2023-09-22

This is PMA's DBGI daily open-notebook.

Today is 2023.09.22

Todo today

Have a look at the DBGI discussion forum

- https://github.com/orgs/digital-botanical-gardens-initiative/discussions

Doing

Meeting Edouard

  • MetaboBlitz / EMIBlitz Vinesh Vineyards

Think about coordination

  • Directus + SampleTracking App

Directus is now up and working on the new Ubuntu 22. release

Edouard started working on Android studio

Do a schema with all example of DBGI ids

  • Information to capture in the SampleTracking App

At id issuing :

  • Timestamp
  • UUID

Think about experimental methods open repositaries. Then Method 1 could have its DOI associated

List of tables to be implemented in DBGI DB

  • Projects

  • Labels (currentky the Samples table)

This table collect the currently reserved and or used labels (corresponds to all printe labels untill now)

  • Field_Samples

This table contains

2 DB

  • EMI DB
  • Project DB (DBGI DB)

Across project DB all headers should be identical.

We now work in Emi Rdb Tables

graph TD Mass_Spectrometer -->|rdf:type|MS_Actuator["sosa:Actuator"] Mass_Spectrometer -->|rdf:type|MS_Sampler["sosa:Sampler"] Mass_Spectrometer -->|sosa:madeActuation|Mass_Spectrometry_Analysis["Mass_Spectrometry_Analysis"] Mass_Spectrometer -->|sosa:madeSampling|Mass_Spectrometry_Analysis["Mass_Spectrometry_Analysis"] Mass_Spectrometry_Analysis -->|rdf:type|MS_Actuation["sosa:Actuation"] Mass_Spectrometry_Analysis -->|sosa:usedProcedure|Mass_Spectrometry_Analysis_Procedure["Mass_Spectrometry_Analysis_Procedure"] Mass_Spectrometry_Analysis -->|sosa:resultTime|ms_time["xsd:dateTime"] Mass_Spectrometry_Analysis -->|"sosa:hasFeatureOfInterest"|Lab_Extract["Lab_Extract"] Mass_Spectrometry_Analysis -->|sosa:hasResult|Mass_Spectrometry_Results["Mass_Spectrometry_Results"]

Schema of an EMI overall procedure

graph TD subgraph field subgraph collection Collector -->|rdf:type|sosa:Sampler Collector -->|sosa:madeSampling|Field_Sampling["Field_Sampling"] Field_Sampling -->|rdf:type|sosa:Sampling["sosa:Sampling"] Field_Sampling -->|sosa:usedProcedure|Sampling_Procedure["Sampling_Procedure"] Field_Sampling -->|sosa:resultTime|fs_time["xsd:dateTime"] end subgraph observation Smartphone -->|rdf:type|sosa:Sensor Smartphone -->|sosa:madeObservation|Field_Observation["Field_Observation"] Smartphone -->|sosa:observes|Pictures["Pictures"] Field_Observation -->|rdf:type|sosa:Observation["sosa:Observation"] Field_Observation -->|sosa:observedProperty|Pictures["Pictures"] Pictures --> |rdf:type|sosa:Observable_property["sosa:Observable_property"] Field_Observation -->|sosa:usedProcedure|Observation_Procedure["Observation_Procedure"] Field_Observation -->|sosa:resultTime|fo_time["xsd:dateTime"] Field_Observation -->|sosa:hasResult|iNaturalist_Observation["iNaturalist_Observation"] Field_Observation -->|"sosa:hasFeatureOfInterest"|Living_System["Living_System"] Field_Sampling -->|"sosa:hasFeatureOfInterest"|Living_System["Living_System"] Living_System -->|skos:narrower|t_a["ex:Taxon_a"] Living_System -->|skos:narrower|t_b["ex:Taxon_b"] end Lab_Extraction -->|"sosa:hasFeatureOfInterest"|Field_Sample["Field_Sample"] t_a -->|rdf:type|w["<a href=http://www.wikidata.org/entity/Q16521>wikidata:Q16521</a>"] t_b -->|rdf:type|w["<a href=http://www.wikidata.org/entity/Q16521>wikidata:Q16521</a>"] t_a -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"] t_b -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"] Field_Sampling -->|sosa:hasResult|Field_Sample["Field_Sample"] subgraph lab direction TB subgraph mass_spectrometry Mass_Spectrometer -->|rdf:type|MS_Actuator["sosa:Actuator"] Mass_Spectrometer -->|rdf:type|MS_Sampler["sosa:Sampler"] Mass_Spectrometer -->|sosa:madeActuation|Mass_Spectrometry_Analysis["Mass_Spectrometry_Analysis"] Mass_Spectrometer -->|sosa:madeSampling|Mass_Spectrometry_Analysis["Mass_Spectrometry_Analysis"] Mass_Spectrometry_Analysis -->|rdf:type|MS_Actuation["sosa:Actuation"] Mass_Spectrometry_Analysis -->|sosa:usedProcedure|Mass_Spectrometry_Analysis_Procedure["Mass_Spectrometry_Analysis_Procedure"] Mass_Spectrometry_Analysis -->|sosa:resultTime|ms_time["xsd:dateTime"] Mass_Spectrometry_Analysis -->|sosa:hasResult|Mass_Spectrometry_Results["Mass_Spectrometry_Results"] end subgraph extraction Extractor -->|rdf:type|sosa:Actuator Extractor -->|sosa:madeActuation|Lab_Extraction["Lab_Extraction"] Lab_Extraction -->|rdf:type|sosa:Actuation["sosa:Actuation"] Lab_Extraction -->|sosa:usedProcedure|Lab_Extraction_Procedure["Lab_Extraction_Procedure"] Lab_Extraction -->|sosa:resultTime|xsd:dateTime Lab_Extraction -->|sosa:resultTime|le_time["xsd:dateTime"] end Lab_Extraction -->|sosa:hasResult|Lab_Extract["Lab_Extract"] Mass_Spectrometry_Analysis -->|"sosa:hasFeatureOfInterest"|Lab_Extract["Lab_Extract"] end
graph TD Field_Sample -->|id_example|dbgi_000001["dbgi_000001"] Field_Sample -->|id_example|dbgi_000001["dbgi_000001"]

Paused

Done

Notes

Todo tomorrow, one day ... or never

Today I learned that