Prototype Germplasm Data Portal, predecessor for the ALIS-Global of the GIGA project. Presentation for the Nordic Gene Bank board meeting on 4th December 2006.
Darwin Core extension for genebanks (germplasm), at Kansas University (May 2012)Dag Endresen
The Darwin Core terms can be seen as an extension to the standard Dublin Core metadata terms. The new Darwin Core extension for genebanks declares the additional terms required for describing genebank datasets, and is based on established standards from the plant genetic resources community. The Global Biodiversity Information Facility (GBIF) provides an information infrastructure for biodiversity data including a suite of software tools for data publishing, distributed data access, and the capture of biodiversity data. The Darwin Core extension for genebanks is a key component that provides access for the genebanks and the plant genetic resources community to the GBIF informatics infrastructure including the new toolkits for data exchange.
Regional Nordic genebank documentation, at the DanBIF seminar in Århus Decemb...Dag Endresen
The Nordic Gene Bank Regional cooperation, for the DanBIF network meeting 9th December 2004, Århus University. Dag Endresen (Nordic Gene Bank). DanBIF is the Danish GBIF node. GBIF is the Global Biodiversity Information Facility, http://gbif.org
Global Information Systems for Plant Genetic Resources, SeedNet training cour...Dag Endresen
The document summarizes information systems for documenting genetic resources. It discusses global information systems like EURISCO, SINGER, and GBIF that provide access to genebank data. Standards for data exchange and description are also covered, such as LSIDs, Darwin Core, Multi-Crop Passport Descriptors, and the Structured Descriptive Data format. Regional networks for sharing plant genetic resource data are mentioned, including SEEDNet, NordGen, and various CGIAR genebanks.
Nordic regional genebank documentation, at a meeting of the Nordic Council of...Dag Endresen
Northern Regional Genebank cooperation. CSO-NB8 meeting of the Nordic Council of Ministers in Vilnius Lithuania, 29th April 2005. Dag Endresen (Nordic Gene Bank).
The document describes AEGIS, an initiative to integrate plant genetic resource conservation efforts across Europe. It aims to establish a virtual European Collection by bringing together unique and important accessions held in different countries under common quality management standards. This will improve collaboration, make resources more accessible, and ensure long-term conservation of important plant genetic materials through activities like safety duplication across genebanks. The initiative builds on existing networks and organizations coordinating European plant genetic resource conservation like ECPGR.
Sharing of germplasm data sets, at the TDWG 2006 conferenceDag Endresen
Data exchange for germplasm data sets with PyWrapper/BioCASE. TDWG 2006 conference, 16th October 2006, St. Louis. Dag Endresen, Johan Bäckman, Helmut Knupffer, Samy Gaiji.
Genebanks as GBIF data providers, the first experiences, at the TDWG 2004 con...Dag Endresen
Genebanks as GBIF data providers - the first experiences. Helmut Knüpffer and Norbert Biermann (IPK Gatersleben), Dag Endresen (Nordic Gene Bank), Pawel Kolasinski and Wieslaw Podyma (IHAR), Javier de la Torre (BGBM, ENBI). Presented at TDWG 2004 conference in Christchurch, New Zealand, 13 October 2004.
Darwin Core extension for genebanks (germplasm), at Kansas University (May 2012)Dag Endresen
The Darwin Core terms can be seen as an extension to the standard Dublin Core metadata terms. The new Darwin Core extension for genebanks declares the additional terms required for describing genebank datasets, and is based on established standards from the plant genetic resources community. The Global Biodiversity Information Facility (GBIF) provides an information infrastructure for biodiversity data including a suite of software tools for data publishing, distributed data access, and the capture of biodiversity data. The Darwin Core extension for genebanks is a key component that provides access for the genebanks and the plant genetic resources community to the GBIF informatics infrastructure including the new toolkits for data exchange.
Regional Nordic genebank documentation, at the DanBIF seminar in Århus Decemb...Dag Endresen
The Nordic Gene Bank Regional cooperation, for the DanBIF network meeting 9th December 2004, Århus University. Dag Endresen (Nordic Gene Bank). DanBIF is the Danish GBIF node. GBIF is the Global Biodiversity Information Facility, http://gbif.org
Global Information Systems for Plant Genetic Resources, SeedNet training cour...Dag Endresen
The document summarizes information systems for documenting genetic resources. It discusses global information systems like EURISCO, SINGER, and GBIF that provide access to genebank data. Standards for data exchange and description are also covered, such as LSIDs, Darwin Core, Multi-Crop Passport Descriptors, and the Structured Descriptive Data format. Regional networks for sharing plant genetic resource data are mentioned, including SEEDNet, NordGen, and various CGIAR genebanks.
Nordic regional genebank documentation, at a meeting of the Nordic Council of...Dag Endresen
Northern Regional Genebank cooperation. CSO-NB8 meeting of the Nordic Council of Ministers in Vilnius Lithuania, 29th April 2005. Dag Endresen (Nordic Gene Bank).
The document describes AEGIS, an initiative to integrate plant genetic resource conservation efforts across Europe. It aims to establish a virtual European Collection by bringing together unique and important accessions held in different countries under common quality management standards. This will improve collaboration, make resources more accessible, and ensure long-term conservation of important plant genetic materials through activities like safety duplication across genebanks. The initiative builds on existing networks and organizations coordinating European plant genetic resource conservation like ECPGR.
Sharing of germplasm data sets, at the TDWG 2006 conferenceDag Endresen
Data exchange for germplasm data sets with PyWrapper/BioCASE. TDWG 2006 conference, 16th October 2006, St. Louis. Dag Endresen, Johan Bäckman, Helmut Knupffer, Samy Gaiji.
Genebanks as GBIF data providers, the first experiences, at the TDWG 2004 con...Dag Endresen
Genebanks as GBIF data providers - the first experiences. Helmut Knüpffer and Norbert Biermann (IPK Gatersleben), Dag Endresen (Nordic Gene Bank), Pawel Kolasinski and Wieslaw Podyma (IHAR), Javier de la Torre (BGBM, ENBI). Presented at TDWG 2004 conference in Christchurch, New Zealand, 13 October 2004.
Estonian National Inventory, at the EPGRIS and EURISCO conference (2 Sept 2003)Dag Endresen
Building a National Inventory for the EPGRIS EURISCO final conference in Prague September 2003. Vahur Kukk (Jogeva PBI), Dag Endresen (Nordic Gene Bank).
http://eurisco.ecprgr.org/
Data Exchange Model Of EPGRIS, seminar at the Vavilov Institute in St Petersb...Dag Endresen
The EPGRIS project aims to create a European plant genetic resources search catalog called EURISCO by collecting passport data from ex situ collections across Europe. It will simplify data flow by having national inventories directly upload standardized data to EURISCO rather than multiple crop databases. The Nordic Gene Bank is coordinating efforts in Region 1, which includes Nordic and Baltic countries. EPGRIS will address character set issues to properly represent data in different languages and evaluate using XML format for improved data exchange.
Darwin Core extension for germplasm (11th December 2013)Dag Endresen
Presentation on the Darwin Core germplasm extension for the "1st International e-Conference on Germplasm Data Interoperability: Session 2", 11th December 2013 (https://sites.google.com/site/germplasminteroperability/). Publishing germplasm information on plant genetic resources and their traits using the Darwin Core standard and the germplasm extension for genebanks.
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.
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
Presentation of some of the major germplasm data sources, including aggregators, networks and individual data providers. Information based on the agINFRA Dossier on Germplasm Data sources (available at http://wiki.aginfra.eu/index.php/Germplasm_Working_Group)
Presented during Session 3 of the 1st International e-Conference on Germplasm Data Interoperability (https://sites.google.com/site/germplasminteroperability/)
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).
GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March...Dag Endresen
Regional NODES meeting of Europe 2010. Presentation of the Global Biodiversity Resources Discovery System (GBRDS, under development) for the NODES. How do we the NODES want the GBRDS to look like. What do we the NODES wish/need the GBRDS to be.
http://www.gbif.org/
http://gbrds.gbif.org/
http://code.google.com/p/gbif-registry/
The document discusses the CIARD (Coherence in Information for Agricultural Research for Development) initiative and how it aims to create a global infrastructure for linked open data. It describes how FAO has worked for decades to make agricultural information more accessible, including through programs like AGRIS and AIMS. The CIARD initiative now involves over 100 partners working to coordinate their efforts and promote common data formats and systems. It outlines FAO's work on vocabularies like AGROVOC and how linked open data can help link distributed data sources in agriculture through applying standards.
Persistent identifiers for digitized specimens (2013)Dag Endresen
Persistent identifiers (PID) for digitized museum collections. Presented at the European GBIF meeting at Digitarium in Jounsuu, Finland, 6 March 2013. A proposed model for assigning UUID PIDs using QR-codes during the imaging and digitization process.
#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
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
The Crop Ontology is a controlled vocabulary for plant breeding data that aims to standardize terminology and enable data sharing and interoperability. It provides definitions and relationships for traits, phenotypes, experimental factors, and other relevant concepts. The ontology is being developed collaboratively by various crop centers and is accessible online. It is aligned with other related ontologies and being converted to semantic web formats to integrate with other plant data resources and enable linked open data.
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.
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
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.
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.
The document discusses India's efforts to access biological collection data from specimens of Indian origin housed in foreign museums and collections. It notes that while digitization initiatives have made foreign data more accessible, developing countries need to undertake coordinated efforts to repatriate their own data from abroad. The National Chemical Laboratory in India has created an online database called "ABCD of Indian Origin" to collate data and images of over 30,000 Indian specimens from 15 foreign museums and collections. The goal is to make this data more available to support biodiversity research and taxonomy in India.
Global Information Systems for Plant Genetic Resources (2009)Dag Endresen
Global information systems for plant genetic resources. For the Caucasus germplasm network training course at the Nordic Genetic Resource Center (NordGen), Alnarp Sweden 29th January 2009.
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)
Estonian National Inventory, at the EPGRIS and EURISCO conference (2 Sept 2003)Dag Endresen
Building a National Inventory for the EPGRIS EURISCO final conference in Prague September 2003. Vahur Kukk (Jogeva PBI), Dag Endresen (Nordic Gene Bank).
http://eurisco.ecprgr.org/
Data Exchange Model Of EPGRIS, seminar at the Vavilov Institute in St Petersb...Dag Endresen
The EPGRIS project aims to create a European plant genetic resources search catalog called EURISCO by collecting passport data from ex situ collections across Europe. It will simplify data flow by having national inventories directly upload standardized data to EURISCO rather than multiple crop databases. The Nordic Gene Bank is coordinating efforts in Region 1, which includes Nordic and Baltic countries. EPGRIS will address character set issues to properly represent data in different languages and evaluate using XML format for improved data exchange.
Darwin Core extension for germplasm (11th December 2013)Dag Endresen
Presentation on the Darwin Core germplasm extension for the "1st International e-Conference on Germplasm Data Interoperability: Session 2", 11th December 2013 (https://sites.google.com/site/germplasminteroperability/). Publishing germplasm information on plant genetic resources and their traits using the Darwin Core standard and the germplasm extension for genebanks.
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.
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
Presentation of some of the major germplasm data sources, including aggregators, networks and individual data providers. Information based on the agINFRA Dossier on Germplasm Data sources (available at http://wiki.aginfra.eu/index.php/Germplasm_Working_Group)
Presented during Session 3 of the 1st International e-Conference on Germplasm Data Interoperability (https://sites.google.com/site/germplasminteroperability/)
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).
GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March...Dag Endresen
Regional NODES meeting of Europe 2010. Presentation of the Global Biodiversity Resources Discovery System (GBRDS, under development) for the NODES. How do we the NODES want the GBRDS to look like. What do we the NODES wish/need the GBRDS to be.
http://www.gbif.org/
http://gbrds.gbif.org/
http://code.google.com/p/gbif-registry/
The document discusses the CIARD (Coherence in Information for Agricultural Research for Development) initiative and how it aims to create a global infrastructure for linked open data. It describes how FAO has worked for decades to make agricultural information more accessible, including through programs like AGRIS and AIMS. The CIARD initiative now involves over 100 partners working to coordinate their efforts and promote common data formats and systems. It outlines FAO's work on vocabularies like AGROVOC and how linked open data can help link distributed data sources in agriculture through applying standards.
Persistent identifiers for digitized specimens (2013)Dag Endresen
Persistent identifiers (PID) for digitized museum collections. Presented at the European GBIF meeting at Digitarium in Jounsuu, Finland, 6 March 2013. A proposed model for assigning UUID PIDs using QR-codes during the imaging and digitization process.
#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
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
The Crop Ontology is a controlled vocabulary for plant breeding data that aims to standardize terminology and enable data sharing and interoperability. It provides definitions and relationships for traits, phenotypes, experimental factors, and other relevant concepts. The ontology is being developed collaboratively by various crop centers and is accessible online. It is aligned with other related ontologies and being converted to semantic web formats to integrate with other plant data resources and enable linked open data.
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.
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
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.
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.
The document discusses India's efforts to access biological collection data from specimens of Indian origin housed in foreign museums and collections. It notes that while digitization initiatives have made foreign data more accessible, developing countries need to undertake coordinated efforts to repatriate their own data from abroad. The National Chemical Laboratory in India has created an online database called "ABCD of Indian Origin" to collate data and images of over 30,000 Indian specimens from 15 foreign museums and collections. The goal is to make this data more available to support biodiversity research and taxonomy in India.
Global Information Systems for Plant Genetic Resources (2009)Dag Endresen
Global information systems for plant genetic resources. For the Caucasus germplasm network training course at the Nordic Genetic Resource Center (NordGen), Alnarp Sweden 29th January 2009.
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)
Maize database is the most important database in the bioinformatics. so i hope it is beneficial to the B.Sc.in Agriculture and M.Sc. in Genetics and Plant Breeding.
This document summarizes a presentation on metadata analysis of germplasm collections in the agINFRA project. It describes two main germplasm data sources - the Chinese Crop Germplasm Information System and the Italian National Germplasm Database. It discusses the schemas and descriptors used, mappings between schemas, and a linked data approach to connecting the different data sources. The overall goal is to facilitate interoperability between global germplasm databases.
EURISCO demo installations of IPT, at GBIF EU Nodes meeting in Alicante (11 M...Dag Endresen
Regional GBIF NODES meeting of Europe in March 2010. Presentation of current activities from the NordGen NODE. Implementations of the GBIF IPT toolkit for genebanks in Europe. Upgrade for selected genebanks from the BioCASE publishing toolkit to the IPT. First step of a scheduled larger implementation planned to start in 2011 as part of the EuroGeneBank application pending EU funding decision. NordGen IPT EURISCO
EURISCO and GBIF IPT, at the Vavilov Institute in St Petersburg (27 April 2010)Dag Endresen
Visit to the NI Vavilov Institute for Plant Industry (VIR) in April 2010. Installation of the GBIF IPT toolkit for data publishing as a test upgrade for the EURISCO data infrastructure of European genebanks.
Marco Brandizi and Keywan Hassani-Pak, Rothamsted Research, Invited Presentation at SWAT4HCLS 2022.
FAIR data principles are being a driving force in life sciences and other scientific domains, helping researchers to share their data and free all of their potential to integrate information and do novel discoveries. Knowledge graphs are an ever more popular paradigm to model data according to such principles, and technologies such as graph databases are emerging as complementary to approaches like linked data. All of this includes the agronomy, farming and food domains. How advanced the adoption of sound data management policies is in these life domains? How does that compare to other life sciences? In this presentation, we will talk about our practical experience, focusing on KnetMiner, a gene and molecular biology discovering platform, which is based on building and publishing knowledge graphs according to the FAIR principles, as well as using a mix of linked data standards for life sciences and recent graph database and API technologies. We will welcome questions and discussions from the audience about similar experience.
Per de Place Bjørn - Revolutionizing taxonomy through an open-access web-regi...ICZN
The document discusses how the Global Biodiversity Information Facility (GBIF) and ZooBank can collaborate to enhance taxonomy. It proposes using globally unique identifiers (GUIDs) to disseminate ZooBank entries through the GBIF portal and network. This would help make ZooBank data more available and allow specimens associated with ZooBank entries to be referenced through GUIDs. The document also discusses enabling retrospective registration of nomenclatural data in ZooBank via GBIF data providers and making ZooBank available to species pages/banks.
Articulo escrito por Hector Sánchez Villeda.
Hector Sánchez ha desarrollado tecnologías de la información para las ciencias biológicas por más de 20 años y actualmente es Fundador y Director de Desarrollo de IT de G2 Apps una empresa de innovación tecnológica basada en Querétaro, México.
G2 APPS se dedica a la implementación de LIMS (Laboratory Information Management Systems) utilizando un enfoque multidisciplinario que desde luego incluye un alto nivel de conocimientos en las ciencias de la vida para llevar a cabo una facil implementación.
Artículo escrito por el MC Hector Sánchez VIlleda acerca de su participación en el desarrollo, diseño e implementacion de un Sistema de Administración de la Información para Laboratorios en la Universidad de Missouri.
Hector Sánchez Villeda ha trabajado por más de 25 años en el desarrollo de TI para las ciencias biologicas y es fundador y Director de Desarrollo de IT en G2 Apps, una compañia de inovación tecnológica basada en la ciudad de Querétaro, Mexico
This document discusses the agINFRA project's efforts to enhance interoperability between agricultural data sources by developing a linked data framework for germplasm data. The agINFRA Germplasm Working Group aims to identify relevant standards, analyze existing schemas and vocabularies, and propose recommendations for exposing germplasm resources as linked open data. Key outcomes include a dossier of germplasm information and engagement with stakeholders. The proposed methodology involves defining a base schema, publishing local classifications as linked data, and linking data from different sources using common vocabularies. Implementation plans include publishing germplasm vocabularies and phenotypic data in 2014.
The Integrated Breeding Platform (IBP) provides breeders with access to high-throughput breeding services, logistics and data management tools, analysis pipelines, decision support tools, and communities of practice to deploy molecular breeding technologies. The IBP aims to be a one-stop-shop for plant breeders. It offers various services, tools, and communities to support the entire breeding workflow from parental selection to final product.
Role of bioinformatics in life sciences researchAnshika Bansal
1. The document discusses bioinformatics and summarizes some of its key applications and tools. It describes how bioinformatics merges biology and computer science to solve biological problems by applying computational tools to molecular data.
2. It provides examples of common bioinformatics tasks like retrieving sequences from databases, comparing sequences, analyzing genes and proteins, and viewing 3D structures.
3. The document lists several popular databases for nucleotide sequences, protein sequences, literature, and other biological data. It also introduces common bioinformatics tools for tasks like sequence alignment, translation, and structure analysis.
INTEGRALL is a freely available database containing over 4,800 sequences related to integrons, integrases, and gene cassettes. It provides scientists with easy access to sequence data, molecular arrangements, and genetic contexts of integrons. The database aims to organize 20 years of integron data in one place and facilitate understanding of integrons' role in bacterial adaptation and interactions. It currently includes sequences from a diverse range of bacteria and environments. Over half of gene cassettes encode antibiotic resistance genes.
AGRIS is the International System for Agricultural Science and Technology. It is supported by a large community of data providers, partners and users. AGRIS is a database that aggregates bibliographic data, and through this core data, related content across online information systems is retrieved by taking advantage of Semantic Web capabilities.
This webinar will present AGRIS international initiative and partnership in the usage of AGRIS bibliographic data as a gateway to enable researchers and policy makers to retrieve agricultural and scientific information. The end-user based webinar will explain the basic fundamentals of AGRIS, overview the AGRIS interface, and how users can initiate their searches using both the simple and advanced search functionalities.
The document discusses various types of gene banks and methods for conserving plant genetic resources ex situ. It describes seed banks, tissue banks, cryo banks, pollen banks, field gene banks, sperm banks and ova banks. It provides details on how each method preserves genetic material and which types of plants each method can be used for. The document also discusses best practices for managing gene bank accessions through electronic databases to facilitate utilization of plant genetic resources.
Similar to Prototype germplasm data portal (2006) (20)
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.
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 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
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
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.
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.
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.
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.
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 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.
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.
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.
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#MongoDB #VectorSearch #AI #SemanticSearch #TechInnovation #DataScience #LLM #MachineLearning #SearchTechnology
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My slides at Nordic Testing Days 6.6.2024
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Building RAG with self-deployed Milvus vector database and Snowpark Container...Zilliz
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Building RAG with self-deployed Milvus vector database and Snowpark Container...
Prototype germplasm data portal (2006)
1. Exchange of germplasm datasets with PyWrapper/BioCASE GAIN Global Accession Information Network December 4, 2006 NGB Board Meeting 2006 Alnarp, Sweden Dag Endresen, Nordic Gene Bank
8. Decentralized model EURISCO (Data Portal Europe) Nordic Gene Bank (Northern Europe) IPK Gatersleben (Germany) IHAR (Poland) (Other European gene banks...) SINGER (Data Portal for CGIAR) (CGIAR International Future Harvest gene banks...) USDA GRIN (Data Portal USA) (USDA ARS National Germplasm Repositories...) WUR CGN (Netherlands) GBIF (Global Biodiversity Data Portal) USER GAIN (Global germplasm Data Portal) [chm.grinfo.net] Internet MCPD MCPD MCPD MCPD MCPD Svalbard International Seed Vault (Safe Backup)
There are more than 6 million ex situ accessions of agricultural and horticultural crops conserved worldwide by genebanks (seed banks) according to FAO.
The passport data from most genebank datasets worldwide are indexed by EURISCO (European genebanks), SINGER (International CGIAR organizations) or USDA-GRIN (USDA ARS National Germplasm Repositories). Summary meta data on the datasets are collected and indexed by the FAO WIEWS database (World Information and Early Warning System on Plant Genetic Resources). FAO WIEWS. The World Information and Early Warning System (WIEWS ) on Plant Genetic Resources for Food and Agriculture (PGRFA) [http://apps3.fao.org/wiews/wiews.jsp]. GRIN Canada [http://pgrc3.agr.gc.ca/index_e.html] This a modification of a slide from Samy Gaiji, from presentation on: “ Information Networking - Challenges for the Plant Genetic Resources Communities, 2004.
* Illustration: Corn earworm pupae that will be used to produce control parasites for release in the field. Photo by Scott Bauer. [http://www.ars.usda.gov/is/graphics/photos/k5554-2.htm] * UBIF is an attempt to define a common foundation for several TDWG/GBIF standards like SDD (see SDD WIKI), ABCD (see ABCD content schema homepage) or TaxonConceptNames (see Taxonomic Concept Transfer Schema WIKI). * Unified Biosciences Information Frameword (UBIF) XML schema for data exchange and integration across knowledge domains. The schema has been design for biological data, but is applicable to other knowledge areas as well. It is based on work of the TDWG SDD and ABCD subgroups and currently jointly authored by the SDD, ABCD, TaxonName subgroups and by GBIF (Global Biodiversity Information Facility). The framework may be used without changes for new schemata, no registration is necessary. * Complex Types are part of the UBIF infrastructure (TDWG common complex type for several schemas, ABCD, SDD, TCS, Lnnean Core, etc.)
GCP_Passport v 1.03 [http://tor.ngb.se/dev/temp/gcp_passport_01_03.xsd] The GCP Passport 1.03 descriptor standard is based on the MCPD and ABCD standards and implemented for the PyWrapper/BioCASE data exchange software. A mapping for automatic “upgrade” between ABCD 2.06 and GCP_Passport_1.03 is also included in the PyWrapper/BioCASE software. The Generation Challenge Programme is a research and capacity building network that uses plant genetic diversity, advanced genomic science, and comparative biology to develop tools and technologies that enable plant breeders in the developing world to produce better crop varieties for resource-poor farmers. [http://www.generationcp.org]
Photo: Field been from Boreal, accession NGB11518, 2005-03-05, Dag Endresen [http://r142b.ngb.se/ngb/2005-03--the-making-of-seeds-pictures/index.php?offset=19&size=medium&stp=1]