Rukaya Sarah Johaadien

• Lieungh, Eva; Bjureke, Kristina; Evju, Marianne; Johaadien, Rukaya Sarah; Olsen, Siri Lie & Skarpaas, Olav [Show all 8 contributors for this article] (2022). Presence-absence of plant habitat specialists in 15 patches of dry calcareous grassland. Biodiversity Data Journal. ISSN 1314-2836. 10. doi: 10.3897/BDJ.10.e94057. Full text in Research Archive Show summary

  Background Dry grasslands on calcareous bedrock in warm climates around the Oslo Fjord are naturally fragmented biodiversity hotspots. This habitat geographically coincides with the most densely populated area of Norway. Many habitat specialists, along with the habitat itself, are red-listed because of land-use change, forest encroachment, and invasive species that cause habitat loss and greater isolation of remaining patches. To ensure effective conservation, data on species presences and absences are necessary to quantify states, changes, and extinction risks in specific populations and habitat patches. New information We present presence-absence data of 49 vascular plant species in 15 patches of dry calcareous grassland habitat, surveyed in 2009, 2019, and in 2020. The species are considered to be habitat specialists and, thus, unlikely to occur between the patches. sampling-event, vascular plants, specialist species, presence-absence data, calcareous grassland, habitat patch, GBIF

• Prylutskyi, Oleh; Abrahamyan, Armine; Voronova, Nina; Aloyan, Tatevik; Borodin, Oleg & Darmostuk, Valerii [Show all 33 contributors for this article] (2019). BioDATA - Biodiversity Data for Internationalisation in Higher Education. Research Ideas and Outcomes (RIO). 5. doi: 10.3897/rio.5.e36276. Full text in Research Archive Show summary

  BioDATA is an international project on developing skills in biodiversity data management and data publishing. Between 2018 and 2021, undergraduate and postgraduate students from Armenia, Belarus, Tajikistan, and Ukraine, have an opportunity to take part in the intensive courses to become certified professionals in biodiversity data management. They will gain practical skills and obtain appropriate knowledge on: international data standards (Darwin Core); data cleaning software, data publishing software such as the Integrated Publishing Toolkit (IPT), and preparation of data papers. Working with databases, creating datasets, managing data for statistical analyses and publishing research papers are essential for the everyday tasks of a modern biologist. At the same time, these skills are rarely taught in higher education. Most of the contemporary professionals in biodiversity have to gain these skills independently, through colleagues, or through supervision. In addition, all the participants familiarize themselves with one of the important international research data infrastructures such as the Global Biodiversity Information Facility (GBIF). The project is coordinated by the University of Oslo (Norway) and supported by the Global Biodiversity Information Facility (GBIF). The project is funded by the Norwegian Agency for International Cooperation and Quality Enhancement in Higher Education (DIKU).

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• Chala, Desalegn; Kusch, Erik; Andrew, Carrie; Torma, Michal; Johaadien, Rukaya Sarah & Kehel, Zakaria [Show all 9 contributors for this article] (2024). BioDT Hackathon: Second End-Users Workshop, January 2024. Full text in Research Archive Show summary

  Three-day hackathon titled Harnessing Digital Twinning for Sustainable Agriculture: Predictive Characterisation and Conservation of Crop Wild Relatives, takes place from January 23rd to 25th, 2024 in Oslo, Norway. The event, promises to unravel the immense potential of digital twinning in revolutionizing global agricultural practices.

• Johaadien, Rukaya Sarah; Torma, Michal; Boer, Hugo de; Meyke, Evgeniy; Schigel, Dmitry & Karimov, Farkhod (2024). GBIF in Central Asia new aspects of development Workshop. Full text in Research Archive Show summary

  Physical workshop and conference with optional digital participation, in Tashkent, Uzbekistan. Providing capacity-building on digitization techniques, data publication, and data cleaning, and co-creating Russian language resources. This project aims to enhance data publication and bioinformatics in Uzbekistan and Tajikistan.

• Kongshavn, Katrine; Endresen, Dag; Johaadien, Rukaya Sarah; Bakken, Vidar & Torma, Michal (2023). University Museum of Bergen - Data publication workshop. Full text in Research Archive Show summary

  The Norwegian Global Biodiversity Information Facility (GBIF) node and the University Museum of Bergen welcomes you to a 2-day workshop to publish biodiversity data as Darwin Core Archives on March 13-14th, 2023.

• Johaadien, Rukaya Sarah; Frøslev, Tobias Guldberg; Plessis, Morne Du; Torma, Michal; Kamenova, Stefaniya & Braathen, Catherine [Show all 7 contributors for this article] (2023). Course on DNA barcode data in BOLD and GBIF - Cape Town, South Africa. Full text in Research Archive Show summary

  Accelerating biodiversity research through DNA barcodes, collection, and observation data. Regional Training Course for M.Sc. and Ph.D. students with expert trainers and trainers-in-training - Cape Town, South Africa.

• Marsden, Luke; Johaadien, Rukaya Sarah; Torma, Michal & Endresen, Dag (2023). Marine data publishing workshop. Full text in Research Archive Show summary

  The Norwegian Global Biodiversity Information Facility (GBIF) node, in collaboration with the Nansen Legacy project, 2-day workshop to help you publish your biodiversity data as Darwin Core Archives! This is a fantastic opportunity to work on your data with the assistance of experts who are involved in developing the Darwin Core standards.

• Johaadien, Rukaya Sarah (2023). Zenodo and usage of communities. Full text in Research Archive Show summary

  What are the pros and cons of different general data archives? Which one suits your needs as researcher? In this Data Managers Network meeting UiO researchers will share their experiences with using different general open research data archives.

• Johaadien, Rukaya Sarah & Torma, Michal (2023). "Publish First": A Rapid, GPT-4 Based Digitisation System for Small Institutes with Minimal Resources. Biodiversity Information Science and Standards (BISS). 7(e112428). doi: 10.3897/biss.7.112428. Full text in Research Archive Show summary

  We present a streamlined technical solution ("Publish First") designed to assist smaller, resource-constrained herbaria in rapidly publishing their specimens to the Global Biodiversity Information Facility (GBIF). Specimen data from smaller herbaria, particularly those in biodiversity-rich regions of the world, provide a valuable and often unique contribution to the global pool of biodiversity knowledge (Marsico et al. 2020). However, these institutions often face challenges not applicable to larger herbaria, including a lack of staff with technical skills, limited staff hours for digitization work, inadequate financial resources for specialized scanning equipment, cameras, lights, and imaging stands, limited (or no) access to computers and collection management software, and unreliable internet connections. Data-scarce and biodiversity rich countries are also often linguistically diverse (Gorenflo et al. 2012), and staff may not have English skills, which means pre-existing online data publication resources and guides are of limited use. The "Publish First" method we are trialing, addresses several of these issues: it drastically simplifies the publication process so technical skills are not necessary; it minimizes administrative tasks saving time; it uses simple, cheap and easily available hardware; it does not require any specialized software; and the process is so simple that there is little to no need for any written instructions. "Publish first" requires staff to attach QR code labels containing identifiers to herbarium specimen sheets, scan these sheets using a document scanner costing around €300, then drag and drop these files to an S3 bucket (a cloud container that specialises in storing files). Subsequently, these images are automatically processed through an Optical Character Recognition (OCR) service to extract text, which is then passed on to OpenAI's Generative Pre-Transformer 4 (GPT-4) Application Programming Interface (API), for standardization. The standardized data is integrated into a Darwin Core Archive file that is automatically published through GBIF's Integrated Publishing Toolkit (IPT) (GBIF 2021). The most technically challenging aspect of this project has been the standardization of OCR data to Darwin Core using the GPT-4 API, particularly in crafting precise prompts to address the inherent inconsistency and lack of reliability in these Large Language Models (LLMs). Despite this, GPT-4 outperformed our manual scraping efforts. Our choice of GPT-4 as a model was a naive one: we implemented the workflow on some pre-digitized specimens from previously published Norwegian collections, compared the published data on GBIF with GPT-4's Darwin Core standardized output, and found the results satisfactory. Moving forward, we plan to undertake more rigorous additional research to compare the effectiveness and cost-efficiency of different LLMs as Darwin Core standardization engines. We are also particularly interested in exploring the new "function calling" feature added to the GPT-4 API, as it promises to allow us to retrieve standardized data in a more consistent and structured format. This workflow is currently under trial in Tajikistan, and may possibly be used in Uzbekistan, Armenia and Italy in the near future.

• Johaadien, Rukaya Sarah (2023). AI seminar. Full text in Research Archive
• Mering, Sabine von; Braun, Paul Jean-Charles; Cubey, Robert W. N.; Groom, Quentin; Haston, Elspeth M. & Hendriksen, Anikka [Show all 12 contributors for this article] (2023). Modelling research expeditions in Wikidata: best practice for standardisation and contextualisation. Biodiversity Information Science and Standards (BISS). 7. doi: 10.3897/biss.7.111427. Full text in Research Archive Show summary

  Expeditions and other collecting events are a major source of objects in natural history museums (e.g., Mesibov 2021). Historically, these trips were often transdisciplinary: biological and Earth science specimens were collected at the same time as ethnological or anthropological objects. As a result, specimens and other material gathered during the same expedition, as well as the related data and metadata, are often distributed across multiple institutions. Many expeditions were driven by colonial agendas, aiming to discover new resources to exploit, and their findings were seldom shared with the source countries and local people. Understanding these expeditions illuminates the colonial origins of museum collections, and contributes to recognizing and addressing their impacts (e.g., Das and Lowe 2018, Ashby and Machin 2021).

• Marsden, Luke; Endresen, Dag; Johaadien, Rukaya Sarah; Torma, Michal & Altenburger, Andreas (2022). Nansen Legacy - Marine data publishing workshop in Tromsø in September 2022. Full text in Research Archive Show summary

  Nansen Legacy (AeN) 3-day workshop to publish marine biodiversity data from the AeN project as Darwin Core Archives on September 20-22, 2022. With support from the Norwegian Global Biodiversity Information Facility (GBIF) node, and the Ocean Biodiversity Information System (OBIS, EurOBIS). https://www.gbif.no/events/2022/nansen-legacy-tromso.html

• Johaadien, Rukaya Sarah; Endresen, Dag & Torma, Michal (2022). An Update on Persistent Identifiers in Norwegian Biodiversity Data. Biodiversity Information Science and Standards (BISS). doi: 10.3897/biss.6.91585. Full text in Research Archive Show summary

  Persistent identifiers (PIDs) are reference keys to pieces of digital information or digital objects (Meadows and Haak 2018). PIDs are long-lasting, trustworthy and ideally globally unique, allowing information to be unambigiously associated with a digital object. This allows, for example, collection objects to be annotated with data (e.g., improved geographic coordinates) from different web services and databases (Page 2008). In 2014, Norway began an initiative to provide all museum specimens at the University of Oslo's Natural History Museum (UiO NHM) with PIDs persistent and globally unique identifiers (PIDs) in the form of universally unique identifiers (UUIDs) prefixed by a persistent uniform resource locator (PURL) (Endresen and Svindseth 2014). This poster provides an update of progress made in this endeavor, and details the technical set up and workflow, as well as problems encountered and reflections on the process. So far, roughly 40% of UiO NHM's collections have PIDs entered in the Darwin Core materialSampleID field for the collections management system. The main technical problem has been in configuring the PURL service to set up redirects correctly. In the future, we plan to migrate from PURLs to the Handle system which provides identifiers for digital objects, or to using DOIs (Digital Object Identifiers), which are an implementation of the Handle system (Paskin 2017).

• Endresen, Dag; Russell, Laura Anne; Schigel, Dmitry; Prylutskyi, Oleh; Johaadien, Rukaya Sarah & Torma, Michal [Show all 11 contributors for this article] (2022). Four-day program on open biodiversity data publishing and high-level data paper publishing, online for Ukraine in August 2022. Full text in Research Archive Show summary

  Regional training course for M.Sc. and Ph.D. students from Ukraine with expert trainers and trainers-in-training, Tuesday 16 to Friday 19 August 2022. Plus preparatory assignments from 1st to 12th August, and post-course assignments from 22nd August to 3rd September. Successful attendees will be issued a certificate of attendance corresponding to 2 ECTS and a digital GBIF Certified Trainer badge. This training model has been tested in the Biodiversity Information for Development (BID) programme and is adapted to BioDATA needs. The course is designed for 16-20 participants. All applicants must submit a motivation letter as part of their registration. Lectures will be in English with teaching materials available both in English and Russian languages, with the support of Ukrainian-speaking mentors. https://www.nhm.uio.no/english/research/projects/biodata/activities/2022-ukraine.html

• Endresen, Dag; Russell, Laura Anne; Schigel, Dmitry; Boer, Hugo de; Johaadien, Rukaya Sarah & Torma, Michal [Show all 10 contributors for this article] (2022). Five-day program curriculum on open biodiversity data publishing, including excursion and bioblitz in Dilijan, Armenia in May 2022. Full text in Research Archive Show summary

  Regional Training course for M.Sc. and Ph.D. students with expert trainers and trainers-in-training - Dilijan, Armenia (5 days), 1 to 5 May 2022. Successful attendees will be issued a certificate of attendance corresponding to 2 ECTS and a digital GBIF Certified Trainer badge. This training model has been tested in the Biodiversity Information for Development (BID) programme and is adapted to BioDATA needs. The course is designed for 16-20 participants. All applicants must submit a motivation letter as part of their registration. The lectures will be in English (with some teaching materials available in Armenian). https://www.nhm.uio.no/english/research/projects/biodata/activities/2022-armenia.html

• Johaadien, Rukaya Sarah; Torma, Michal; Rindal, Eirik & Barotov, Samariddin (2022). CESP mentoring - data publication and digitisation course for Tajikistan September 2022. Full text in Research Archive Show summary

  GBIF data mobilization and publication course for the Tajikistan GBIF Node at the Institute of Botany, Plant Physiology and Genetics, Tajikistan National Academy of Sciences, Armenia (3 days). https://www.gbif.no/events/2022/cesp-tajikistan.html https://www.gbif.org/project/CESP2022-001/

• Endresen, Dag; Johaadien, Rukaya Sarah & Bakken, Vidar (2021). Node update from GBIF Norway: Wikidata, Agent identifiers, Material Sample. Full text in Research Archive Show summary

  Node update from GBIF Norway: Wikidata, Agent identifiers, MaterialSample. Presentation by GBIF Norway

• Endresen, Dag & Johaadien, Rukaya Sarah (2021). Update on BioDATA - DNA metabarcoding data management. Full text in Research Archive Show summary

  GNM 2021 (Virtual) Group 1 – data mobilization training and guidance on sequence-derived data mobilization, presentation by Dag Terje Filip Endresen, GBIF Node Manager

• Johaadien, Rukaya Sarah; Endresen, Dag & Bakken, Vidar (2021). Norwegian GBIF marine datasets from OBIS. Full text in Research Archive Show summary

  GNM 2021 (Virtual) Marine data mobilization session presentation by Norwegian GBIF Node

• Endresen, Dag Terje Filip; Johaadien, Rukaya Sarah & Bakken, Vidar (2021). Capacity development activities from GBIF Norway. Full text in Research Archive Show summary

  Capacity building is an essential component of the GBIF community, a "soft" skill that (even with all the pandemic-related practice) is exceedingly hard to do well. Ahead of a summer calendar that includes the GBIF Global Nodes Meeting and the start of dozens of new projects funded through the BID, BIFA and CESP programmes, this session of the GBIF community webinar will take a deeper look into current training activities across the network.

• Goodson, Hillary; Johaadien, Rukaya Sarah; Bakken, Vidar & Endresen, Dag Terje Filip (2021). Presentation of GBIF for the Norwegian Oil & Gas environment monitoring network meeting on April 7th 2021. Full text in Research Archive Show summary

  Presentation of GBIF for the Norwegian Oil & Gas environment monitoring network meeting on April 7th, 2021. Participants from: Lundin, Total, Conoco Phillips, Okea, AkerBP, Equinor, Wintershall, Spirit Energy, Aker BP, Shell, Lotos upstream, Repsol, Vår energi.

• Endresen, Dag Terje Filip; Bakken, Vidar; Johaadien, Rukaya Sarah & Ihlen, Per Gerhard (2020). Møte om biologiske mangfolddata for privat sektor. Full text in Research Archive Show summary

  GBIF Capacity Enhancement Support Programme, Project CESP2019-004, OpenPSD: Promoting publication and use of private-sector data on biodiversity

• Endresen, Dag Terje Filip; Abrahamyan, Armine; Mirzorakhimov, Akobir; Melikyan, Andreas; Verstraete, Brecht & Schigel, Dmitry [Show all 17 contributors for this article] (2019). BioDATA: Biodiversity data mobilisation and data publication training in Eurasia. Biodiversity Information Science and Standards (BISS). 3(e37543). doi: 10.3897/biss.3.37543. Full text in Research Archive Show summary

  BioDATA (Biodiversity Data for Internationalisation in Higher Education) is an international project to develop and deliver biodiversity data training for undergraduate and postgraduate students from Armenia, Belarus, Tajikistan, and Ukraine. By training early career (student) biodiversity scholars, we aim at turning the current academic and education biodiversity landscape into a more open-data-friendly one. Professional practitioners (researchers, museum curators, and collection managers involved in data publishing) from each country were also invited to join the project as assistant teachers (mentors). The project is developed by the Research School in Biosystematics - ForBio and the Norwegian GBIF-node, both at the Natural History Museum of the University of Oslo in collaboration with the Secretariat of the Global Biodiversity Information Facility (GBIF) and partners from each of the target countries. The teaching material is based on the GBIF curriculum for data mobilization and all students will have the opportunity to gain the respective GBIF certification. All materials are made freely available for reuse and even in this very early phase of the project, we have already seen the first successful reuse of teaching materials among the project partners. The first BioDATA training event was organized in Minsk (Belarus) in February 2019 with the objective to train a minimum of four mentors from each target country. The mentor-trainees from this event will help us to teach the course to students in their home country together with teachers from the project team. BioDATA mentors will have the opportunity to gain GBIF certification as expert mentors which will open opportunities to contribute to future training events in the larger GBIF network. The BioDATA training events for the students will take place in Dushanbe (Tajikistan) in June 2019, in Minsk (Belarus) in November 2019, in Yerevan (Armenia) in April 2020, and in Kiev (Ukraine) in October 2020. Students from each country are invited to express their interest to participate by contacting their national project partner. We will close the project with a final symposium at the University of Oslo in March 2021. The project is funded by the Norwegian Agency for International Cooperation and Quality Enhancement in Higher Education (DIKU).

• Endresen, Dag Terje Filip; Russell, Laura Anne; Schigel, Dmitry; Johaadien, Rukaya Sarah; Tykarski, Piotr & Shashkov, Maxim [Show all 11 contributors for this article] (2019). BioDATA Capacity Enhancement Training: Biodiversity Data Mobilization, Train-the-mentors. Full text in Research Archive Show summary

  The goal of the train-the-mentors course is to equip the target group, the most advanced and appropriate trainers in the target countries, with the necessary training skills to apply these as assistants in the main training activities in Dushanbe (June 2019), Minsk (November 2019), Yerevan (April 2020), and Kiev (October 2020).

• Endresen, Dag Terje Filip; Tykarski, Piotr; Archambeau, Anne-Sophie; Lysaght, Liam; Johaadien, Rukaya Sarah & Bakken, Vidar [Show all 8 contributors for this article] (2019). European GBIF Nodes meeting 2019 in Oslo. Full text in Research Archive Show summary

  The 2019 annual European GBIF Nodes meeting will be in Oslo 22 to 24 May at the UiO Natural History Museum in Oslo.

• Bianchini, Federico; Birkeland, Even; Bösl, Korbinian; Gade, Alexandra; Holmen, Oddgeir Lingaas & Hu, Xian [Show all 14 contributors for this article] (2021). BioMedData Deliverable D2.1 - Report on data management plan needs/gaps. Zenodo. Full text in Research Archive Show summary

  The BioMedData project was established in 2020 to connect the largest research infrastructures within the Life Sciences in Norway with the scope of improving their data management practices, aiming at the production of findable, accessible, interoperable and reusable (FAIR) data. This report marks the conclusion of the first phase within the project, aimed at assessing the data management routines at these infrastructures and the gap with respect to the FAIR data principles. This study is supported by a questionnaire, compiled by all the infrastructures involved, covering international requirements (Science Europe, Horizon2020) as well as the FAIR data principles. The investigation revealed a lack of internationally recognised metadata standards and repositories within specific domains. In other cases, the international metadata standards lack attributes representing provenance information of steps prior to data generation. On top of this, the main responsibility for data management implementation is found to often lie with individual researchers and not infrastructures. A more systematic organisation of data management duties and associated budgeting by the research projects would allow the infrastructures to operate a cost recovering support model.

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