2023-09-17
This is PMA's DBGI daily open-notebook.
Today is 2023.09.17
Todo today
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Doing
Loooking into the next BioDigiCon 2023 program https://www.idigbio.org/content/biodigicon-2023-0
- Poelen Jorrit jhpoelen+biodigicon@jhpoelen.nl Ronin Institute / UC Santa Barbara Cheadle Center for Biodiversity and Ecological Restoration Independent Biodiversity Informatician
Building a Digital Extended Specimen One Association at a Time: What Does It Take to Extend OBI Herbarium Records with their Associated GenBank Sequences? "Specimen from Natural History Collections are physical repositories of genetic information. Genetic sequences extracted from specimen are stored in genetic sequence databases like the openly accessible GenBank at NCBI, DNA DataBank of Japan, or the European Nucleotide Archive (ENA). While researchers and collection managers make efforts to associate (or link) Natural History Collection records with their derived genetic accession records, extra work is need to make these associations explicit. We describe how a collaboration between a biodiversity informatics expert and collection managers of the Hoover/OBI Herbarium at CalPoly, San Luis Obispo, CA was forged with the aim to extend OBI specimen records to include their associated GenBank records. In addition, we quantify the costs of creating these specimen extensions, and discuss the socio-economic capacity needed to repeat this digital specimen extension process for the hundreds of millions of specimen records available globally today." Katelin, Pearson, Arizona State University; Jenn, Yost, Cal Poly State University San Luis Obispo, Cal
- Fitzsimmons Grant support@specifysoftware.org Specify Collections Consortium Technical Support Manager Advancing Biological Collections with Specify 7 "The Specify Collections Consortium has been working hard to engineer new features for its flagship collections management platform, Specify 7. Specify 7 has undergone improvements to its architecture, data operations, and user interface. We have updated and streamlined the software while introducing new capabilities.
These enhancements improve productivity in managing and sharing collections data with the biodiversity community. They involve deduplicating and merging records, adding a customizable statistics panel, integrating Specify Network links to data aggregators like GBIF and iDigBio, expanding Extended Specimen integration, and adhering to the FAIR principles.
We have also introduced the form “meta menu”, accessible from any data form. It includes functions like running reports and labels, configuring carry forward and auto-numbering, inspecting edit history, ordering results, switching subview display formats, editing form definitions, and sharing URL links. Furthermore, we have enhanced the functionality of Specify's tree interface, WorkBench, Query Builder, and system configuration tools for editing App Resources. Navigation within the application has been improved by creating unique URLs for each page. We have integrated Weblate, a continuous localization service, for crowdsourced translation of Specify 7 into any language.
We are excited to showcase the numerous capabilities of Specify, which provide effective digitization, management, and integration for biological collections." Grant, Fitzsimmons
- Levy Rick richard.levy@botanicgardens.org Denver Botanic Gardens Scientific Data Manager Rapid and reproducible specimen data formatting
"The Darwin Core has worked wonders in terms of making biodiversity data readily accessible and consistent among institutions. However, it is not necessarily designed in a way that best suits the needs of those on the ground working to record data consistently and efficiently. For example, broad fields such as occurrenceRemarks may contain the existence of associated material samples, associated digital records, or contextual information describing the project for which a specimen was collected. The field dynamicProperties can contain valuable variable descriptions of organisms but requires JavaScript Object Notation formatting that is not typically the way a field or lab researcher records notes. In this presentation I will share our process for rapid and reproducible data formatting for incoming specimens at the Kathryn Kalmbach Herbarium of Vascular Plants and the Sam Mitchel Herbarium of Fungi. Repositories for each method, respectively, can be found at the following locations: https://github.com/DenverBotanicGardens/khd_voucherDataProcessingScript https://github.com/DenverBotanicGardens/dbg_voucherDataProcessingScript" Ernie, Marx, Colorado State University
Paused
Done
Notes
https://github.com/bio-guoda/preston/issues/250 https://linker.bio/hash://sha256/f849c870565f608899f183ca261365dce9c9f1c5441b1c779e0db49df9c2a19d