GBIF is exploring strategies to guide its work towards 2030. Key areas of focus include:
1. Increasing engagement with the scientific community through training, tools, and enabling nodes to better support national and regional research.
2. Filling data gaps in taxonomy, geography, and time through prioritizing mobilization of new data resources and checklists.
3. Developing new infrastructure and services like data annotation, machine learning tools, and metrics to improve data quality, reuse, and support digitization of legacy collections.
GBIF is a global biodiversity data infrastructure that provides open access to over 1.6 billion species occurrence records. It connects over 1,600 data publishers through a voluntary network of participants and aims to facilitate research and policy related to biodiversity and sustainable development. Data shared through GBIF is cited with digital object identifiers to give credit to data publishers and encourage further data sharing. The presentation reviewed GBIF's role in open science and data citation principles, provided statistics on global and Norwegian contributions to the network, and explained how to publish and cite biodiversity data through GBIF.
GBIF and Biodiversity informatics for museums, 15 March 2021Dag Endresen
This document discusses open data and open science practices in natural history museums. It summarizes that very few museum specimens have been digitized, with GBIF publishing around 1.6 billion records including 200 million specimens. This represents only about 10% of the estimated 1.2-3 billion total specimens. The document promotes open data practices and FAIR data principles. It outlines the role of GBIF in providing infrastructure for open data publishing and how this can enable new research opportunities while supporting policy goals. Museums are encouraged to adopt open science approaches to remain relevant in an era of open data and big biodiversity data.
Museum collections as research data - October 2019Dag Endresen
This document discusses how natural history museums can embrace open science principles by making their collections openly available as research data. It provides context on initiatives like GBIF and DiSSCo that aim to publish biodiversity data according to common standards. While only around 5-10% of specimen records are currently digitized globally, the push for open access to publicly funded research means that museums need to develop new approaches to remain relevant providers of scientific resources. Open science practices like data sharing, citation and reuse can help address reproducibility issues and enable new discovery.
This document discusses the landscape of biodiversity informatics from a systematics perspective. It covers the background of the domain including key problems integrating biodiversity research. It also discusses social challenges like openness, collaboration and communities, as well as standards, identifiers and protocols. Finally, it briefly touches on (big) data challenges and synthetic challenges related to data aggregation, linking, visualization and modeling in biodiversity informatics. The overall goal appears to be providing an integrated view of the current state and opportunities in the field.
The role of biodiversity informatics in GBIF, 2021-05-18Dag Endresen
The document discusses the role of biodiversity informatics and the Global Biodiversity Information Facility (GBIF) in making biodiversity data available through open access. GBIF provides free and open access to over 1.6 billion species occurrence records from over 1600 data publishers. The document highlights how digitizing natural history collections and integrating diverse biodiversity data sources can support research and policy goals. It emphasizes best practices like using common data standards, publishing datasets on GBIF to make them widely discoverable and reusable, and citing data with DOIs to incentivize open data sharing.
Lecture for a course at NTNU, 27th January 2021
CC-BY 4.0 Dag Endresen https://orcid.org/0000-0002-2352-5497
See also http://bit.ly/biodiversityinformatics
https://www.gbif.no/events/2021/lecture-ntnu-gbif.html
GBIF and reuse of research data, Bergen (2016-12-14)Dag Endresen
Biodiversity informatics seminar at the Department of Biology, University of Bergen on data publication and reuse of GBIF-mediated biodiversity data on 14th December 2016. Organized by the Norwegian GBIF Node and the Norwegian Biodiversity Information Center (NBIC, Artsdatabanken).
See also: http://www.gbif.no/events/2016/data-publishing-seminar-in-bergen.html
See also: http://doi.org/10.13140/RG.2.2.24290.32969
GBIF is a global biodiversity data infrastructure that provides open access to over 1.6 billion species occurrence records. It connects over 1,600 data publishers through a voluntary network of participants and aims to facilitate research and policy related to biodiversity and sustainable development. Data shared through GBIF is cited with digital object identifiers to give credit to data publishers and encourage further data sharing. The presentation reviewed GBIF's role in open science and data citation principles, provided statistics on global and Norwegian contributions to the network, and explained how to publish and cite biodiversity data through GBIF.
GBIF and Biodiversity informatics for museums, 15 March 2021Dag Endresen
This document discusses open data and open science practices in natural history museums. It summarizes that very few museum specimens have been digitized, with GBIF publishing around 1.6 billion records including 200 million specimens. This represents only about 10% of the estimated 1.2-3 billion total specimens. The document promotes open data practices and FAIR data principles. It outlines the role of GBIF in providing infrastructure for open data publishing and how this can enable new research opportunities while supporting policy goals. Museums are encouraged to adopt open science approaches to remain relevant in an era of open data and big biodiversity data.
Museum collections as research data - October 2019Dag Endresen
This document discusses how natural history museums can embrace open science principles by making their collections openly available as research data. It provides context on initiatives like GBIF and DiSSCo that aim to publish biodiversity data according to common standards. While only around 5-10% of specimen records are currently digitized globally, the push for open access to publicly funded research means that museums need to develop new approaches to remain relevant providers of scientific resources. Open science practices like data sharing, citation and reuse can help address reproducibility issues and enable new discovery.
This document discusses the landscape of biodiversity informatics from a systematics perspective. It covers the background of the domain including key problems integrating biodiversity research. It also discusses social challenges like openness, collaboration and communities, as well as standards, identifiers and protocols. Finally, it briefly touches on (big) data challenges and synthetic challenges related to data aggregation, linking, visualization and modeling in biodiversity informatics. The overall goal appears to be providing an integrated view of the current state and opportunities in the field.
The role of biodiversity informatics in GBIF, 2021-05-18Dag Endresen
The document discusses the role of biodiversity informatics and the Global Biodiversity Information Facility (GBIF) in making biodiversity data available through open access. GBIF provides free and open access to over 1.6 billion species occurrence records from over 1600 data publishers. The document highlights how digitizing natural history collections and integrating diverse biodiversity data sources can support research and policy goals. It emphasizes best practices like using common data standards, publishing datasets on GBIF to make them widely discoverable and reusable, and citing data with DOIs to incentivize open data sharing.
Lecture for a course at NTNU, 27th January 2021
CC-BY 4.0 Dag Endresen https://orcid.org/0000-0002-2352-5497
See also http://bit.ly/biodiversityinformatics
https://www.gbif.no/events/2021/lecture-ntnu-gbif.html
GBIF and reuse of research data, Bergen (2016-12-14)Dag Endresen
Biodiversity informatics seminar at the Department of Biology, University of Bergen on data publication and reuse of GBIF-mediated biodiversity data on 14th December 2016. Organized by the Norwegian GBIF Node and the Norwegian Biodiversity Information Center (NBIC, Artsdatabanken).
See also: http://www.gbif.no/events/2016/data-publishing-seminar-in-bergen.html
See also: http://doi.org/10.13140/RG.2.2.24290.32969
Introduction to GBIF. GBIF seminar in Bergen. 2016-12-14Dag Endresen
GBIF Norway provides a summary of biodiversity data publishing and access activities in Norway through the Global Biodiversity Information Facility (GBIF). Over 22 million occurrence records with locations in Norway have been published through GBIF from 31 countries worldwide. The GBIF node team at the University of Oslo works to publish Norwegian biodiversity data and facilitate its use. They collaborate with other Norwegian institutions like Artsdatabanken and NTNU University Museum to advance open data policies and research utilizing GBIF.
GBIF data publishing. GBIF seminar in Bergen. 2016-12-14Dag Endresen
GBIF data publishing seminar at the Department for Biology at the University of Bergen. http://www.gbif.no/events/2016/data-publishing-seminar-in-bergen.html
GBIF & GRScicoll, Høstseminar Norges museumsforbunds Seksjon for natur, 2021-...Dag Endresen
This document discusses digitalization efforts and open biodiversity data infrastructure. It provides an overview of GBIF (Global Biodiversity Information Facility), including its goals of providing open access to biodiversity data worldwide. It notes that over 1.9 billion species occurrence records have been published through GBIF from over 1,700 data publishers. The document encourages museums to engage in open science and digitalization to remain relevant and take advantage of new opportunities and funding. It discusses using identifiers like DOIs to cite biodiversity data and link it to publications and people.
Digital research: Collections, data, tools and methods Stella Wisdom
Presentation for the Economic and Social Research Council North West Social Sciences Doctoral Training Partnership event on 26th November 2021, by Stella Wisdom, Digital Curator, British Library
Global Biodiversity Information Facility (GBIF) - 2012Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF) and GBIF Norway for the Department of Technical and Scientific Conservation (CONSERV) at the Natural History Museum, University of Oslo. Tøyen, Oslo, 7 November 2012.
GBIF data portal, ECPGR working group (2017-03-16)Dag Endresen
GBIF data portal. Invited speaker at the ECPGR Barley and Forage working group meeting in Malmö, 2017-03-14 to 16. The workshop included publication of genebank accession and collection data in the European Genebank Search Catalog (EURISCO). Topics also included demonstrations on how to publish characterization & evaluation (C&E) trait data in EURISCO.
See also
* GBIF.no home page: http://www.gbif.no/news/2017/ecpgr-workshop.html
* GBIF/Bioversity task group report on data fitness for use in agrobiodiversity: http://www.gbif.org/resource/82283
* ECPGR Documentation & Information meeting in May 2014: https://www.slideshare.net/DagEndresen/european-agrobidioversity-ecpgr-network-meeting-on-eurisco-central-crop-databases-and-users-prague-may-2014
#HepaticaWeek April 2016, GBIF data publishingDag Endresen
Citizen science species observation reporting and data publishing with the Global Biodiversity Information Facility (GBIF). Video feed available at: https://youtu.be/t22QmFPcvOM?t=34m4s
Global Biodiversity Information Facility - 2013Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF), GBIF-Norway and the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken) at the Norwegian Institute for Forestry and Landscape (Skog og Landskap) at Ås outside Oslo on the 17th October 2013. Seminar together with the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken).
GBIF-Norway node story lightning talk at GB26 in Leiden, October 2019Dag Endresen
The Nodes training at the start of the Nodes meeting focussed on Nodes strategies, administration, and governance tools. Some of the nodes stories were presented at the Global Nodes Meeting. Norway has an operational GBIF Node providing nationally important data pathways that are very well integrated into national information systems. However, there is not yet any solution in place for funding after 2019. In less than 3 months the node might be left without any node budget. Unfortunately, this is a situation far too many of the GBIF Nodes recognize alarmingly well - if they even have any appropriate node budget at all.
Trait Mining, prediction of agricultural traits in plant genetic resources with ecological parameters. Focused Identification of Germplasm Strategy (FIGS). For the Vavilov seminars at the IPK Gatersleben 13th June 2007. Dag Endresen, Michael Mackay, Kenneth Street.
GBIF BIFA mentoring, Day 1 GBIF intro, July 2016Dag Endresen
GBIF enables free and open access to biodiversity data online. It is an international initiative focused on making biodiversity data available for scientific research, conservation and sustainable development. The document provides statistics on the number of species occurrence records, datasets, and data publishing institutions in GBIF as of June 2016. It also shows graphs of the growth in biodiversity data through GBIF over time and the number of data publishers and downloads by country.
Data publication meeting at the Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences (NMBU), GBIF Norway and the Norwegian Biodiversity Information Centre (Artsdatabanken).
BioDATA capacity enhancement curriculum at GBIF GB26 Global Nodes Meeting in ...Dag Endresen
BioDATA Biodiversity Data for Internationalization in Higher Education is funded by the Norwegian Agency for International Cooperation and Quality Enhancement in Higher Education (DIKU) -- and is based on reusing training materials from the GBIF Biodiversity Information for Development (BID) program funded by the European Commission.
Biodiversity Informatics: An Interdisciplinary ChallengeBryan Heidorn
"Impacto de la Informática en el Conocimiento de la Biodiversidad: Actualidad y Futuro” at Universidad Nacional de Colombia on August 12, 2011. https://sites.google.com/site/simposioinformaticaicn/home
European agrobiodioversity, ECPGR network meeting on EURISCO, Central Crop Da...Dag Endresen
Presentation on the Darwin Core standard for data exchange and the germplasm extension for genebanks during the 2014 workshop of the ECPGR Documentation and Information Working Group "Tailoring the Documentation of Plant Genetic Resources in Europe to the Needs of the User" (http://www.ecpgr.cgiar.org/working_groups/documentation_information/docinfo2014.html) in Prague-Ruzyně, Czech Republic, 20th May 2014.
Short URL: https://goo.gl/C5UEnU
DOI: http://doi.org/10.13140/RG.2.2.10865.28006
GBIF BIFA mentoring, Day 4b Event core, July 2016Dag Endresen
GBIF BIFA mentoring in Los Banos, Philippines for the South-East Asian ASEAN Biodiversity Heritage Parks. With Dr. Yu-Huang Wang, Dr. Po-Jen Chiang, and Guan-Shuo Mai from TaiBIF the GBIF node of Taiwan (Chinese Tapei); and the Biodiversity Informatics team at ASEAN Centre For Biodiversity. http://www.gbif.no/events/2016/gbif-bifa-mentoring.html
Intro to GBIF: Infrastructures and Platforms for Environmental Crowd Sensing ...Kyle Copas
Slides presented while representing GBIF—the Global Biodiversity Information Facility (http://gbif.org)—at 'Infrastructures and Platforms for Environmental Crowd Sensing and Big Data' at the European Environment Agency on 9 Sept 2015. The session was part of EnviroInfo and ICT for Sustainability, a three-day conference in Copenhagen hosted by the University of Copenhagen in collaboration with the European Environment Agency.
GBIF BIFA mentoring, Day 2 Publish data, July 2016Dag Endresen
GBIF BIFA mentoring in Los Banos, Philippines for the South-East Asian ASEAN Biodiversity Heritage Parks. With Dr. Yu-Huang Wang, Dr. Po-Jen Chiang, and Guan-Shuo Mai from TaiBIF the GBIF node of Taiwan (Chinese Tapei); and the Biodiversity Informatics team at ASEAN Centre For Biodiversity. http://www.gbif.no/events/2016/gbif-bifa-mentoring.html
The Global Biodiversity Information Facility and Africa RisingFatima Parker-Allie
This document summarizes a conference on mobilizing Africa's biodiversity data. It discusses GBIF's efforts to engage countries and partners in Africa and increase participation. It outlines GBIF's priorities for 2017-2021, which include delivering relevant data, improving data quality, filling data gaps, organizing biodiversity knowledge, and empowering the global network. It also summarizes efforts in Africa led by GBIF and partners to develop a strategy and regional plan of action to mobilize policy-relevant biodiversity data in Africa to support sustainable development.
Introduction to GBIF. GBIF seminar in Bergen. 2016-12-14Dag Endresen
GBIF Norway provides a summary of biodiversity data publishing and access activities in Norway through the Global Biodiversity Information Facility (GBIF). Over 22 million occurrence records with locations in Norway have been published through GBIF from 31 countries worldwide. The GBIF node team at the University of Oslo works to publish Norwegian biodiversity data and facilitate its use. They collaborate with other Norwegian institutions like Artsdatabanken and NTNU University Museum to advance open data policies and research utilizing GBIF.
GBIF data publishing. GBIF seminar in Bergen. 2016-12-14Dag Endresen
GBIF data publishing seminar at the Department for Biology at the University of Bergen. http://www.gbif.no/events/2016/data-publishing-seminar-in-bergen.html
GBIF & GRScicoll, Høstseminar Norges museumsforbunds Seksjon for natur, 2021-...Dag Endresen
This document discusses digitalization efforts and open biodiversity data infrastructure. It provides an overview of GBIF (Global Biodiversity Information Facility), including its goals of providing open access to biodiversity data worldwide. It notes that over 1.9 billion species occurrence records have been published through GBIF from over 1,700 data publishers. The document encourages museums to engage in open science and digitalization to remain relevant and take advantage of new opportunities and funding. It discusses using identifiers like DOIs to cite biodiversity data and link it to publications and people.
Digital research: Collections, data, tools and methods Stella Wisdom
Presentation for the Economic and Social Research Council North West Social Sciences Doctoral Training Partnership event on 26th November 2021, by Stella Wisdom, Digital Curator, British Library
Global Biodiversity Information Facility (GBIF) - 2012Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF) and GBIF Norway for the Department of Technical and Scientific Conservation (CONSERV) at the Natural History Museum, University of Oslo. Tøyen, Oslo, 7 November 2012.
GBIF data portal, ECPGR working group (2017-03-16)Dag Endresen
GBIF data portal. Invited speaker at the ECPGR Barley and Forage working group meeting in Malmö, 2017-03-14 to 16. The workshop included publication of genebank accession and collection data in the European Genebank Search Catalog (EURISCO). Topics also included demonstrations on how to publish characterization & evaluation (C&E) trait data in EURISCO.
See also
* GBIF.no home page: http://www.gbif.no/news/2017/ecpgr-workshop.html
* GBIF/Bioversity task group report on data fitness for use in agrobiodiversity: http://www.gbif.org/resource/82283
* ECPGR Documentation & Information meeting in May 2014: https://www.slideshare.net/DagEndresen/european-agrobidioversity-ecpgr-network-meeting-on-eurisco-central-crop-databases-and-users-prague-may-2014
#HepaticaWeek April 2016, GBIF data publishingDag Endresen
Citizen science species observation reporting and data publishing with the Global Biodiversity Information Facility (GBIF). Video feed available at: https://youtu.be/t22QmFPcvOM?t=34m4s
Global Biodiversity Information Facility - 2013Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF), GBIF-Norway and the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken) at the Norwegian Institute for Forestry and Landscape (Skog og Landskap) at Ås outside Oslo on the 17th October 2013. Seminar together with the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken).
GBIF-Norway node story lightning talk at GB26 in Leiden, October 2019Dag Endresen
The Nodes training at the start of the Nodes meeting focussed on Nodes strategies, administration, and governance tools. Some of the nodes stories were presented at the Global Nodes Meeting. Norway has an operational GBIF Node providing nationally important data pathways that are very well integrated into national information systems. However, there is not yet any solution in place for funding after 2019. In less than 3 months the node might be left without any node budget. Unfortunately, this is a situation far too many of the GBIF Nodes recognize alarmingly well - if they even have any appropriate node budget at all.
Trait Mining, prediction of agricultural traits in plant genetic resources with ecological parameters. Focused Identification of Germplasm Strategy (FIGS). For the Vavilov seminars at the IPK Gatersleben 13th June 2007. Dag Endresen, Michael Mackay, Kenneth Street.
GBIF BIFA mentoring, Day 1 GBIF intro, July 2016Dag Endresen
GBIF enables free and open access to biodiversity data online. It is an international initiative focused on making biodiversity data available for scientific research, conservation and sustainable development. The document provides statistics on the number of species occurrence records, datasets, and data publishing institutions in GBIF as of June 2016. It also shows graphs of the growth in biodiversity data through GBIF over time and the number of data publishers and downloads by country.
Data publication meeting at the Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences (NMBU), GBIF Norway and the Norwegian Biodiversity Information Centre (Artsdatabanken).
BioDATA capacity enhancement curriculum at GBIF GB26 Global Nodes Meeting in ...Dag Endresen
BioDATA Biodiversity Data for Internationalization in Higher Education is funded by the Norwegian Agency for International Cooperation and Quality Enhancement in Higher Education (DIKU) -- and is based on reusing training materials from the GBIF Biodiversity Information for Development (BID) program funded by the European Commission.
Biodiversity Informatics: An Interdisciplinary ChallengeBryan Heidorn
"Impacto de la Informática en el Conocimiento de la Biodiversidad: Actualidad y Futuro” at Universidad Nacional de Colombia on August 12, 2011. https://sites.google.com/site/simposioinformaticaicn/home
European agrobiodioversity, ECPGR network meeting on EURISCO, Central Crop Da...Dag Endresen
Presentation on the Darwin Core standard for data exchange and the germplasm extension for genebanks during the 2014 workshop of the ECPGR Documentation and Information Working Group "Tailoring the Documentation of Plant Genetic Resources in Europe to the Needs of the User" (http://www.ecpgr.cgiar.org/working_groups/documentation_information/docinfo2014.html) in Prague-Ruzyně, Czech Republic, 20th May 2014.
Short URL: https://goo.gl/C5UEnU
DOI: http://doi.org/10.13140/RG.2.2.10865.28006
GBIF BIFA mentoring, Day 4b Event core, July 2016Dag Endresen
GBIF BIFA mentoring in Los Banos, Philippines for the South-East Asian ASEAN Biodiversity Heritage Parks. With Dr. Yu-Huang Wang, Dr. Po-Jen Chiang, and Guan-Shuo Mai from TaiBIF the GBIF node of Taiwan (Chinese Tapei); and the Biodiversity Informatics team at ASEAN Centre For Biodiversity. http://www.gbif.no/events/2016/gbif-bifa-mentoring.html
Intro to GBIF: Infrastructures and Platforms for Environmental Crowd Sensing ...Kyle Copas
Slides presented while representing GBIF—the Global Biodiversity Information Facility (http://gbif.org)—at 'Infrastructures and Platforms for Environmental Crowd Sensing and Big Data' at the European Environment Agency on 9 Sept 2015. The session was part of EnviroInfo and ICT for Sustainability, a three-day conference in Copenhagen hosted by the University of Copenhagen in collaboration with the European Environment Agency.
GBIF BIFA mentoring, Day 2 Publish data, July 2016Dag Endresen
GBIF BIFA mentoring in Los Banos, Philippines for the South-East Asian ASEAN Biodiversity Heritage Parks. With Dr. Yu-Huang Wang, Dr. Po-Jen Chiang, and Guan-Shuo Mai from TaiBIF the GBIF node of Taiwan (Chinese Tapei); and the Biodiversity Informatics team at ASEAN Centre For Biodiversity. http://www.gbif.no/events/2016/gbif-bifa-mentoring.html
The Global Biodiversity Information Facility and Africa RisingFatima Parker-Allie
This document summarizes a conference on mobilizing Africa's biodiversity data. It discusses GBIF's efforts to engage countries and partners in Africa and increase participation. It outlines GBIF's priorities for 2017-2021, which include delivering relevant data, improving data quality, filling data gaps, organizing biodiversity knowledge, and empowering the global network. It also summarizes efforts in Africa led by GBIF and partners to develop a strategy and regional plan of action to mobilize policy-relevant biodiversity data in Africa to support sustainable development.
GBIF data mobilisation for the Nansen Legacy, Tromsø, 2022-09-20Dag Endresen
Nansen Legacy (Arven etter Nansen, AeN) - Marine data publishing workshop. 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
Developing the field of Biodiversity Informatics in South Africa through the ...Fatima Parker-Allie
This document discusses developing the field of biodiversity informatics in South Africa. It outlines how biodiversity data and informatics tools can help address key biodiversity challenges. It discusses establishing a Centre for Biodiversity Information Management to develop the field through curriculum, research on data management, and niche modeling. The research project aims to model fish species distributions under climate change using primary biodiversity data from GBIF to assess impacts on commercially exploited species important for food security. Establishing the field involves various partnerships and building human capital through training and research.
GBIF (Global Biodiversity Information Facility) Position Paper: Data Hosting ...Phil Cryer
The document discusses categories of biodiversity data and examples of existing data sources. It notes that while biodiversity data is being generated at an unprecedented rate, significant amounts are being lost after projects end due to poor data management and preservation practices. It proposes the establishment of Biodiversity Data Hosting Centers (BDHC) to provide long-term hosting and archiving of biodiversity data in order to prevent further loss and make data accessible. The document outlines types of biodiversity data, features BDHCs should possess, and barriers to effective data management that need to be addressed.
This document summarizes the findings of a study on the use of the Global Biodiversity Information Facility (GBIF) by scientists in the Netherlands. The study found that while the number of studies using GBIF data is increasing, many researchers remain unfamiliar with or skeptical of GBIF due to concerns about data quality and the effort required to clean and validate the data. Researchers who are most skeptical tend to work on smaller-scale topics where high-quality data is more readily available. The study provides recommendations for how the Dutch node of GBIF (NLBIF) can increase awareness and use of GBIF, such as establishing user communities and supporting promising research that uses GBIF data.
This document discusses GBIF's efforts to bridge biodiversity evidence through data standards by incorporating molecular data like sequences. It describes an experiment to add a non-Linnaean checklist of fungi from the UNITE database to the GBIF backbone taxonomy. This would allow indexing and displaying georeferenced sequence data in the same way as specimen and observation data. Checklists are seen as key, and stable but dynamic digitally citable sources are needed. Successful examples like Norway adding Barcode of Life Data are held up. The document advocates cross-linking all biodiversity data through open sharing on platforms like GBIF and tracking use through data citation.
This presentation summarizes the advancements towards the completing the work described in GBIF Work Programme Update 2016.
It was composed by different members from the GBIF Secretariat. This particular version was shared during the European Nodes Meeting in Lisbon the 19 April 2016.
Joint GBIF Biodiversa+ symposium in Helsinki on 2024-04-16Dag Endresen
GBIF Norway contributed to a symposium organized jointly by Biodiversa+ and GBIF, to discuss the requirements for national biodiversity monitoring hubs in the context of proposals for a European Biodiversity Observation Coordination Centre.
Scientific Advisory Committee (SAC) meeting May 2023 for the Global Information System (GLIS) of the Plant Treaty (ITPGRFA) of the United Nations Food and Agriculture Organization (FAO)
The document summarizes the recommendations of the GBIF Governing Board's Global Strategy and Action Plan for Mobilization of Natural History Collections Data task group. The task group recommends that GBIF facilitate discovery of non-digital collection resources, increase efficiency of data capture and quality of digitized specimens, and improve infrastructure for publishing digitized collection data globally.
The document summarizes recommendations from the GBIF GSAP-NHC Task Group on improving the publishing of natural history collections data. It recommends that GBIF facilitate access to information about non-digital collections, work to increase the efficiency of digitizing specimen data and enhance data quality, and improve the global infrastructure for publishing digitized collections data.
The document summarizes recommendations from the GBIF GSAP-NHC Task Group on improving the digitization and publication of natural history collection data. It recommends that GBIF facilitate discovery of non-digital collection resources, increase efficiency and quality of data capture, and improve global infrastructure for publishing digitized collection data. Specifically, it calls for GBIF to publicize non-digital metadata, assess the scale of undigitized specimens, support technological innovations for digitization, and strengthen hosting and identification of published data.
The RDA started through collaboration between the European Commission, NSF/NIST in the US, and Australia. Various meetings in 2012 led to the decision to call the organization the Research Data Alliance (RDA). The RDA held its first plenary meeting in Gothenburg, Sweden in March 2013, which saw 240 participants. The RDA has since grown to over 1000 members from 55 countries working in various interest groups and working groups to develop infrastructure and standards to enable open sharing of research data.
The document summarizes the challenges and progress of the Global Biodiversity Information Facility (GBIF) in improving interoperability and access to biodiversity data across local, national, and international scales. GBIF has expanded its network from 70 million records in 2007 to over 300 million records today from over 300 data publishers. Key efforts include developing simplified data standards, tools to help publish data, integrating additional data sources, and addressing issues around accurate interpretation of data across scales and languages to improve usability.
Open biodiversity information: international perspectives summarizes:
1. The document discusses global biodiversity data sources and uses, highlighting collections, observations, citizen science, and literature. It also reviews organizations that manage and use biodiversity data like GBIF, Catalogue of Life, and Biodiversity Heritage Library.
2. GBIF is a global network that publishes over 500 million species occurrence records from over 600 data publishers. It is increasing the amount of digitized biodiversity data and number of data publishers each year. The data is used in research on taxonomy, conservation, and more.
3. Finland is an active participant in GBIF, having published over 1 million records and 19 million occurrence records in total
High-level Meeting & Workshop on Environmental and Scientific Open Data for Sustainable Development Goals in Developing Countries. Madagascar, 4-6 December 2017
NLBIF state of the art presentation provided at symposium "Connecting Research Data - Good Practices for Data Integration and Reuse" Amsterdam (VU) 19 October 2015.
Modelling Research Expeditions in Wikidata: Best Practice for Standardisation...Dag Endresen
TDWG 2023 Hobart, 2023-10-10.
Sabine von Mering, Paul Jean-Charles Braun, Robert W. N. Cubey, Quentin Groom, Elspeth M Haston, Annika Hendriksen, Rukaya Johaadien, Siobhan Leachman, Luke Marsden, Heimo Rainer, Joaquim Santos, Dag Endresen. https://doi.org/10.3897/biss.7.111427
See also https://www.wikidata.org/wiki/Wikidata:WikiProject_Research_expeditions
Ontologies for biodiversity informatics, UiO DSC June 2023Dag Endresen
GBIF Norway was invited to the UiO Digital Scholar Centre Data (DSC) Managers Network meeting on 2023-06-08 to present how we use biodiversity ontologies. https://www.gbif.no/news/2023/biodiversity-ontologies.html
The UiO Natural History Museum (GBIF Norway) presented the evacuation of the Kherson herbarium in Ukraine at the 2023 annual conference for the Norwegian Association of Archives. Plenary 2023-06-01.
More information at: https://www.gbif.no/news/2023/privatarkivkonferansen.html
Video at: https://www.gbif.no/news/2023/video/2023-06-kherson-herbarium.mp4
BioDT for the UiO Science section meeting 2023-03-24Dag Endresen
Presentation of the Biodiversity Digital Twin (BioDT) project for the University of Oslo (UiO) Natural History Museum (NHMO) Science department on 2023-03-24.
BioDATA final conference in Oslo, November 2022Dag Endresen
BioDATA – Biodiversity data management skills for students (2018-2022). BioDATA is an international project on developing skills in biodiversity data management and data publishing for undergraduate and postgraduate students from Armenia, Belarus, Norway, Tajikistan, and Ukraine. 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 Directorate for Higher Education and Skills (HKDir). The final closing symposium for all partner universities was organized at the University of Oslo Natural History Museum in Oslo from 11th to 12th November 2022.
GBIF at Living Norway Open Science Lab 2022-03-03Dag Endresen
Presentation of GBIF at the Living Norway Open Science Lab on 2022-03-03. See program at
https://livingnorway.no/join-the-living-norway-ecological-data-network-through-our-open-science-lab/
https://livingnorway.no/2022/02/10/join-our-open-science-lab/
https://www.gbif.no/events/2022/open-science-lab-1.html
Råd fra GBIF-Norge til datainfrastrukturutvalget i dialogmøte 2021-11-19Dag Endresen
[Råd 1] Norske forskningsdata bør publiseres i henhold til internasjonale data-standarder. Internasjonale data-standarder sikrer interoperabilitet og reelle muligheter for gjenbruk av data. Etablerte data-standarder innenfor et fagområde gir ofte best effekt for realisert gjenbruk, men kan hindre gjenbruk av data i nye og uforutsette tverrfaglige studier og sammenhenger. Norge bør derfor også bidra til tverrfaglig videreutvikling av interoperabilitet på tvers av data-standarder som er i anvendelse innenfor de enkelte fagområder.
[Råd 2] Måloppnåelse for økt deling av forskningsdata blir enklere med effektive insentiver. Vi tror at etablering av forskningsdata som siterbart vitenskapelig produkt slik som DORA (sfdora.org, 2012) og Force11 (force11.org, 2011) beskriver gir viktige retningslinjer som datainfrastrukturutvalget bør forsøke å integrere i nye Norske retningslinjer.
[Råd 3] Metrikk for å måle gjennomslag og innflytelse (impact) av forskning ("tellekanter") bør utvides til å inkludere metrikk for anerkjennelse av datakilde (data-publikasjon, data-sitering) for både forsker og institusjon. Publisering av forskningsdata bør fortrinnsvis utføres gjennom en profesjonell infrastruktur (slik som GBIF) der opphavsmann og de ulike bidragsytere til produksjon, innsamling, tilretteleggelse, håndtering, og bevaring av data kan registreres. Dataset bør tilordnes stabil digital identitet, gjennom løsninger slik som DOI (digital object identifier). Personer bør knyttes til stabil digital identitet gjennom løsninger slik som ORCID (Open Researcher and Contributor ID, orcid.org). Institusjoner bør knyttes til stabil digital identitet gjennom system løsninger slik som ROR (Research Organization Registry, ror.org).
[Råd 4] Etablering av infrastruktur for forskningsdata tar tid og behøver derfor kontinuitet og forutsigbare rammer, mandat, og langsiktig strategisk investering. Effektiv langsiktig investering i felles internasjonale løsninger krever ofte bedre kontinuitet enn det som er mulig innenfor handlingsrommet for basisfinansiering for enkelte forskningsinstitusjoner og universiteter. Samtidig som felles multi-nasjonal investering i fellesløsninger ofte har en betydelig lavere kostnad enn en alternativ mere fragmentert infrastruktur.
GBIF Norge (GBIF.no) er den norske deltagernoden i Global Biodiversity Information Facility (GBIF.org). GBIF er en internasjonal organisasjon som arbeider for fri og åpen tilgang til globalt dekkende informasjon om biologisk mangfold. GBIF ble etablert i 2001 etter en beslutning i OECDs Science Forum i 1999. Norge ble medlem av GBIF i 2004 og den norske deltagernoden, GBIF Norge, ble etablert med sekretariat ved Universitet i Oslo Naturhistorisk Museum i nært samarbeid med Artsdatabanken og med finansiering fra Forskningsrådet. GBIF Norges mandat omfatter nasjonal deltagelse i GBIF med internasjonal publisering av norske artsdata i henhold til internasjonale data-standarder som er forvaltet av GBIF.
Open science curriculum for students, June 2019Dag Endresen
Living Norway seminar on Open Science in Trondheim 12th June 2019.
https://livingnorway.no/2019/04/26/living-norway-seminar-2019/
https://www.gbif.no/events/2019/living-norway-seminar.html
Event core and new datatypes in GBIF - 10th European GBIF Nodes Meeting in Ta...Dag Endresen
Integrating event-core and other new and complex data types (data models) in GBIF. Data types inside Darwin Core not yet supported in GBIF. Introduction for starting the discussions at the 10th European GBIF Nodes Meeting in Tallinn Estonia 15th May 2018. See also: http://bit.ly/gbifEu2018_datatypes | http://bit.ly/gbifEu2018_new_datatypes | DOI: 10.13140/RG.2.2.16667.36641
GBIF/OBIS hackathon in Brussels January 2018Dag Endresen
From 16 to 17 January 2018 biological data experts was meeting in Brussels to exchange experiences and use cases for the (relatively) new Darwin Core Event core and how the standard can be used in Marine and terrestrial contexts. By discussing use cases we aimed at providing guidelines on best practices of this new standard.
See also:
http://www.gbif.no/news/2018/gbif_obis_event_core_workshop.html
http://www.gbif.no/news/2018/documents/2018-01-17_event_core_mof_dwciri.pptx
Reuse of biodiversity data published in GBIF, November 2017Dag Endresen
UiO CEES Friday seminar: Open and reusable research data with the Global Biodiversity Information Facility (GBIF)
If a tree falls in the forest and nobody reuses this information in peer review validated research — for what purpose did we then publish the event in GBIF?
Easy access to large data volumes is a new paradigm that researchers in many fields are starting to get used with. Production of good quality research data is very expensive and research councils and governments around the world, including Norway, are looking for scientific practices to maximize the reuse of research data for other purposes than what it was originally collected for. The Global Biodiversity Information Facility (GBIF.org) is an open-data research infrastructure funded by the world’s governments and aimed at providing anyone, anywhere access to data about all types of life on Earth. GBIF was established in March 2001, following a recommendation from the OECD Mega-science Forum in 1999. Norway became a voting member in April 2004.
Dag Endresen is the national coordinator for the Norwegian participant node in GBIF. The Norwegian GBIF Node (GBIF.no) is hosted by the UiO Natural History Museum in Oslo and provides support (gbif-drift@nhm.uio.no) for publishing and using biodiversity data made available in GBIF to researchers and other users in Norway. In this presentation Dag Endresen will present the GBIF organisation with focus on examples for reuse of biodiversity data in ecological research and provide guidelines for publishing your own research data in GBIF.
Organizer: UiO CEES - Centre for Ecological and Evolutionary Synthesis, University of Oslo
http://www.gbif.no/events/2017/cees-seminar.html
http://www.mn.uio.no/cees/english/research/news/events/research/guest-lectures/friday-seminars/2017/gbif-seminar.html
DOI: 10.13140/RG.2.2.33765.50403
GBIF lunch seminar at UiO Natural History Museum in Oslo, 2017-03-30Dag Endresen
If a tree falls in the forest and nobody publish the event in GBIF, did it really happen?
If a tree falls in the forest and nobody bring a sample to a museum herbarium, how can we verify that it really did happen?
Short URL: http://goo.gl/xJraxb
Sudheer Mechineni, Head of Application Frameworks, Standard Chartered Bank
Discover how Standard Chartered Bank harnessed the power of Neo4j to transform complex data access challenges into a dynamic, scalable graph database solution. This keynote will cover their journey from initial adoption to deploying a fully automated, enterprise-grade causal cluster, highlighting key strategies for modelling organisational changes and ensuring robust disaster recovery. Learn how these innovations have not only enhanced Standard Chartered Bank’s data infrastructure but also positioned them as pioneers in the banking sector’s adoption of graph technology.
HCL Notes und Domino Lizenzkostenreduzierung in der Welt von DLAUpanagenda
Webinar Recording: https://www.panagenda.com/webinars/hcl-notes-und-domino-lizenzkostenreduzierung-in-der-welt-von-dlau/
DLAU und die Lizenzen nach dem CCB- und CCX-Modell sind für viele in der HCL-Community seit letztem Jahr ein heißes Thema. Als Notes- oder Domino-Kunde haben Sie vielleicht mit unerwartet hohen Benutzerzahlen und Lizenzgebühren zu kämpfen. Sie fragen sich vielleicht, wie diese neue Art der Lizenzierung funktioniert und welchen Nutzen sie Ihnen bringt. Vor allem wollen Sie sicherlich Ihr Budget einhalten und Kosten sparen, wo immer möglich. Das verstehen wir und wir möchten Ihnen dabei helfen!
Wir erklären Ihnen, wie Sie häufige Konfigurationsprobleme lösen können, die dazu führen können, dass mehr Benutzer gezählt werden als nötig, und wie Sie überflüssige oder ungenutzte Konten identifizieren und entfernen können, um Geld zu sparen. Es gibt auch einige Ansätze, die zu unnötigen Ausgaben führen können, z. B. wenn ein Personendokument anstelle eines Mail-Ins für geteilte Mailboxen verwendet wird. Wir zeigen Ihnen solche Fälle und deren Lösungen. Und natürlich erklären wir Ihnen das neue Lizenzmodell.
Nehmen Sie an diesem Webinar teil, bei dem HCL-Ambassador Marc Thomas und Gastredner Franz Walder Ihnen diese neue Welt näherbringen. Es vermittelt Ihnen die Tools und das Know-how, um den Überblick zu bewahren. Sie werden in der Lage sein, Ihre Kosten durch eine optimierte Domino-Konfiguration zu reduzieren und auch in Zukunft gering zu halten.
Diese Themen werden behandelt
- Reduzierung der Lizenzkosten durch Auffinden und Beheben von Fehlkonfigurationen und überflüssigen Konten
- Wie funktionieren CCB- und CCX-Lizenzen wirklich?
- Verstehen des DLAU-Tools und wie man es am besten nutzt
- Tipps für häufige Problembereiche, wie z. B. Team-Postfächer, Funktions-/Testbenutzer usw.
- Praxisbeispiele und Best Practices zum sofortigen Umsetzen
Driving Business Innovation: Latest Generative AI Advancements & Success StorySafe Software
Are you ready to revolutionize how you handle data? Join us for a webinar where we’ll bring you up to speed with the latest advancements in Generative AI technology and discover how leveraging FME with tools from giants like Google Gemini, Amazon, and Microsoft OpenAI can supercharge your workflow efficiency.
During the hour, we’ll take you through:
Guest Speaker Segment with Hannah Barrington: Dive into the world of dynamic real estate marketing with Hannah, the Marketing Manager at Workspace Group. Hear firsthand how their team generates engaging descriptions for thousands of office units by integrating diverse data sources—from PDF floorplans to web pages—using FME transformers, like OpenAIVisionConnector and AnthropicVisionConnector. This use case will show you how GenAI can streamline content creation for marketing across the board.
Ollama Use Case: Learn how Scenario Specialist Dmitri Bagh has utilized Ollama within FME to input data, create custom models, and enhance security protocols. This segment will include demos to illustrate the full capabilities of FME in AI-driven processes.
Custom AI Models: Discover how to leverage FME to build personalized AI models using your data. Whether it’s populating a model with local data for added security or integrating public AI tools, find out how FME facilitates a versatile and secure approach to AI.
We’ll wrap up with a live Q&A session where you can engage with our experts on your specific use cases, and learn more about optimizing your data workflows with AI.
This webinar is ideal for professionals seeking to harness the power of AI within their data management systems while ensuring high levels of customization and security. Whether you're a novice or an expert, gain actionable insights and strategies to elevate your data processes. Join us to see how FME and AI can revolutionize how you work with data!
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
GraphSummit Singapore | The Art of the Possible with Graph - Q2 2024Neo4j
Neha Bajwa, Vice President of Product Marketing, Neo4j
Join us as we explore breakthrough innovations enabled by interconnected data and AI. Discover firsthand how organizations use relationships in data to uncover contextual insights and solve our most pressing challenges – from optimizing supply chains, detecting fraud, and improving customer experiences to accelerating drug discoveries.
Programming Foundation Models with DSPy - Meetup SlidesZilliz
Prompting language models is hard, while programming language models is easy. In this talk, I will discuss the state-of-the-art framework DSPy for programming foundation models with its powerful optimizers and runtime constraint system.
Unlock the Future of Search with MongoDB Atlas_ Vector Search Unleashed.pdfMalak Abu Hammad
Discover how MongoDB Atlas and vector search technology can revolutionize your application's search capabilities. This comprehensive presentation covers:
* What is Vector Search?
* Importance and benefits of vector search
* Practical use cases across various industries
* Step-by-step implementation guide
* Live demos with code snippets
* Enhancing LLM capabilities with vector search
* Best practices and optimization strategies
Perfect for developers, AI enthusiasts, and tech leaders. Learn how to leverage MongoDB Atlas to deliver highly relevant, context-aware search results, transforming your data retrieval process. Stay ahead in tech innovation and maximize the potential of your applications.
#MongoDB #VectorSearch #AI #SemanticSearch #TechInnovation #DataScience #LLM #MachineLearning #SearchTechnology
Dr. Sean Tan, Head of Data Science, Changi Airport Group
Discover how Changi Airport Group (CAG) leverages graph technologies and generative AI to revolutionize their search capabilities. This session delves into the unique search needs of CAG’s diverse passengers and customers, showcasing how graph data structures enhance the accuracy and relevance of AI-generated search results, mitigating the risk of “hallucinations” and improving the overall customer journey.
Removing Uninteresting Bytes in Software FuzzingAftab Hussain
Imagine a world where software fuzzing, the process of mutating bytes in test seeds to uncover hidden and erroneous program behaviors, becomes faster and more effective. A lot depends on the initial seeds, which can significantly dictate the trajectory of a fuzzing campaign, particularly in terms of how long it takes to uncover interesting behaviour in your code. We introduce DIAR, a technique designed to speedup fuzzing campaigns by pinpointing and eliminating those uninteresting bytes in the seeds. Picture this: instead of wasting valuable resources on meaningless mutations in large, bloated seeds, DIAR removes the unnecessary bytes, streamlining the entire process.
In this work, we equipped AFL, a popular fuzzer, with DIAR and examined two critical Linux libraries -- Libxml's xmllint, a tool for parsing xml documents, and Binutil's readelf, an essential debugging and security analysis command-line tool used to display detailed information about ELF (Executable and Linkable Format). Our preliminary results show that AFL+DIAR does not only discover new paths more quickly but also achieves higher coverage overall. This work thus showcases how starting with lean and optimized seeds can lead to faster, more comprehensive fuzzing campaigns -- and DIAR helps you find such seeds.
- These are slides of the talk given at IEEE International Conference on Software Testing Verification and Validation Workshop, ICSTW 2022.
GraphRAG for Life Science to increase LLM accuracyTomaz Bratanic
GraphRAG for life science domain, where you retriever information from biomedical knowledge graphs using LLMs to increase the accuracy and performance of generated answers
Goodbye Windows 11: Make Way for Nitrux Linux 3.5.0!SOFTTECHHUB
As the digital landscape continually evolves, operating systems play a critical role in shaping user experiences and productivity. The launch of Nitrux Linux 3.5.0 marks a significant milestone, offering a robust alternative to traditional systems such as Windows 11. This article delves into the essence of Nitrux Linux 3.5.0, exploring its unique features, advantages, and how it stands as a compelling choice for both casual users and tech enthusiasts.
Let's Integrate MuleSoft RPA, COMPOSER, APM with AWS IDP along with Slackshyamraj55
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Cosa hanno in comune un mattoncino Lego e la backdoor XZ?Speck&Tech
ABSTRACT: A prima vista, un mattoncino Lego e la backdoor XZ potrebbero avere in comune il fatto di essere entrambi blocchi di costruzione, o dipendenze di progetti creativi e software. La realtà è che un mattoncino Lego e il caso della backdoor XZ hanno molto di più di tutto ciò in comune.
Partecipate alla presentazione per immergervi in una storia di interoperabilità, standard e formati aperti, per poi discutere del ruolo importante che i contributori hanno in una comunità open source sostenibile.
BIO: Sostenitrice del software libero e dei formati standard e aperti. È stata un membro attivo dei progetti Fedora e openSUSE e ha co-fondato l'Associazione LibreItalia dove è stata coinvolta in diversi eventi, migrazioni e formazione relativi a LibreOffice. In precedenza ha lavorato a migrazioni e corsi di formazione su LibreOffice per diverse amministrazioni pubbliche e privati. Da gennaio 2020 lavora in SUSE come Software Release Engineer per Uyuni e SUSE Manager e quando non segue la sua passione per i computer e per Geeko coltiva la sua curiosità per l'astronomia (da cui deriva il suo nickname deneb_alpha).
Threats to mobile devices are more prevalent and increasing in scope and complexity. Users of mobile devices desire to take full advantage of the features
available on those devices, but many of the features provide convenience and capability but sacrifice security. This best practices guide outlines steps the users can take to better protect personal devices and information.
Pushing the limits of ePRTC: 100ns holdover for 100 daysAdtran
At WSTS 2024, Alon Stern explored the topic of parametric holdover and explained how recent research findings can be implemented in real-world PNT networks to achieve 100 nanoseconds of accuracy for up to 100 days.
UiPath Test Automation using UiPath Test Suite series, part 6DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 6. In this session, we will cover Test Automation with generative AI and Open AI.
UiPath Test Automation with generative AI and Open AI webinar offers an in-depth exploration of leveraging cutting-edge technologies for test automation within the UiPath platform. Attendees will delve into the integration of generative AI, a test automation solution, with Open AI advanced natural language processing capabilities.
Throughout the session, participants will discover how this synergy empowers testers to automate repetitive tasks, enhance testing accuracy, and expedite the software testing life cycle. Topics covered include the seamless integration process, practical use cases, and the benefits of harnessing AI-driven automation for UiPath testing initiatives. By attending this webinar, testers, and automation professionals can gain valuable insights into harnessing the power of AI to optimize their test automation workflows within the UiPath ecosystem, ultimately driving efficiency and quality in software development processes.
What will you get from this session?
1. Insights into integrating generative AI.
2. Understanding how this integration enhances test automation within the UiPath platform
3. Practical demonstrations
4. Exploration of real-world use cases illustrating the benefits of AI-driven test automation for UiPath
Topics covered:
What is generative AI
Test Automation with generative AI and Open AI.
UiPath integration with generative AI
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Essentials of Automations: The Art of Triggers and Actions in FMESafe Software
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We’ll kick things off by showcasing the most commonly used event-based triggers, introducing you to various automation workflows like manual triggers, schedules, directory watchers, and more. Plus, see how these elements play out in real scenarios.
Whether you’re tweaking your current setup or building from the ground up, this session will arm you with the tools and insights needed to transform your FME usage into a powerhouse of productivity. Join us to discover effective strategies that simplify complex processes, enhancing your productivity and transforming your data management practices with FME. Let’s turn complexity into clarity and make your workspaces work wonders!
Essentials of Automations: The Art of Triggers and Actions in FME
GBIF towards 2030 (November 2018)
1. GBIF towards
2030
Photo: ForBio/GBIF training at Baikal lake September 2018, CC-BY Dag Endresen
UiO Natural History Museum in Oslo, Department of Research and
Collections, November 8th 2018 CC-BY Dag Endresen
2. GBIF data
surpassed
1 billion species
occurrence
data points in
July 2018
So what …? “What can we do with a billion data points that we could NOT do with,
say, a hundred million?” (GBIF Science Chair Rod Page on Twitter 4 July 2018).
With this observation of a frilled anemone (Metridium dianthus) off Saint-
Pierre and Miquelon, a French archipelago in the northwestern Atlantic.
#GBIF1Billion
4. Status 7th Nov 2018
Occurrence records 1 033 809 115
Datasets 41 536; Publishing institutions 1 305
5. GBIF is a success … so, do we just
continue to deliver more of the same?
Illustration by Rod Page (former GBIF Science committee chair) 5 July 2018.
11. GBIF.no towards a permanent
research infrastructure
Funding periods (15 years, 2005-2019, 50 MNOK)
• 2005-2007 (3 years, RCN 4,5 MNOK, total 5,6 MNOK)
• 2008-2011 (4 years, RCN 6,3 MNOK, total 12,1 MNOK)
• 2012-2016 (5 years, RCN 13,0 MNOK, total 20,0 MNOK)
• 2017-2019 (3 years, RCN 9,2 MNOK, total 12,1 MNOK)
• 2020 --> permanent long-term infrastructure
Forskningsrådet (RCN)
UiO Naturhistorisk museum
Artsdatabanken (NBIC)
13. Node team at NHM, University of Oslo
Dag Endresen, Node manager
Chris/an Svindseth, Data manager
Fridtjof Mehlum, Research director
Vidar Bakken, part-8me (30%)
Artsdatabanken, Trondheim
Wouter Koch, node member
Nils Valland, board member
NTNU University Museum
Anders Finstad, GBIF Science commiCee
Solveig Bakken, board member
Research Council of Norway
Chris/an Wexels Riser
Per Backe-Hansen (un8l 2016)
Contact us at: helpdesk@gbif.no
Status 2018
14. Node team at NHM, University of Oslo
Dag Endresen, Node manager
Vidar Bakken, part-time
Vacancy, Data manager
Artsdatabanken, Trondheim
Wouter Koch, node member
Nils Valland, board member
Stein A. Hoem, IT Manager
NTNU University Museum
Anders Finstad, GBIF Science committee
Solveig Bakken, board member
Data scientist (?)
Norwegian Institute for Nature Research
Erlend B. Nilsen, Science ambassador
Roald Vang, IT Manager
Frank Hanssen, node member
Research Council of Norway
Research Infrastructure Team
16. GBIF Governing Board 2018, GB25, October 2018
GBIF Science Committee: “Focus Forward
on increase usage and relevance”.
Thomas M. Orrell (chair)
Smithsonian Institution, Washington, USA
Greg Riccardi (1st vice chair)
Florida State University, Tallahassee, USA
Anders G. Finstad (2nd vice chair )
NTNU University Museum, Trondheim, Norway
Philippe Grandcolas (3rd vice chair)
Muséum naAonal d'Histoire naturelle, Paris, France GBIF Science
CommiFee
17. Almost 700 – about 2 papers a day
Peer-reviewed publications using GBIF-mediated data
GBIF Gove r ni ng Boa rd 2018, GB25, Oc tobe r 2018
Slide from the GBIF Science Committee Report, GB25, Kilkenny, Ireland, October 2018
18. GBIF Governing Board 2018, GB25, October 2018
Who are currently using GBIF?
▇ Using GBIF data
▇ All citations
Slide from the GBIF Science CommiFee Report, GB25, Kilkenny, Ireland, October 2018
GBIF Science
CommiFee
We could focus on
increasing GBIF relevance
over here?
GBIF citation per category (status 2018-1-15)
19. ● Consolidate data indexing
● Expand data models
● Build strong linkages with
reference catalogues
GBIF infrastructure directions
Bringing data together
brings science together
GBIF Gove r ni ng Boa rd 2018, GB25, Oc tobe r 2018
Slide from the GBIF Science CommiAee Report, GB25 , Kilkenny, Ireland, October 2018
20. Engaging the (wider) science community
● Proper recogni(on of data-users as GBIF
stakeholders.
● Engage and involve through teaching and
relevant tools (e.g. R).
● Enable nodes to engage more closely on
naBonal / regional level.
Slide from the GBIF Science Committee Report, GB25, Kilkenny, Ireland, October 2018
GBIF Gove r ni ng Boa rd 2018, GB25, Oc tobe r 2018
21. Recommendations from the GBIF Nodes chair
● Focus on people (Secretariat, Nodes, Publishers
and Users).
● Training, especially for new Node managers.
● Identify a mechanism locally to:
○ Take part in the GBIF work program.
○ Invest in more sustainable Nodes:
■ Stable funding
■ Capacitated staff
■ Development plan
GBIF Gove r ni ng Boa rd 2018, GB25, Oc tobe r 2018
Slide from the GBIF Nodes Committee Report (Andre
Heughebaert), GB25, Kilkenny, Ireland, October 2018
22. GBIF Gove r ni ng Boa rd 2018, GB25, Oc tobe r 2018
Slide from the GBIF ExecuAve
Secretary (Donald Hobern)
Report, GB25, Kilkenny,
Ireland, October 2018
24. Priority 1: Empower global
network
Ensure that governments, researchers and users are
equipped and supported to share, improve and use data
through the GBIF network, regardless of geography,
language or institutional affiliation.
• Remove barriers to participation
• Increase benefits associated with publishing
biodiversity data
• Address capacity needs
G B I F S t r a t e g i c p l a n 2 0 1 7 - 2 0 2 1
25. Priority 2: Enhance biodiversity
information infrastructure
Provide leadership, expertise and tools to support the
integration of all biodiversity information as an
interconnected digital knowledgebase.
• Coordinate vision and strengthen partnerships with major
biodiversity informatics initiatives
• Promote standardization and common mechanisms for
exchange of biodiversity data
• Provide stable and persistent data infrastructure to
support research
G B I F S t r a t e g i c p l a n 2 0 1 7 - 2 0 2 1
26. Priority 3. Fill data gaps
Prioritize and promote mobilization of new data resources
which combine with existing resources to maximize the
coverage, completeness and resolution of GBIF data,
particularly with respect to taxonomy, geography and time.
• Expand checklists to cover all taxonomic groups
• Identify and prioritize gaps in spatial and temporal data
• Engage institutions and researchers with
complementary data
G B I F S t r a t e g i c p l a n 2 0 1 7 - 2 0 2 1
27. Priority 4. Improve data quality
Ensure that all data within the GBIF network are of
the highest-possible quality and associated with
clear indicators enabling users to assess their origin,
relevance and usefulness for any application.
• Enhance automated data validation
• Implement tools for expert curation
• Provide clear quality indicators for all data
G B I F S t r a t e g i c p l a n 2 0 1 7 - 2 0 2 1
28. Priority 5. Deliver relevant data
Ensure that GBIF delivers data in the form and
completeness required to meet the highest-priority
needs of science and, through science, society.
• Engage with expert communities to manage data
to the highest quality possible
• Deliver well-organized and validated data to
support key applications
G B I F S t r a t e g i c p l a n 2 0 1 7 - 2 0 2 1
29. Does GBIF provide access to the
appropriate tools needed to
address the current challenges
for biological diversity?
If you have a hammer, everything looks like a nail …
31. • Darwin Core occurrence data
provide different types of evidence
for the occurrence of a species in
6me and space.
• Museum specimens & collec6ons
• Material samples & sequence data
• Species or ecosystem monitoring data
• Ci6zen species observa6ons
• … focus on adding new data types?
32. Focus efforts on Data standards?
Genomic Standards Consortium (GSC)
MIMARKS - Minimum
information about a marker
gene sequence
Biodiversity Information
Standards TDWG
Darwin Core
occurrenceID
materialSampleID
eventIDGlobal Genome Biodiversity
Network (GGBN)
33. 79.2% (ci*zen science)
Observa*on data
14,6%
specimens
Rapid increase in GBIF of (ci*zen science) observa*on data…!
Data for natural history specimens was the beginning and remains at the core of
GBIF’s scope
Focus efforts on collection specimens and vouchered and curated physical
samples?
(biobank-samples)
Troudet et al. (2018) The Increasing Disconnection of Primary Biodiversity Data from Specimens doi:10.1093/sysbio/syy044
34. Bias in distribution from uneven reporting efforts!
Distribution of species occurrence records made available to GBIF by citizen
science data providers. https://www.gbif.org/citizen-science
Chandler et al. (2017) Contribution of citizen science towards international biodiversity monitoring. Biological Conservation doi:10.1016/j.biocon.2016.09.004
Focus efforts on filling gaps in species distribution coverage?
36. Total ≈ 8.7 millions species?
(excluding bacteria and micro-organisms)
Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How Many Species Are
There on Earth and in the Ocean? PLoS Biology doi:10.1371/journal.pbio.1001127
Caley J, Fisher R, and Mengersen K (2014) Global species richness have not
converged. Trends in Ecology and evolution doi:10.1016/j.tree.2014.02.002
Caley et al. 2014
The Catalogue of Life is a quality-assured checklist
of more than 1.8 million species known to science.
Focus efforts on mobilizing nomenclature resources?
37. New Species Concepts indexed in GBIF
Species concepts based on Opera8onal Taxon Units (OTUs) (from
PlutoF UNITE) are indexed into the GBIF taxon backbone.
Species concepts based on BOLD barcode index numbers (BINs)
are indexed into the GBIF taxon backbone.
Focus efforts on mobilizing yet unnamed species concepts?
38. Capacity building: Data capture & data publishing
• Tajikistan, Belarus, Ukraine, Armenia & Norway
• UiO NHM, ForBio, GBIF Norway & GBIF Secretariat
• 64 students & staff trained
• 8 events over three years:
– 2018 Sep Oslo Kick-off
– 2019 Feb Minsk Belarus
– 2019 Jun Dushanbe Tajikistan
– 2019 Nov Minsk Belarus
– 2020 Apr Yerevan Armenia
– 2020 Oct Kiev Ukraine
– 2021 March Oslo Norway
• DIKU/SIU grant 2018–2021
Focus efforts on capacity building & training?
40. Example of data cleaning workflow
verbatimEventDate:
18 Mayo 2016
year: 2016
month: 5
day: 18
eventDate: 2016-05-18
startDayOfYear: 139
endDayOfYear: 139
DwC-ArchiveSource
Data
cleaning
41. Biased representa,on in country membership
Focus efforts on increasing the country membership coverage?
Low membership coverage in Asia and Africa
42. Asia (gap in data coverage)
Africa (gap in data)
M
ostdataarefrom
morerecentdates
Focus on filling data coverage and gaps in space and 3me?
43. The total number of
specimens in natural history
collec4ons worldwide is
es4mated to 1.2 to 3 billion.
(Ariño 2010; Duckworth et al. 1993)
GBIF indexes 876 million records –
including 128 million specimens
=> 4% to 10% coverage?
Photo: Botany Collection, Algae, Smithsonian National
Museum of Natural History Museum, by Chip Clark.
Focus efforts on services
for supporting digitizing of
legacy specimens?
44. Data fitness depends on data being
• accessible
• timely
• easy to read
• relevant
• consistent
• complete
• specific
• comprehensive
The true value of biodiversity
data can be measured by the
extent to which it is used.
Focus efforts on data re-use metrics and other incen2ves?
47. New services for Annotating biodiversity data
Tschöpe et al. (2013) Annotating biodiversity data via the Internet.
48. "Machine learning algorithms have
successfully identified plant species in massive
herbaria just by looking at the dried
specimens. According to researchers, similar
AI approaches could also be used identify the
likes of fly larvae and plant fossils"
Researchers trained... algorithms on more than 260,000 scans of
herbarium sheets, encompassing more than 1,000 species. The
computer program eventually identified species with nearly 80%
accuracy: the correct answer was within the algorithms’ top 5 picks
90% of the time. That, says (Penn State paleobotanist Peter) Wilf,
probably out-performs a human taxonomist by quite a bit.
Carranza-Rojas J, Goeau H, Bonnet P, Mata-Montero E, and Joly A (2017) Going deeper
in the automated identification of Herbarium specimens. BMC Evolutionary Biology
17:181. https://doi.org/10.1186/s12862-017-1014-z
Ledford H (2017) Artificial intelligence identifies plant species for science: Deep-learning
methods successfully classify thousands of herbarium samples. Nature News 11 August
2017. doi:10.1038/nature.2017.22442
Carranza-Rojas J, Joly A, Bonnet P, Goëau H, Mata-Montero E (2017) Automated
Herbarium Specimen Identification using Deep Learning. Proceedings of TDWG 1:
e20302. https://doi.org/10.3897/tdwgproceedings.1.20302
Focus efforts on new machine learning services?
51. "Scien&fic irreproducibility
— the inability to repeat
others' experiments and
reach the same conclusion
— is a growing concern”.
Baker (2016) Nature
doi:10.1038/533452a
52. Open Access (OA): Research results distributed online and free
of costs or other barriers – often meaning free access to
research articles.
Open Science: researchers to share their methods, computer
code and research data in central data repositories.
Open Data: based on FAIR principles: findable, accessible,
interoperable and reusable (biodiversity) data - is the primary
objective of GBIF.
For full reproducibility we also need access to the physical
biological material – to be deposited in museum collections
and biobank-repositories.
"Scientific irreproducibility — the inability to repeat others'
experiments and reach the same conclusion” (Nature 2016)
53. "FAIR" data
• Findable
– assign persistent IDs, provide rich metadata, register in
a searchable resource (such as GBIF)
• Accessible
– Retrievable by their ID using a standard protocol,
metadata remain accessible even if data aren’t
• Interoperable
– Use formal, broadly applicable languages, use standard
vocabularies, qualified references (e.g. Darwin Core)
• Reusable
– Rich, accurate metadata, clear licences, provenance,
use of community standards (e.g. Dublin Core, EML)
www.force11.org/group/fairgroup/fairprinciples
• Wilkinson, M. D. et al. (2016) The FAIR Guiding Principles for scientific data
management and stewardship. Sci. Data 3:160018
[doi:10.1038/sdata.2016.18]
Slide source: OpenAIRE & EUDAT, CC-BY-4.0, 2013
54. Data Citation Principles
1. Data to be legitimate citable products of research.
2. Data citations giving scholarly credit and attribution.
3. In scholarly literature, whenever claims are based on data, data should
always be cited.
4. Persistent method for identification of data, that is machine actionable,
globally unique, universal.
5. Data citation facilitate access to data or at least to metadata.
6. Unique identifiers that persist even beyond the lifespan of the data.
7. Data citation identify and access the specific data that support
verification of the claim (provenance, time-slice, version).
8. Flexible, but attention to interoperability of practices across
communities.
Data Cita'on Synthesis Group: Joint Declara'on of Data Cita'on Principles. Martone M. (ed.) San Diego CA: FORCE11; 2014
55. Open research data
Forskningsrådet (2014). ISBN: 978-82-12-03361-0
The Research Council of Norway expects all research data from projects
funded by the Research Council to be made freely available as open data.
In some situations there can be valid and justified reasons for exceptions.
(2014)
56. Open Science
Kunnskapsdepartementet (2016)
EU (2016) Compe<<veness Council, 26-27/05/2016
EU (2007) INSPIRE Direc<ve
Norway is to be a careful pioneer in open access to research results.
Norway to follow the ambi6on of EU on full open access to publicly
funded research by 2020.
Results of research supported by public and public-private funds freely available to and reusable by anyone.
57. ARKIVERING AV FORSKNINGSDATA OG
MATERIALPRØVER (BIOBANK)
• Åpen arkivering og deling av data og fysiske
materialprøver sikrer at dine forskningsresultater er
reproduserbare.
• Profesjonell kuratering av data og materialprøver sparer
deg forskningstid fordi du selv, dine samarbeidspartnere
og andre finner, forstår, og får tilgang til dine
forskningsdata og prøver.
• Deling av data og materialprøver gir deg bredere
spredning og påvirkningskraft for din forskning.
• Tilrettelegging for gjenbruk av forskningsdata og
materialprøver forsterker åpen og nyskjerrighets-dreven
forskning og kan lede til uventede forsknings-
gjennombrudd!