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Difference between revisions of "Task Force Data Standards and Data Access"
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*Developing tutorials for publishing genetic sample data on GGBN | *Developing tutorials for publishing genetic sample data on GGBN | ||
*Reducing bottlenecks for updating genetic sample data from providers | *Reducing bottlenecks for updating genetic sample data from providers | ||
| − | *Implementation of GGBN data standard in Symbiota, Plutof and ZIMS. | + | *Implementation of GGBN data standard in [http://symbiota.org/docs/ Symbiota], [https://plutof.ut.ee/ Plutof] and [https://www.species360.org/products-services/zoo-aquarium-animal-management-software-2/ ZIMS]. |
| − | *Migration of GGBN institutional registry to GBIF | + | *Migration of GGBN institutional registry to [https://www.gbif.org/ GBIF] |
*Modifications of the GGBN data standard for environmental DNA and environmental samples, along with HTS library samples. | *Modifications of the GGBN data standard for environmental DNA and environmental samples, along with HTS library samples. | ||
*Performing a user review of the GGBN website to inform improvements to its data architecture. | *Performing a user review of the GGBN website to inform improvements to its data architecture. | ||
*Performing a review of GGBN’s permit fields, including any impediments to implementation by users. | *Performing a review of GGBN’s permit fields, including any impediments to implementation by users. | ||
*Collaboration with sequencing portals to provide best practices for documentation and citation of samples and make the GGBN data standard the global standard for implementation of the Nagoya Protocol. | *Collaboration with sequencing portals to provide best practices for documentation and citation of samples and make the GGBN data standard the global standard for implementation of the Nagoya Protocol. | ||
| − | *As part of [https://www.synthesys.info/ SYNTHESYS+] Work Package 3, developing a best practices for usage of molecular collections handbook. | + | *As part of [https://www.synthesys.info/ SYNTHESYS+] Work Package 3, developing a best practices for usage of molecular collections handbook. |
=Accomplishments= | =Accomplishments= | ||
*[https://wiki.ggbn.org/ggbn/GGBN_Data_Standard GGBN Data Standard for Tissue and DNA] | *[https://wiki.ggbn.org/ggbn/GGBN_Data_Standard GGBN Data Standard for Tissue and DNA] | ||
*Tutorials on publishing genetic sample data using the [https://www.youtube.com/watch?v=0WhK5HpXEY0&feature=emb_title Integrated Publishing Toolkit] and [https://www.youtube.com/watch?v=OuqTCM6FcJU BioCase] provider software. | *Tutorials on publishing genetic sample data using the [https://www.youtube.com/watch?v=0WhK5HpXEY0&feature=emb_title Integrated Publishing Toolkit] and [https://www.youtube.com/watch?v=OuqTCM6FcJU BioCase] provider software. | ||
| − | *Implementation of GGBN data standard in data management systems Arctos and Specify. | + | *Implementation of GGBN data standard in data management systems [https://arctosdb.org/ Arctos] and [https://www.sustain.specifysoftware.org/ Specify]. |
*Implementation of a new algorithm for the taxonomic backbone in the GGBN Data Portal to provide robust counts on taxa needed for gap analysis. | *Implementation of a new algorithm for the taxonomic backbone in the GGBN Data Portal to provide robust counts on taxa needed for gap analysis. | ||
| − | *Implementation of GGBN Data Portal [http://data.ggbn.org/ggbn_portal/usagestats/ usage statistics]. | + | *Implementation of GGBN Data Portal [http://data.ggbn.org/ggbn_portal/usagestats/ usage statistics]. |
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=Related Resources= | =Related Resources= | ||
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*Mike Trizna, Smithsonian Institution (2017-present) | *Mike Trizna, Smithsonian Institution (2017-present) | ||
*Xiao Feng (Vincent) Wei, China National Gene Bank (2018-present) | *Xiao Feng (Vincent) Wei, China National Gene Bank (2018-present) | ||
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| + | [[Category:Data standards]] | ||
| + | [[Category:Help]] | ||
Latest revision as of 12:30, 9 January 2023
Contents
[hide]Program of Work
- Development of a data standard for sharing DNA and tissue information
- Development and subsequent expansion of a global data platform for aggregating relevant data sources of genomic samples, vouchers, molecular analysis, publications, and images
Current Activities
- Developing tutorials for publishing genetic sample data on GGBN
- Reducing bottlenecks for updating genetic sample data from providers
- Implementation of GGBN data standard in Symbiota, Plutof and ZIMS.
- Migration of GGBN institutional registry to GBIF
- Modifications of the GGBN data standard for environmental DNA and environmental samples, along with HTS library samples.
- Performing a user review of the GGBN website to inform improvements to its data architecture.
- Performing a review of GGBN’s permit fields, including any impediments to implementation by users.
- Collaboration with sequencing portals to provide best practices for documentation and citation of samples and make the GGBN data standard the global standard for implementation of the Nagoya Protocol.
- As part of SYNTHESYS+ Work Package 3, developing a best practices for usage of molecular collections handbook.
Accomplishments
- GGBN Data Standard for Tissue and DNA
- Tutorials on publishing genetic sample data using the Integrated Publishing Toolkit and BioCase provider software.
- Implementation of GGBN data standard in data management systems Arctos and Specify.
- Implementation of a new algorithm for the taxonomic backbone in the GGBN Data Portal to provide robust counts on taxa needed for gap analysis.
- Implementation of GGBN Data Portal usage statistics.
Related Resources
- The Global Genome Biodiversity Network (GGBN) Data Standard specification
- The Global Genome Biodiversity Network (GGBN) Data Portal
Current Members
- Gabi Droege, Botanic Garden and Botanical Museum Berlin-Dahlem (2011-present), Chair
- Katie Barker, Smithsonian National Museum of Natural History (2011-present)
- Margaret Cawsey, Commonwealth Scientific and Industrial Research Organisation (CSIRO) (2014-present)
- Jonathan Coddington, Smithsonian National Museum of Natural History (2011-present)
- Jeremy deWaard, Centre for Biodiversity Genomics, University of Guelph (2018-present)
- Tim Fulcher, Royal Botanic Gardens, Kew (2016-present)
- Peter Grobe, Zoological Research Museum Alexander Koenig (2016-present)
- Chris Hunter, China National Gene Bank/GigaScience (2018-present)
- Lars Erik Johannessen, Natural History Museum, Oslo (2016-present)
- Kim Labuschagne, National Zoological Gardens of South Africa (2014-present)
- Chris Meyer, Smithsonian National Museum of Natural History (2011-present)
- Glen Newton, Agriculture and Agri-Food Canada (2016-present)
- Thomas Orrell, Smithsonian National Museum of Natural History (2011-present)
- Björn Quast, Zoological Research Museum Alexander Koenig (2016-present)
- Dmitry Schigel, Global Biodiversity Information Facility (2016-present)
- Mike Trizna, Smithsonian Institution (2017-present)
- Xiao Feng (Vincent) Wei, China National Gene Bank (2018-present)
