Archive Format Research Articles

Sharing of data archive of radiation exposure animal experiments in QST/NIRS and IES.

Institute for Radiological Science (NIRS), National Institutes for Quantum Science and Technology (QST), and Institute for Environmental Sciences (IES) have conducted large-scale animal experiments for radiation risk analyses in terms of life shortening and cancer prevalence. It is important to store data and biological samples from these large-scale experiments for sharing and future use since the economic and practical limitations, as well as the ethical considerations, make it difficult. QST/NIRS established an archive called the Japan Storehouse of Animal Radiobiology Experiments (J-SHARE) for the purpose of storing and sharing these historic collections. We plan to integrate the data and tissue specimen images obtained at the IES into J-SHARE by standardizing the archive format, with the aim of maximizing the results of radiation biology research. This integration is expected to contribute to the generation of new knowledge for radiation risk assessment and the provision of scientifically based information on radiation protection.

Deceiving Dichotomies: On the Interrelation of the Archive and the Cultural Memory Canon

ABSTRACTThis paper explores the conceptual relationship between archives and canonization by amending Aleida Assmann's cultural memory framework of Canon and Archive to consider ongoing debates in archival theory and practice. The process of canonization concerns the selection, value, and duration of cultural memory. The formation and function of archives are marked by processes of appraisal (record evaluation and selection), acquisition (record transfer), and preservation (record duration). Placing A. Assmann's framework in conversation with the informational frameworks of de Fremery and Buckland, we observe how at any given time (a past/present context), records (documents) are selected (perception) because of their value in signaling memories and community histories (affordances) while serving as a durable medium for restabilizing identities (use) across time (a present/future context).

PyDwCA: A Tool for Integrating Biodiversity Data

The Darwin Core Archive (DwC-A) format, based on the Darwin Core standard (Wieczorek et al. 2012), facilitates the exchange, management, and integration of biodiversity data from multiple sources. This ability to collate biodiversity data allows datasets to be aggregated at community-supported infrastructures, merged in different combinations, meta-analyzed and submitted to public repositories (Baker et al. 2014). Thus, the DwC-As serve as unifying archives in concatenated collective efforts, such as biodiversity inventories at different spatial and taxonomic scales. Here we describe PyDwCA*1, 2, a Python library implemented to handle the "star scheme" of DwC-A. This new library reads compressed zip files containing the expected meta.xml and uses it to assign the core component and its extensions. It also provides Python classes to define the core, the extensions, and the metadata file for creating an archive and writing it into a compressed zip file. PyDwCA also implements functionality to select, filter and merge DwC-A files. We present this new tool in the context of the construction of the Chilean National Biodiversity Inventory (Fig. 1), but PyDwCA serves as a versatile technical solution applicable to different contexts in the field of biodiversity informatics (e.g., integration of datasets from biological collection and sampling events). To exemplify how PyDwCA works, we present the step-by-step integration of the Chilean Catalogue of Vascular Plants (Rodriguez et al. 2018) on a matrix provided by the Catalogue of Life (Banki 2024), filtered with the species with occurrences recorded for Chile in the Global Biodiversity Information Facility (GBIF) (GBIF.Org 2023).

Ideas and perspectives: Human impacts alter the marine fossil record

Abstract. The youngest fossil record is a crucial source of data documenting the recent history of marine ecosystems and their long-term alteration by humans. However, human activities that reshape communities and habitats also alter sedimentary and biological processes that control the formation of the sedimentary archives recording those impacts. These diverse physical, geochemical, and biological disturbances include changes in sediment fluxes due to the alteration of alluvial and coastal landscapes, seabed disturbance by bottom trawling and ship traffic, ocean acidification and deoxygenation, removal of native species, and introduction of invasive ecosystem engineers. These novel processes modify sedimentation rates, the depth and intensity of sediment mixing, the pore-water saturation state, and the preservation potential of skeletal remains – the parameters controlling the completeness and spatiotemporal resolution of the fossil record. We argue that humans have become a major force transforming the nature of the marine fossil record in ways that can both impede and improve our ability to reconstruct past ecological and climate dynamics. A better understanding of the feedback between human impacts on ecosystem processes and their preservation in the marine fossil record offers new research opportunities and novel tools for interpreting geohistorical archives of the ongoing anthropogenic transformation of the coastal ocean.

Концептуальные основы веб-архивирования в библиотеках

An electronic web document as an object for recording scientific and cultural communications is considered in the paradigm of library documentology. The research significance of preserving network documents as having a specific temporality of media objects is substantiated. Ego-documents, which include online documents (blogs and forums), are considered as part of media culture that is subject to archiving and has research potential. The problem of the disappearance of web documents and ways to solve it are considered. Archiving web documents as a practice for preserving cultural heritage is justified from the point of view of media archeology. An overview of the activities of domestic and foreign libraries in the formation and development of web archives is presented. Cases of cooperation between national and municipal libraries in the formation of web archives and providing access to electronic documents are presented. Recommendations for the development of web archiving in Russia are proposed.

Integrity Check Value, Are You a Spy? Information Leakage Attack on Archive Formats

Integrity Check Value, Are You a Spy? Information Leakage Attack on Archive Formats

СТАНОВЛЕНИЕ И РАЗВИТИЕ СИСТЕМЫ РАЙОННЫХ И ГОРОДСКИХ АРХИВОВ В 1934-1991 ГГ.: НА ПРИМЕРЕ СВЕРДЛОВСКОЙ ОБЛАСТИ

The paper deals with the issue of forming a system of local archives in Russia on the example of functioning of district (city) archives of the Sverdlovsk region from 1934 to 1991. The subject of the study is the network of the lower level archives in the Middle Urals. Based on the historical-institutional approach, an attempt is made to reconstruct the state policy in the field of archiving. The article provides a comprehensive analysis of archival policy, the institutional system of the local archives management and the activity areas as well as the dynamics of the change in the number of archival institutions. Separate consideration is given to the special role of the departments and branches in the regional archival systems. The stages of creating an archival network are dealt with sequentially: the search for a model of a local archival system in Soviet Russia, its implementation (1919–1934), the beginning of the formation of local archives in the Sverdlovsk region (1934–1938), the subordination of the archives to the NKVD-MVD (1939–1956) and their reassignment to the district executive committees (1956–1991). The article concludes on the specific features of the information culture in the USSR, the essential principles of the Soviet archival system and the contradictory trends in the development of the key element of the Russian archival system. The research was carried out on the basis of the documents from the State Archives of the Sverdlovsk Region.

WEB HISTORIES IN THE MAKING: WEB ARCHIVES & THE LOGICS OF PRACTICE

Historically-situated accounts of the Web have a long history within the field of internet studies. Drawing on diverse methodologies and forms of data, web histories of platforms, cultures and communities of practice have illuminated the rich, but often transient and shifting nature of life online. Many web histories rely upon researchers capturing, collecting, and generating their own data through time, though some have also engaged with web archives as a means for studying the past online. However, web archive data have never fulfilled the requirements of positivist ideals such as ‘representativeness’ or objectivity, and the methodological consequences of this observation currently do not go far enough. This panel aims to shift and reframe current discussions of the ‘promise’ of web archives for web historiography, towards identifying what underlying logics or ideals drive and motivate various actors engaged in this work. We argue that not only do the logics underpinning the practices of collecting and archiving the Web deserve further attention, but also the practices of internet researchers who aim to use these materials for studying the Web. Each paper contribution in this panel builds on web archive criticism by situating archived web material as fundamentally tied to the logics of practice. These underpinnings affect not only the formation of web archives, but also the methodological approaches researchers take. We therefore suggest new ways for conceptualising the ‘doing’ of web histories, tying them to an assemblage of people, practice and data that shape how we can come to understand the Web.

Tacit Narratives in the Manuscript Collections of Matthew Parker and Robert Cotton

Over the past two decades, the history of early modern archives has been a topic of considerable interest among historians, and their research has drawn attention to the complex motives and commitments that inspired individuals, communities, and institutions to create, collect, preserve, and use archives in the early modern period. Their research also offers insights into what Eric Ketelaar has called the “tacit narratives of power and knowledge” woven into the formation, preservation, and use of archives and opens up new avenues for exploring the social history of archives. The English Protestant Reformation has provided the backdrop for some of this work, highlighting the ways in which post-Reformation libraries functioned as “polemical weapons” in political and religious struggles to control the historical narrative about the roots of the Reformation. The libraries built by the antiquarian collectors Matthew Parker and Robert Cotton in the 16th and 17th centuries furnish useful examples of the kinds of tacit narratives embedded in the selection, preservation, and use of post-Reformation manuscript collections. This article draws on the research undertaken by early modern historians into the collecting and compiling practices underpinning the formation and use of the Parker and Cotton manuscript collections to demonstrate how their work is helping to illuminate the tacit narratives embedded in early modern archives as well as broadening and deepening the social history of archives.

The premise of temperature effect playing in regions with complex moisture sources – Evidence from high-resolution water vapor isotopes

Atmospheric precipitation has widely taken part in the formation and accumulation of many geological archives. In these processes, the isotope fractionations are tightly related to the meteorological factors, such as temperature and precipitation amount. Therefore, precipitation isotopes are usually regarded as an effective proxy to reconstruct the paleoclimate and paleoenvironmental changes. However, with the deepening of research, it is found that the temperature effect is not suitable for all regions and time scales, especially in regions with complex moisture sources. Moreover, the applicable mechanism of the temperature effect is still unclear. Here, we chose Xi’an as our study site, because it is located in the transition zone of the East Asian Summer Monsoon (EASM) and the westerlies with relatively complex water vapor sources. Through conducting a three-year, high-resolution, relatively continuous water vapor isotopic composition measurements in Xi’an, we defined the duration of the EASM here, which normally starts in June and is over in September. By separating the δ18Op into monsoon and non-monsoon seasons, we found a significant temperature effect in the non-monsoon seasons, with a correlation coefficient of 0.54, while no temperature effect is observed in the monsoon seasons and the whole year. Our water vapor isotopic results suggested that the establishment of temperature effect of precipitation isotopes should follow two prerequisites: 1. single water vapor source; 2. large temperature gradient. Our results specify the applicable conditions of temperature effect and potentially help us to better use precipitation isotopes to understand the paleo-temperature variations in different regions.

Dataset of benthic copepods in the littoral zones of Lake Maggiore

Copepods (Crustacea: Copepoda) are widespread in aquatic ecosystems worldwide and represent an important component of the meiobenthic metazoan assemblages of lake littorals. Yet, little is currently known about the diversity of benthic copepods in lentic habitats. We gathered information on the benthic copepod assemblages of the littoral zone of Lake Maggiore as part of the Interreg Italy-Switzerland 2014-2020 Parchi Verbano Ticino project (ID: 481668), funded by the European Regional Development Fund (ERDF). Lake Maggiore is a large and deep temperate lake in north-western Italy human-managed from mid-March to mid-September. This contributes to substantial changes in water levels in relation to human activities such as hydropower, industrial and agricultural uses. We compiled a dataset listing 234 occurrences of benthic copepod species recorded from three littoral sampling sites situated in three protected areas, two of which are part of the Natura 2000 network in Italy and one is part of the Emerald Network in Switzerland. We collected the specimens during the summer-autumn period in 2019-2021. We identified the copepods at the species level and created a dataset with individual georeferenced occurrence records for each species, organized in a standardized Darwin Core Archive format. We made available, through the Global Biodiversity Information Facility (GBIF), a total of 13 distinct taxonomic entities and 234 unique georeferenced occurrence records related to the benthic copepod assemblages of the littoral zone of Lake Maggiore (Tabilio Di Camillo et al., 2023). The dataset has the potential to support the authorities in charge of managing Lake Maggiore’s water levels in addressing the ecological risk relevant to the littoral zone and in developing shared implementation strategies for sustainable water management.

Littoral chironomids and oligochaetes in the subalpine Lake Maggiore: a first dataset

A dataset of 227 oligochaetes and 373 chironomids occurrence records from the subalpine Lake Maggiore, a large and deep temperate lake in Northern-Western Italy and Switzerland was developed within the Interreg Italy-Switzerland 2014-2020 Parchi Verbano Ticino Project (ID:481668) funded by the European Regional Development Fund (ERDF). The lake belongs to the national (LTER-Italy), European (LTER-Europe) and International (ILTER) long-term ecological research networks. Data were collected during the summer-autumn period in 2019-2021. Chironomids (Insecta, Diptera) and oligochaetes (Annelida, Clitellata) were identified to genus/species gr./species level by the authors. All 600 occurrence records are georeferenced and organised in a standardised Darwin Core Archive format. These data gathered along the littoral areas of Lake Maggiore will contribute to the development of common implementation strategies for shared and sustainable water management level of the lake, with particular reference to the protected natural areas (sites belonging to Natura 2000 network in Italy and to the Emerald Network in Switzerland). The authors strongly believe in the great potential of open access occurrence records in biogeographical studies and ecological research in the context of global environmental changes. For that reason, the dataset has been uploaded to the Global Biodiversity Information Facility (GBIF), an intergovernmental free and open access biodiversity data infrastructure.

The diversity of cultivable endophytic fungi of the sand coast plant Ipomoeapes-caprae in Taiwan.

Ipomoeapes-caprae is a plant of sand coasts and it can tolerate stresses, such as high salinity, strong wind and sand movements and lack of nutrients. It plays an important role in coast protection and preventing erosion. Fungal endophytes show high biodiversity and have a strong influence on the survival of plants under different stress factors. Although this plant is important for sand coast ecosystems, little is known about the associated fungi. In this study, we isolated and identified endophytic fungi of Ipomoeapes-caprae, a dominant plant along the shore of Taiwan. The dataset contains 896 records, which correspond to 177 species. The geographical scope of the dataset covers the northern subtropical area of the main island of Taiwan, with its sand coasts in New Taipei, Taoyuan, Hsinchu and Taichung and two botanical gardens in Taipei and Taichung. The detailed original data of fungal diversity are rarely publicly shared under strictly formalised and, thus, reusable standards. As an example for such an approach, the complete occurrence dataset was made available in the Darwin Core Archive format via the Global Biodiversity Information Facility (GBIF) under Version 1.13, Taiwan Biodiversity Information Facility (TaiBIF) https://doi.org/10.15468/9h9rcg. In this first data paper on endophytic fungi, the scientific name and associated DNA sequence in the dataset were directly linked to other free online resource (Index Fungorum, GenBank), which shows the potential of GBIF for linking together different online data repositories. We describe a dataset, in which the diversity of endophytic fungi of the sand coast plant Ipomoeapes-caprae in Taiwan was investigated.

Simulating a lead-cooled reactor campaign using the EUCLID/V1 code

The paper presents the results of the development of the EUCLID/V1 integrated dynamic code designed to analyze and justify the safety of fast neutron reactor facilities with a liquid-metal coolant, in terms of simulating the reactor campaign. The relevance of this study lies in the need to simulate the behavior of the core at any time during the campaign. It lets us to obtain a full dataset for subsequent simulations of the reactor dynamic conditions (including transient states or accidents). The authors have developed a fuel archive to store calculated data in HDF5 format, created a computational model editor to generate input data in the fuel archive format, and also provided an example of computing the campaign of a lead-cooled fast reactor for three core design models shown in this paper. The main array of fuel assemblies was simulated as a single unit in the first model, as three units in the second model, and in the third every single assembly was unique. In addition, the authors have shown changes in the total masses of actinides in the core, revealed that the different core models have an insignificant effect on the evolution of the total masses of actinides, and given the fuel assembly burnup values for the three core models. For the third model, the largest difference between the minimum and maximum burnup values was obtained with an almost identical average over the fuel assemblies. The reactivity margin over time for the three core models was presented. It was shown that the values and behavior of the reactivity margin during the three micro-campaigns are almost equal. From the fourth to the sixth cycle, the reactivity margin value for the third core model was lower than for the first and the second ones. Finally, the authors conclude that it is desirable to evaluate the behavior of the reactivity margin for lead-cooled fast reactor campaigns based on the detailed model of the core.

NIAGADS Alzheimer’s Genomics Database: version GRCh38

AbstractBackgroundThe Alzheimer’s Genomics Database (GenomicsDB) is an interactive knowledgebase for Alzheimer's disease (AD) genetics that offers a platform for data sharing, discovery, and analysis to accelerate research on AD and AD related dementias (ADRD). The resource provides unrestricted access to GWAS summary statistics datasets, variant annotations, and meta‐analysis results deposited at the NIA Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS). Here we introduce an updated version of the GenomicsDB, now mapped against the latest human genome assembly, GRCh38.MethodThe GenomicsDB allows users to interactively mine AD/ADRD summary statistics datasets or visually inspect them and compare with annotated variant tracks and GRCh38 aligned functional genomics tracks from the FILER functional genomics repository (Kuksa et al. 2022). Available tracks include key AD datasets from large‐scale sequencing projects such as IGAP (Lambert et al. 2013; Kunkle et al. 2019) and the ADGC (e.g., Naj et al. 2011) that have been lifted over from earlier genome builds. Available annotated variants include those from the AD Sequencing Project’s (ADSP) Release3 WGS, called from nearly 17k samples. All variants reported in the GenomicsDB are annotated using an assembly specific version of ADSP annotation pipeline (Butkiewicz et al. 2018). The GenomicsDB provides a REST API for programmatic access. Supported queries return complete annotations for single or bulk lookups of GenomicsDB entries (genes, variants, genomic loci) and ranged queries of datasets as JSON documents.ResultThe GenomicsDB currently hosts >70 datasets and reports >150 million annotated variants from the ADSP and 23 AD/ADRD GWAS studies, mapped to GRCh38. Keeping up with community standards allows this resource to provide ongoing support for AD/ADRD research by making it possible to integrate AD/ADRD relevant `omics datasets generated by the ADSP and others who have adopted GRCh38 as their reference genome.ConclusionThe NIAGADS Alzheimer’s Genomics Database v. GRCh38 (www.niagads.org/genomics) provides an up‐to‐date and accessible platform that facilitates unrestricted sharing of genetic knowledge underpinning AD/ADRD. To best serve our user community, NIAGADS will continue to provide the GRCh37.p19 version of the Alzheimer’s Genomics Database (including programmatic access) in archival format.

Погляд на ранню історію аудіовізуального архівування в Україні

The purpose of the investigation is to look into the early history of national audiovisual archiving, which began with the founding in 1932 and the formation of the All-Ukrainian CinePhoto Archives in Kyiv (now the Central State Audiovisual and Electronic Archives), which in time coincided with the establishment of totalitarianism in the USSR, and to reveal the infl uence of the latter on the formation of relevant archival practices and methodologies. The research methodology is based on general scientifi c principles of the unity of theory and practice, complexity, historicism, comprehensiveness of knowledge, and the application of interdisciplinary and sociocultural approaches. The basic approaches are complemented by a complex of research methods, in particular, problem-chronological, historical-cultural, critical-comparative, structuralfunctional analysis, as well as source studies methods (archival and bibliographic heuristics, systematization and interpretation of sources). Scientifi c novelty. The article describes the prerequisites for the creation and initiation of activities of the All-Ukrainian CinePhoto Archives in Kyiv as the fi rst national center for collecting and storing audiovisual heritage. The content, specifi cs, principles and directions of activity of the audiovisual archive are defi ned, the interconnection and interdependence of the archival reality and the political regime are revealed. The conclusion is formulated that the problem retains research perspectives, in particular in terms of comparing the Ukrainian experience with foreign models of audiovisual archiving and their results in the pre-war period.

Representing Biases, Inequalities and Silences in National Web Archives: Social, Material and Technical Dimensions

Contemporaneous collecting of the publicly available web has provided researchers with an invaluable source with which to interpret various aspects of the recent past. With millions of websites gathered, stored and made accessible in national web archives over the past 25 years, this paper argues for the need to reflect upon, and respond to, the biases, inequalities and silences that exist in these vast repositories. This article presents a research agenda for web archivists and web historians to together think broadly about the social, material and technical dimensions that shape what is included in web archives, and what is excluded. A key challenge impacting this effort is that various complexities and contingencies of archival formation are obscured. These include wider social inequalities, the entanglement of human and machine decision-making in the archiving process, changing dynamics of power over information online and the environmental impact of technical systems. Accounting for these social, material and technical factors that shape the formation of web archives provides opportunities to develop and use archives in ways that better acknowledge both the strengths and limitations of national web archives as a proxy for the web’s past.

Leveraging ecocomDP as a Flexible Intermediate Data Pattern to Expose NEON Biodiversity Data in GBIF

The Environmental Data Initiative (EDI) and the National Ecological Observatory Network (NEON) have been developing a flexible intermediate data design pattern for ecological community data called “ecocomDP”, which is intended to promote FAIR data principles. Specifically, this effort will enhance the discoverability of and access to biodiversity data from NEON and EDI data holdings, including data from the United States Long Term Ecological Research (USLTER) program (O'Brien et al. 2021). The ecocomDP data model is applied in the ecocomDP R (programming language) library, which provides tools for independent researchers to format their data following the ecocomDP standard, as well as tools to search and visualize data from NEON and EDI data holdings in their R environment. The flexibility of the ecocomDP data model allows for much of the ancillary data associated with observation events to be preserved. Here we describe a modular workflow that is under development to expose ecocomDP-formatted data packages in the Global Biodiversity Information Facility (GBIF) data portal (Fig. 1). Specifically, we highlight an effort to apply this workflow to create a pipeline to convert and submit NEON biodiversity data products to GBIF. EDI now has more than 70 data packages reformatted to the ecocomDP model, and has nearly finished developing a conversion of that intermediate format to a Darwin Core Archive (DwC-A, event core) format (Wieczorek et al. 2012) for submission to GBIF. This workflow takes advantage of EDI’s dataset subscription service, which triggers creation of an updated DwC-A when an original dataset is revised. Because ecocomDP provides a standardized input to this submission process, any data package in the ecocomDP format can be exposed in GBIF through this workflow. Thus, we are working to leverage the EDI-managed conversion and submission process to expose NEON data in GBIF, which is possible because of the existing mappings of NEON data products to ecocomDP (Li et al. 2022). This will include data products representing terrestrial and aquatic organisms (Table 1) from all NEON sites, spanning the entire United States. The overall goal of this effort is to provide an automated, modular workflow with complete provenance to submit NEON and EDI datasets to GBIF, built in such a way that datasets can be properly updated as new samples are collected and the data are published. The development of such a submission pipeline will provide a standardized process to expose biodiversity data from two continental scale networks, NEON and the U.S. National Science Foundation's Long-term Ecological Research network in GBIF. Further, the modularity of the workflow will allow independent researchers to adapt tools developed in this effort for their data archiving and publishing needs.

Rhakhis: A workflow for managing the WFO taxonomic backbone

In 2021, the World Flora Online (WFO) Council agreed that the team at the Royal Botanic Garden Edinburgh would take on the technical role of managing the WFO Taxonomic Backbone (WFO-TB). This presentation outlines the implementation of a system to manage the associated data and explores possible future developments. The WFO-TB is a global concensus checklist of plants including bryophytes, pteridophytes, gymnosperms and angiosperms. The checklist data consists of two parts: facts concerning the nomenclatural acts that establish the names under the nomenclatural code, and consensus expert opinion on the placement of those names into a single, authoritative taxonomy. WFO-TB is unique in that it is both global in scope and curated by a large team of experts from multiple institutions. There are currently around 280 specialist contributors organised into 37 Taxonomic Expert Networks (TENs). The primary function of the WFO-TB is to provide structure to the hundreds of thousands of descriptions, images and other pieces of Content that make up the WFO’s main web portal, but periodic snapshots of the taxonomic data are also made available as public downloads and published as the WFO Plant List. The WFO Plant List is unique in that it remembers each version of WFO-TB that was published and links between them thus providing a stable, citable resource. In addition, data can be released in any format that researchers may find useful including through ChecklistBank and so be potentially incorporated into the Catalogue of Life and GBIF (Global Biodiversity Information Facility). All checklist data are released with a Creative Commons (CC) license of CC0 so that others may freely build upon, enhance and reuse the works for any purposes without restriction under copyright or database law. Prior to 2022, the WFO-TB was managed as part of the main WFO data resources supporting the WFO Portal by the team at Missouri Botanical Garden. Moving responsibility for hosting the backbone to the team at Edinburgh added significant resources to the project as a whole, but created technical challenges. The first requirement of the new system (called Rhakhis, a Greek form of rachis, the ‘backbone’ of a leaf or inflorescence) was to demonstrate that it could feed data back to Missouri in a way that could be incorporated into the WFO infrastructure without causing disruption to the Content curation process. This was completed in early 2022, and, by June, the primary copy of the WFO-TB data had been entrusted to Rhakhis. The June 2022 version of the WFO Plant List and the WFO-TB was published using the previous system, switching to publication from Rhakhis in December 2022. The system architecture of Rhakhis is quite simple. A MySQL database holds all the data and is exposed via a GraphQL API to a web-based user interface written in Javascript using React and Bootstrap. User authentication is handled via a link to ORCiD (Open Researcher and Contributor ID). Authorisation for editors is delegated hierarchically down the taxonomic tree. This provides the ability for TENs and the TEN Manager to oversee and manage the live data directly and to delegate authority to colleagues. The TEN Manager has access to a plain HTML bulk loader interface that enables the ingestion of CSV and files in DwC-A (Darwin Core Archive) format supplied by TENs as well as updates from other data sources, such as IPNI (International Plant Names Index) and WCVP (RBG Kew’s World Checklist of Vascular Plants). Rhakhis is designed as a standalone data management tool for taxonomists involved in the project rather than a public website, and is hosted on a WFO server on the Google Cloud. The WFO Plant List is run on a separate system and designed to be a performant public-facing website. Periodic snapshots of the WFO-TB are imported into a Solr Index that is then exposed via another GraphQL API as well as Semantic Web-compliant HTTPS URIs. A web-based user interface to WFO Plant List is implemented as part of the Craft CMS (Content Management System) that also runs the About pages of the WFO Web Portal, but it would be possible to build other interfaces to this data. The periodic snapshots of the WFO-TB, which are published through the WFO Plant List, are archived in Zenodo and assigned a DOI (Digital Object Identifier), as well as contributed to Catalogue of Life ChecklistBank. The archive formats currently supported include: Darwin Core Archive and Catalogue of Life Data Package, but other formats will be considered in the future. We are interested in investigating the creation of data papers, e.g., through the Biodiversity Data Journal at Pensoft, to provide additional accreditation for contributors and exposure of their data.

Indexing Biotic Interactions in GBIF data

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 available in GBIF, showing that biotic interaction claims can be automatically found and extracted from GBIF. Our results suggest that much can be gained by an increased focus on development of tools that help to index and curate biotic interaction data in existing datasets. Combined with data standardization and best practices for sharing biotic interactions, such as the initiative on plant-pollinators interaction (Salim 2022), this approach can rapidly contribute to and meet open data principles (Wilkinson 2016). We used Preston (Elliott et al. 2020), open-source software that versions biodiversity datasets, to copy all GBIF-indexed datasets. The biodiversity data graph version (Poelen 2020) of the GBIF-indexed datasets used during this study contains 58,504 datasets in Darwin Core Archive (DwC-A) format, totaling 574,715,196 records. After retrieval and verification, the datasets were processed using Elton. Elton extracts biotic interaction data and supports 20+ existing file formats, including various types of data elements in DwC records. Elton also helps align interaction claims (e.g., host of, parasite of, associated with) to the Relations Ontology (RO, Mungall 2022), making it easier to discover datasets across a heterogeneous collection of datasets. Using specific mapping between interaction claims found in the DwC records to the terms in RO*1, Elton found 30,167,984 potential records (with non-empty values for the scanned DwC terms) and 15,248,478 records with recognized interaction types. Taxonomic name validation was performed using Nomer, which maps input names to names found in a variety of taxonomic catalogs. We only considered an interaction record valid where the interaction type could be mapped to a term in RO and where Nomer found a valid name for source and target taxa. Based on the workflow described in Fig. 1, we found 7,947,822 interaction records (52% of the potential interactions). Most of them were generic interactions (interacts_with, 87.5%), but the remaining 12.5% (993,477 records) included host-parasite and plant-animal interactions. The majority of the interactions records found involved plants (78%), animals (14%) and fungi (6%). In conclusion, there are many biotic interactions embedded in existing datasets registered in large biodiversity data indexers and aggregators like iDigBio, GBIF, and BioCASE. We exposed these biotic interaction claims using the combined functionality of biodiversity data tools Elton (for interaction data extraction), Preston (for reliable dataset tracking) and Nomer (for taxonomic name alignment). Nonetheless, the development of new vocabularies, standards and best practice guides would facilitate aggregation of interaction data, including the diversification of the GBIF data model (GBIF 2022b) for sharing biodiversity data beyond occurrences data. That is the aim of the TDWG Interest Group on Biological Interactions Data (TDWG 2022).