[tdwg] Public review - metadata for HTS libraries based on the GGBN Data Standard - deadline 22. September 2017

Dröge, Gabriele G.Droege at bgbm.org
Wed Aug 23 18:14:00 UTC 2017

Dear colleagues,

Last year the Global Genome Biodiversity Network (GGBN, http://www.ggbn.org ) has published the GGBN Data Standard, which covers terms related to DNA and tissue samples (https://terms.tdwg.org/wiki/GGBN_Data_Standard,  Droege et al. 2016 (https://library.ggbn.org/share/s/E3qbuKsJSwaI67IWItXCKw)). Many of you were part of the public revision process.

In addition to genomic DNA the development and use of high-throughput next generation sequencing (HTS) have outstripped current plans of SYNTHESYS (http://www.synthesys.info) and GGBN to join natural history (NH) collection data with DNA and tissue collection data.  HTS libraries can be considered a preparation of the genetic material of an organism(s), the actual physical molecular representation of a collection/specimen. These libraries come with specific adaptors that limit their transferability to other sequencing systems. They are prepared at great expense, but usually are only used for a single project, whilst a great deal of additional useful information may be available within these libraries. To increase the potential of the HTS libraries to be used for multiple projects they would need to be discoverable and metadata information made available. HTS library searches require the metadata to be queried on specific standardized keywords (by e.g. organism, HTS method etc.).

HTS library parameters already in the GGBN Data Standard have been reviewed and augmented in order to incorporate library metadata of existing as well as future techniques. This is being realized by preparation of use-cases incorporating a range of different HTS techniques (e.g. whole genome shotgun sequencing, RADseq sequencing, single molecule MinIon sequencing).

The result is a set of terms dedicated to library preparation including the pipeline parameters.

Use cases are available in the GGBN Sandbox and will kept stable for at least three years. (http://wiki.ggbn.org/ggbn/Use_Cases_HTS_library_samples)
Now we are kindly seeking your help with reviewing the terms and also ask for your general feedback on this initiative. GGBN does not want to reinvent the wheel, but work together with other organisations and initiatives, such as MIxS, GBIF, BOLD, INSDC.

The template with the proposed HTS terms can be found in our Document Library (https://library.ggbn.org/share/s/dbHuLYuGQOiv5v8avKhhPw) for your review. We would appreciate if you could send the filled out excel sheet back before 22. September 2017 to support at ggbn.org<mailto:support at ggbn.org>. We are planning to present the results at TDWG 2017. This email text can also be found in our wiki: http://wiki.ggbn.org/ggbn/HTS_Public_Consultation

Please feel free to forward this email to interested colleagues.

With Warm Regards,

Gabi Droege
Technical Manager, Global Genome Biodiversity Network
Botanic Garden and Botanical Museum Berlin-Dahlem
Berlin, Germany


Katie Barker
Program Manager, Global Genome Initiative and Global Genome Biodiversity Network
National Museum of Natural History
Smithsonian Institution
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