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 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"]