BioSamples submission (2023 samples)

[xtrojak]

Goal: Submit basic metadata for (all) 2023 Trec samples Deadline: ~15.9.2024

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TODO:

• [ ] Double-check all key attributes for Tara and LSI samples (#1 #2 #3 #4)
  • [ ] GPS, datetime, protocol
  • [ ] depth - fixed for Tara, for LSI get from protocol
  • [ ] altitude - Tara only sea level (aerosols on boat?), LSI we can get from logsheets
• [x] geopolitical location - use API, use getGazetteerRecordsByLatLong to retrieve nation or EEZ
• [ ] Create naming scheme for samples
  • TREC_[tara/LSI/plugin]_[SDL]_[date]_[protocol]_[replicate]_[BioSampleID]
• [ ] Include sampling design label based on alignment
• [x] collection date - deal with timezones
• [ ] transfer editing rights for samples from AtlantEco
• [x] organism - e.g. marine metagenome
• [x] Term Source REF - NCBITAXON
• [x] Term Accession Number
• [x] sample Identifier - SAMEA[ID]
• [ ] sample description - multiple attribute merged into a sentence
• [ ] prepare submission script (or use drag & drop web interface)
• [ ] complete and unify protocol names
• [x] metals aliquotes

Optionally include samples from these plugins:

• [ ] Model organisms - sampling inventory under development
• [x] Plankton
  • [x] process logsheets
  • [x] Vincent group samples
• [ ] Decelle group - they should have digitalised data, ask for it
• [x] Aerosols - same template as LSI, potentially doable
• [x] VV club

[xtrojak]

We often have start and end time/location - do we want to include both? If only one, which one it should be?

EDIT: Let's use only start for now.