From f6b3d0966fd185b37829ca5134e0cb1de8f6697f Mon Sep 17 00:00:00 2001 From: PMA Date: Mon, 18 Sep 2023 15:50:11 +0200 Subject: [PATCH] Dendron workspace sync ## Synced vaults: - dendron-dbgi Dendron version: 0.124.0 Hostname: vpn-client-43-15.unifr.ch --- vault/emi-semantic-model.md | 136 +++++++++++++++++- .../open-notebook.dbgi.pmallard.2023.09.17.md | 6 +- 2 files changed, 140 insertions(+), 2 deletions(-) diff --git a/vault/emi-semantic-model.md b/vault/emi-semantic-model.md index 1c7fe5f2ae6..b29ff9298c8 100644 --- a/vault/emi-semantic-model.md +++ b/vault/emi-semantic-model.md @@ -2,7 +2,7 @@ id: u3r5ovqpurmj36nsvmetsl8 title: Emi Semantic Model desc: '' -updated: 1693574568667 +updated: 1695045009288 created: 1693548771769 --- @@ -126,3 +126,137 @@ classDiagram } ``` + +#### Schema of an EMI Observation procedure + +```mermaid +graph TD + 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|xsd:dateTime + Field_Observation -->|"sosa:hasFeatureOfInterest"|Living_System["Living_System"] + Field_Observation -->|sosa:hasResult|iNaturalist_Observation["iNaturalist_Observation"] + Living_System -->|skos:narrower|t_a["ex:Taxon_a"] + Living_System -->|skos:narrower|t_b["ex:Taxon_b"] + t_a -->|rdf:type|w["wikidata:Q16521"] + t_b -->|rdf:type|w["wikidata:Q16521"] + t_a -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"] + t_b -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"] +``` + +#### Schema of an EMI Collection procedure + +```mermaid +graph TD + 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|xsd:dateTime + Field_Sampling -->|"sosa:hasFeatureOfInterest"|Living_System["Living_System"] + Field_Sampling -->|sosa:hasResult|Field_Sample["Field_Sample"] + Living_System -->|skos:narrower|t_a["ex:Taxon_a"] + Living_System -->|skos:narrower|t_b["ex:Taxon_b"] + t_a -->|rdf:type|w["wikidata:Q16521"] + t_b -->|rdf:type|w["wikidata:Q16521"] + t_a -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"] + t_b -->|"emi:isClassifiedWith (optional)"|w2["Specimen Type Vocabulary"] +``` + +#### Schema of an EMI Extraction procedure + +```mermaid +graph TD + 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:hasFeatureOfInterest"|Field_Sample["Field_Sample"] + Lab_Extraction -->|sosa:hasResult|Lab_Extract["Lab_Extract"] +``` + + +#### Schema of an EMI Mass Spectrometry analysis procedure + +```mermaid +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 + + +```mermaid +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"] + end + 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["wikidata:Q16521"] + t_b -->|rdf:type|w["wikidata:Q16521"] + 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 +``` + diff --git a/vault/open-notebook.dbgi.pmallard.2023.09.17.md b/vault/open-notebook.dbgi.pmallard.2023.09.17.md index 7ddea3c025e..df5a0361d8c 100644 --- a/vault/open-notebook.dbgi.pmallard.2023.09.17.md +++ b/vault/open-notebook.dbgi.pmallard.2023.09.17.md @@ -2,7 +2,7 @@ id: uchpm4tt1enj34vr209qauc title: '2023-09-17' desc: '' -updated: 1694932520626 +updated: 1694935574463 created: 1694932202779 traitIds: - open-notebook-dbgi-pmallard @@ -53,6 +53,10 @@ https://www.idigbio.org/content/biodigicon-2023-0 ## Notes +https://github.com/bio-guoda/preston/issues/250 +https://linker.bio/hash://sha256/f849c870565f608899f183ca261365dce9c9f1c5441b1c779e0db49df9c2a19d + + ## Todo tomorrow, one day ... or never ###