Vocabulary - a Contribution to Interaction Data Standardization." Biodiversity Information Science and Standards 5 (September 23, 2021): e75636. https://doi.org/10.3897/biss.5.75636.

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Human demands on resources such as food and energy are increasing through time while global challenges such as climate change and biodiversity loss are becoming more complex to overcome, as well as more widely acknowledged by societies and governments. Reports from initiatives like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) have demanded quick and reliable access to high-quality spatial and temporal data of species occurrences, their interspecific relations and the effects of the environment on biotic interactions. Mapping species interactions

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Casaer, Jim, Tanja Milotic, Yorick Liefting, Peter Desmet, and Patrick Jansen. "Agouti: A platform for processing and archiving of camera trap images." Biodiversity Information Science and Standards 3 (September 24, 2019): e46690. https://doi.org/10.3897/biss.3.46690.

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Camera traps placed in the field, photograph warm-bodied animals that pass in front of an infrared sensor. The imagery represents a rich source of data on mammals larger than ~200 grams, providing information at the level of species and communities. Camera-trap surveys generate observations of specific mammals at a certain location and time, including photo evidence that can be evaluated by experts to map species distribution patterns. The imagery also provides information on the species composition of local communities, identifying which species co-occur and in what proportion. Moreover, the

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Gueta, Tomer, Rahul Chauhan, Thiloshon Nagarajah, et al. "bddashboard: An infrastructure for biodiversity dashboards in R." Biodiversity Information Science and Standards 5 (September 27, 2021): e75684. https://doi.org/10.3897/biss.5.75684.

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<u>The bdverse</u> is a collection of packages that form a general framework for facilitating biodiversity science in R (programming language). Exploratory and diagnostic visualization can unveil hidden patterns and anomalies in data and allow quick and efficient exploration of massive datasets. The development of an interactive yet flexible dashboard that can be easily deployed locally or remotely is a highly valuable biodiversity informatics tool. To this end, we have developed 'bddashboard', which serves as an agile framework for biodiversity dashboard development. This project is built in

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Groom, Quentin, Chloé Besombes, Josh Brown, et al. "Progress in Authority Management of People Names for Collections." Biodiversity Information Science and Standards 3 (June 13, 2019): e35074. https://doi.org/10.3897/biss.3.35074.

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The concept of building a network of relationships between entities, a knowledge graph, is one of the most effective methods to understand the relations between data. By organizing data, we facilitate the discovery of complex patterns not otherwise evident in the raw data. Each datum at the nodes of a knowledge graph needs a persistent identifier (PID) to reference it unambiguously. In the biodiversity knowledge graph, people are key elements (Page 2016). They collect and identify specimens, they publish, observe, work with each other and they name organisms. Yet biodiversity informatics has b

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Vattakaven, Thomas, Harikrishnan Surendran, and Prabhakar Rajagopal. "A decade of the India Biodiversity Portal: Planning ahead with technology to enhance citizen science participation in India." Biodiversity Information Science and Standards 3 (June 19, 2019): e37202. https://doi.org/10.3897/biss.3.37202.

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The India Biodiversity Portal (IBP) was initiated a decade ago, aiming to aggregate data on all species within India. The portal has been running a citizen science module for the past 8 years, aggregating observation data from the general public. The portal runs many flagship citizen science campaigns, such as the Neighborhood Trees Campaign, National Moth Week, Spotting Alien Invasive species, Mapping Indian Snails and Slugs and Frogwatch. We have learnt valuable lessons in harnessing participation in citizen science, implementing functionality and in integrating technological advancements in

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Little, Holly, Talia Karim, and Erica Krimmel. "Improving the Adoption and Evolution of Data Standards for Fossil Specimens." Biodiversity Information Science and Standards 5 (September 23, 2021): e75646. https://doi.org/10.3897/biss.5.75646.

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As we atomize and expand the digital representation of specimen information through data standards, it is critical to evaluate the implementation of these developments, including how well they serve discipline-specific needs. In particular, fossil specimens often present challenges because they require information to be captured that is seemingly parallel to, but not entirely aligned with, that of their extant counterparts. Previous work to evaluate data sharing practices of paleontology collections has shown an imbalance in the use of Darwin Core (DwC) (Wieczorek et al. 2012) terms and many i

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Alshahrani, Mohammed, Vedant Parikh, Brandon Foley, and Gennady Verkhivker. "Ensemble-Based Binding Free Energy Profiling and Network Analysis of the KRAS Interactions with DARPin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants and Universal Architecture of Regulatory Hotspots and Allosteric Binding." Biomolecules 15, no. 6 (2025): 819. https://doi.org/10.3390/biom15060819.

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KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS allostery remain poorly understood. In this study, we employ microsecond molecular dynamics simulations, mutational scanning, and binding free energy calculations together with dynamic network modeling to dissect how engineered DARPin proteins K27, K55, K13, and K19 engage KRAS through diverse molecular mechanisms ranging from effector mimicry to conform

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Sterner, Beckett, Nathan Upham, Atriya Sen, and Nico Franz. "Avenues into Integration: Communicating taxonomic intelligence from sender to recipient." Biodiversity Information Science and Standards 4 (October 9, 2020): e59006. https://doi.org/10.3897/biss.4.59006.

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<em>"What is crucial for your ability to communicate with me… pivots on the recipient's capacity to interpret—to make good inferential sense of the meanings that the declarer is able to send" </em>(Rescher 2000, p148).Conventional approaches to reconciling taxonomic information in biodiversity databases have been based on string matching for unique taxonomic name combinations (Kindt 2020, Norman et al. 2020). However, in their original context, these names pertain to specific usages or taxonomic concepts, which can subsequently vary for the same name as applied by different authors. Name-based

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Fichtmueller, David, Walter G. Berendsohn, Gabriele Droege, et al. "ABCD 3.0 Ready to Use." Biodiversity Information Science and Standards 3 (June 19, 2019): e37214. https://doi.org/10.3897/biss.3.37214.

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The TDWG standard ABCD (Access to Biological Collections Data task group 2007) was aimed at harmonizing terminologies used for modelling biological collection information and is used as a comprehensive data format for transferring collection and observation data between software components. The project ABCD 3.0 (A community platform for the development and documentation of the ABCD standard for natural history collections) was financed by the German Research Council (DFG). It addressed the transformation of ABCD into a semantic web-compliant ontology by deconstructing the XML-schema into indiv

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